TaSIP overexpression lead to transcriptomic reprogramming. Most of the mitochondrial dysfunction stimulon (MDS) genes, including AtAOX1a, were upregulated substantially by the overexpression of TaSIP1-∆C.

ginseng hairy roots grew significantly under Ro-0.5 mg/L stress. Inhibition, the specificity of root tip cell injury was obvious, promoted the accumulation of endogenous hormones IAA and SA, and inhibited the accumulation of ABA and JA. The accumulation of ginsenosides was significantly inhibited (except Rg3) under Ro-0.5 mg/L stress. The mRNA analysis of the Ro-0.5 mg/L group and CK group showed that the differentially expressed genes were mostly concentrated in the hormone signal transduction pathway. The genes ARF7 and EFM were up-regulated, and XTH23 and ZOX1 were down-regulated, which can be used as important candidates for hormone-responsive continuous cropping disorders. Gene. 74 differentially expressed miRNAs were identified based on miRNA sequencing, of which 22 were up-regulated and 52 were down-regulated. The target genes of ptc-miR156k_L+1, mtr-miR156b-5p, gma-miR156a_R+1, and mtr-miR156e were all TRINITY_DN14567_c0_g4, TRINITY_DN14567_c0_g4 is a gene in the plant hormone signal transduction pathway, and the four miRNAs are all negatively correlated with mRNA, indicating that ptc-miR156k_L+1, mtr-miR156b-5p, gma-miR156a_R+1, and mtr-miR156e are very likely involved in ginseng Response to continuous cropping disorders and regulation of ginsenoside synthesis.

We found that both cultivars had common mechanisms to cope with cold stress, including common differentially expressed genes (DEGs), similar time-point-related differential expression profile of genes, and similar NtCBF gene co-expression modules, suggesting conservation of adaptation strategies for cold responses. Importantly, we found that YT experienced DEGs even under normal growth condition and had less DEGs in early stage of cold stress (0.5-2 h) when compared to TT, reflecting occurrence of genotype-dependent gene transcription. Moreover, a gene co-expression module (brown) with stress-related genes up-regulated in YT instead of TT at late stage (4-8 h), which might contribute to contrasting phenotypic changes during cold stress between TT and YT.

SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves.

neo-tetraploid Arabidopsis thaliana plants using RNAseq and ICP-MS to evaluate the effect of mutations and ploidy on the gene expression and shoot ionome. We are able to show that neo-tetraploid plants induce low-potassium (K) signaling to increase their shoot K content. However, we also show that this low-K signaling is distinct form previously studied, externally applied low-K signaling. In this way, we are able to identify new components of the K homeostasis network, which are required to regulate K demand. Additionally we are able to show that while individual components of the K uptake system are not sufficient to increase shoot K, a loss of root hairs abolished the ploidy K phenotype (PPP) as does a defective Casparian strip. Root hairs are the site of entry of K into the root and neo-tetraploids increase their root hair length and density (RHI) to facilitate their higher K demand. The Casparian strip on the other hand enables higher K concentration in the stele of the root, which is required for the increased K content in neo-tetraploids.

Under control conditions, using a stringent cut-off (DESeq, adjusted to FDR < 0.01 and LogFC ≥ 1), we found only four differentially expressed genes (DEGs) between jar1-11 and Col-0, all of them downregulated. By contrast, we found 339 DEGs between JAR1-OE and Col-0, of which 134 were downregulated and 205 were upregulated. A comparison of the RNA-seq data from Col-0 between control and drought conditions revealed 3401 DEGs, of which 2023 were down- and 1378 upregulated. By comparison, jar1-11 plants, which were most heavily affected by drought stress, showed a much higher number (6139 in total; 2616 up- and 3523 down-regulated) of DEGs, while the more drought-tolerant JAR1-OE line displayed a lower number (2025 in total; 971 up- and 1054 down-regulated) of DEGs. 2411 DEGs were found between Col-0 and jar1-11 under drought among which 966 genes showed a higher and 1445 genes a lower expression level in jar1-11. On the other hand, out of 998 DEGs found between Col-0 and JAR1-OE under drought, 737 genes showed a higher and 261 genes a lower expression level in JAR1-OE. Moreover, we found 391 DEGs counter-regulated between jar1-11 and JAR1-OE.

We identified 4414 DEGs between WT (+iron) and WT (-iron). WT minus was used as the baseline to compare transcriptome landscape between cell specific localization lines. Compared to WT minus iron, pye-1 had 3878 DEGs, SHR23 had 3697 DEGs, PEP45 had 3678 DEGs, WER13 had 4696 DEGs, and WER65 had 3920 DEGs.

Transcriptional reprogramming plays a key role in drought stress responses, preceding the onset of morphological and physiological adaptations. The best characterised signal regulating gene expression in response to drought is the phytohormone abscisic acid (ABA). ABA-regulated gene expression, biosynthesis and signalling are highly organised in a diurnal cycle, so that ABA-regulated physiological traits occur at the appropriate time of the day. The mechanisms that underpin such diel oscillations in ABA signals are poorly characterised. Here we uncover GIGANTEA (GI) as a key gate keeper of ABA-regulated transcriptional and physiological responses. Time-resolved RNAseq under different irrigation scenarios indicate that gi mutants produce an exaggerated ABA response at midday, despite accumulating wild-type levels ABA. The direct comparison with ABA-deficient mutants confirms the role of GI in controlling ABA-regulated genes and enabled us to distinguish a phase of high ABA sensitivity at dawn, characterized by low GI accumulation.

Arsenic is one of the most relevant environmental pollutants and human health threats. Several arsenic species occur in soil pore waters. Recently it was discovered that these include inorganic and organic thioarsenates. Dimethylmonothioarsenate (DMMTA) belong to organic thioarsenates and in mammalian cells its toxicity was found to exceed even that of arsenite. We investigated DMMTA toxicity in Arabidopsis thaliana (Col-0) and we found strong transcriptome changes dominated by stress-responsive genes.

Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research has shown that A. thaliana retains memory of a first cold stress (priming) and improves its primed freezing tolerance even further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic (gas chromatography–mass spectrometry) and transcriptomic (RNA-Seq) changes during 24 h of cold priming or cold triggering at 4°C. During triggering higher expression of genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or proteins function as detoxifiers of reactive oxygen species (ROS) was observed compared to cold priming. Examples of early responders to triggering were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling while late responders were identified to act in fine-tuning of stress response and development regulation. Four transcription factors, CBF2/DREB1C, CBF4/DREB1D, DDF2/DREB1E and DDF1/DREB1F were strongly and uniquely significantly induced throughout the entire triggering response. The induction of unusual members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced genes of the CBF regulon and slower accumulation of selected cold stress associated metabolites proposes that a cold triggering stimulus might be sensed as milder stress in plants compared to priming. Further, the strong induction of CBF4 throughout triggering suggests a unique function of this gene during cold stress memory.

the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana. We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T (FT), CONSTANS (CO), and BROTHER OF FT (BFT). Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental associated genes.

up to 26 CqCrRLK1L members were identified in quinoa genome. To systematically investigate their tissue-specific expression pattern and gene expression profiles in response to abiotic stresses, different quinoa samples including leaf, pistil, stamen, root, and leaf treated with NaCl were harvested for transcrioptome analysis with three biological replicates for each sample. Finally,we mapped about 30 million sequence reads per sample to the quinoa genome (NL-6) and combining the four different tissues (leaf, pistil, stamen, and root), totally 40382 genes were detected, accounting for 69% of total genes in quinoa. The expression of most CqCrRLK1Ls genes were detected in all four kind of tissues, and they showed tissue-specific expression pattern. In salt-treated leaves, we observe that about 6-thosands genes changed their expression, with log2FoldChange < -1 or >1 and p value <0.05. And four CqCrRLK1L genes largely altered their transcript levels, implying that these genes are involved in the regulation of salt stress response in quinoa. The present study provides a base for future research on elucidating the varied biological functions of CqCrRLK1Ls and their contributions to stress responses.

induced secondary dormancy to address the transcriptional heterogeneity among seeds that leads to binary germination/non-germination outcomes. We developed a single seed RNA-seq strategy that allowed us to observe a reduction in seed transcriptional heterogeneity as seeds enter stress conditions, followed by an increase during recovery. We identified groups of genes whose expression showed a specific pattern through a time course and used these groups to position the individual seeds along the transcriptional gradient of germination competence. In agreement, transcriptomes of dormancy-deficient seeds (mutant of DELAY OF GERMINATION 1 gene) showed a shift towards higher values of the germination competence index. Interestingly, a significant fraction of genes with variable expression encoded translation-related factors. In summary, interrogating hundreds of single seed transcriptomes during secondary dormancy-inducing treatment revealed variability among the transcriptomes that could result from the distribution of population-based sensitivity thresholds. Our results also showed that single seed RNA-seq is the method of choice for analyzing seed bet-hedging-related phenomena.

To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress.

The loss-of-function mutant, rs33, showed increased sensitivity to salt and low-temperature stress. Genome-wide analyses of gene expression and splicing in seedlings subjected to these stresses identified multiple splice isoforms from stress-responsive genes dependent on RS33. The number of RS33-regulated genes is much higher under low-temperature stress as compared to salt stress.

General translational repression is predicted as a key process to reduce energy consumption under hypoxia. We have previously showed that mRNA loading onto polysome is reduced in Arabidopsis under submergence. Here, we showed that plant stress activated GCN2 (general control nonderepressible 2) can phosphorylate eIF2a (Eukaryotic Initiation Factor 2a) in Arabidopsis under submergence, and this process is reversible after desubmergence. Compared to the wild-type, the reduction in polysome loading during submergence was less severe in the gcn2 mutant. Transgenic lines overexpressing GCN2 had more ATP and conferred better tolerance under submergence, suggesting that GCN2 might modulate the dynamics of translation to adjust the energy homeostasis under hypoxia. Interestingly, GCN2-eIF2a signaling was activated by ethylene under submergence. However, GCN2 activity was not affected in ein2-5 and eil1ein3 under submergence, suggesting that GCN2 activity was regulated by noncanonical ethylene signaling. In addition, the polysome loading was retained in both ein2-5 and etr1-1 under submergence, implying that ethylene modulated the dynamic translation under submergence via EIN2 and GCN2. Notably, our NGS analysis also demonstrated that EIN2 and GCN2 regulated the translation of 23 core hypoxia genes as well as 53% translational repressed genes under submergence. On the other hand, EIN2 and GCN2 also affected the expression of genes involved in hypoxic response, ethylene response, biotic stress and negative regulation of cytokinin signaling. Taken together, these demonstrated that entrapped ethylene triggers GCN2 and EIN2 to ensure the translation of stress required proteins under submergence and also provide a step stone for future investigation how eukaryotic cells modulate the translation to response for the changeable environments.

MiRNA-seq followed by bioinformatic analysis identified a large number of small RNAs with size ranging from 17bp to 35bp. A total 1380 miRNAs were identified in plants experiencing long-term Ca deficiency, while 1495 miRNAs were identified in the control plants. Among the miRNAs identified in this study, 161 miRNAs were known, and 348 miRNAs were novel while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs. Based on gene ontology (GO) analysis, the target genes were found to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some of the miRNAs were specifically enriched in roots or shoots of low calcium treated plants as compared to control plants.

Using samples from Apollo 11, 12 and 17, we show that the terrestrial plant Arabidopsis thaliana germinates and grows in diverse lunar regoliths. However, our results show that growth is challenging; the lunar regolith plants were slow to develop, expressed genes indicative of ionic stresses, and many showed severe stress morphologies. Therefore, although in situ lunar regolith can be useful for plant production in lunar habitats, they are not benign substrates.

In this work the transcriptional response of rapeseed to one aspect of waterlogging, hypoxia in the root zone, was analyzed, including two rapeseed cultivars from different origin, Avatar from Europe and Zhongshuang 9 from Asia. Both cultivars showed a high number of differentially expressed genes in roots after 4 and 24 h of hypoxia. The response included many well-known hypoxia-induced genes such as genes coding for glycolytic and fermentative enzymes. Leaves hardly responded to the root stress after a 24-h-stress treatment, and photosynthesis seemed to be not affected by the stress applied to roots. There was no clear difference in either gene expression or tolerance to waterlogging between the two genotypes used in this study.

At least 20 million reads were uniquely mapped to the Arabidopsis reference genome with an average length of about 300 bp for paired-end reads. A total of 1057 and 3390 DEGs were identified for suvh5 and suvh6 versus Col-0, respectively, under noninfected conditions. Upon infection of BCN, Col-0 had 4566 DEGs compared to the noninfected wild type. BCN-infected single mutants suvh5 and suvh6 had 2487 and 846 DEGs compared to BCN-infected Col-0, respectively. Of these DEGs, 1277 and 592 or about 51% and 70% are also differentially expressed in BCN-infected Col compared to noninfected Col-0, respectively, and 324 of the 1277 and 592 DEGs are common to BCN-infected suvh5 and suvh6 compared to the control. DEGs common to BCN-infected Col-0 and/or suvh5, and suvh6 are involved in stress and defense responses, primary and secondary metabolism, signal transduction, cell wall organization and other cellular processes. This suggests that SUVH5 and SUVH6 play a major role in transcriptome reprogramming to facilitate cellular, molecular, and metabolic processes involved in the compatible plant-nematode interaction.

the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.

In this study, the interaction between the salt stress tolerance-inducing beneficial bacterium Enterobacter sp. SA187 and Arabidopsis was investigated with a special focus on the plant immune system. Among the immune signalling mutants, the Lys-motif receptors LYK4 strongly affected the beneficial interaction. Overexpression of the chitin receptor components LYK4 compromised the beneficial effect of SA187 on Arabidopsis. Transcriptome analysis revealed that the role of LYK4 in immunity is intertwined with a function in remodeling defense responses. Overall, our data indicate that components of the plant immune system are key elements in mediating beneficial metabolite-induced plant abiotic stress tolerance.

Here we aim to characterized the gene expression profile in Populus ussuriensis roots at 0, 6, 12, 24, 48 and 120 h after the start of PEG-induced drought stress. A total of 2 μg RNA per sample was used to generate sequencing libraries using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA). Libraries were sequenced in 150 bp paired-end mode, using an Illumina HiSeq X Ten platform. Our results provide a global view of gene expression profile that contributes to drought resistance in Populus ussuriensis, and meaningful information for genetic engineering research in the future.

Gene Ontology terms for hormone signaling, abiotic stress, and biotic stress were significantly enriched among mis-expressed transcripts, proteins, and/or mis-phosphorylated proteins, in agreement with FER’s known roles in these processes. Analysis of multi-omics data and subsequent experimental evidence identified previously unknown functions of FER in ER (Endoplasmic Reticulum) body formation, glucosinolate biosynthesis. FER functions through transcription factor NAI1 to mediate ER body. FER also negatively regulates indole glucosinolates biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors are hypo-phosphorylated in the fer mutant and demonstrated that FER acts through ABI5 to negatively regulate the ABA response during germination. Our integrated-omics study therefore reveals novel functions of FER and provides new insights into the underlying mechanisms of FER function.

To identify the differetially expressed genes under nitrate stress, RNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were mapped to rice (IRGSP-1) genome.

Grapevines cv Sauvignon Blanc were subjected to different stress regimes by simulating the most common extreme weather events occurring within the current climate change scenario. During spring, just before bud break, the vines were either flooded or kept under normal conditions. Both vines were then split in two groups and put in differnt tunnels, either undergoing a simulated heatwave or not. Berry samples were collected from the four groups of plants (control, only flooded, only heatwave, flooded + heatwave) at different timepoints before, during and after the stress. Transcriptomic analyses were carried out on these samples along with some metabolomic assessments to characterize the response to stress in the different samples and the effect of the combined stresses.

the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.

Results:Out of total 32,190 genes, we identified 3,912, as DT responsive genes, 2,339 and 4,635 as , heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively.Conclusion: Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.

We compared the transcriptomic response of polarized microspore stage tomato anthers to long-term mild heat (LTMH-) stress of wild-type and three lines that display increased pollen thermo-tolerance. Our results indicated distinct differences between the thermo-tolerant lines and wild-type, suggesting a dampened response to LTMH in the tolerant lines than in wild-type.

V. inaequalis causes apple scab disease, the most economically important disease of apples. In this study, we generated a comprehensive RNA-seq transcriptome of V. inaequalis during host colonization of apple, with six in planta time points (12hpi, 24hpi, 2dpi, 3dpi, 5dpi, 7dpi) and one in culture reference (fungus grown on cellophane membranes overlaying potato dextrose agar). Analysis of this transcriptome identified five in planta gene expression clusters or waves corresponding to three specific infection stages: early, mid and mid-late infection of subcuticular biotrophic host-colonization. In our analysis we focus on general fungal nutrition (plant cell wall degrading enzymes and transporters) as well as effectors (proteinaceous effectors and secondary metabolites). Early infection was characterized by the expression of genes that encode plant cell wall-degrading enzymes (PCWDEs) and proteins associated with oxidative stress responses. Mid-late infection was characterized by genes that encode PCWDEs and effector candidates (ECs).

Plants are exposed to regular diurnal rhythms of light and dark. Changes in the photoperiod by the prolongation of the light period cause photoperiod stress in short day-adapted Arabidopsis thaliana. Here we report on the transcriptional response to photoperiod stress of wild-type A. thaliana and photoperiod stress-sensitive cytokinin signaling and clock mutants. Transcriptomic changes induced by photoperiod stress included numerous changes in reactive oxygen species (ROS)-related transcripts and showed a strong overlap with alterations occurring in response to ozone stress and pathogen attack, which have in common the induction of an apoplastic oxidative burst. A core set of photoperiod stress-responsive genes has been identified, including salicylic acid (SA)-biosynthesis and -signaling genes. Genetic analysis revealed a central role for NPR1 in the photoperiod stress response as npr1-1 mutants were stress-insensitive. Photoperiod stress treatment led to a strong increase in camalexin levels which is also observed in response to pathogen infections. Photoperiod stress induced the resistance of Arabidopsis plants to a subsequent infection by Pseudomonas syringae pv. tomato DC3000 indicating priming of the defence response. Together, photoperiod stress causes transcriptional reprogramming resembling plant pathogen defence responses and induces systemic acquired resistance in the absence of a pathogen.

Dwarfed stature is a desired trait for modern orchard production systems. One effective strategy of dwarfing is exogenously applying plant growth retardants (PGRs) to plants. However, for many economic fruit trees, the current knowledge on the regulatory mechanisms underlying the dwarfing effect of PGRs were limited, which largely restricts their agricultural application. In this study, we exogenously applied three kinds of PGRs (paclobutrazol, B9 and mannitol) to the seedlings of pomegranate (Punica granatum L.) and performed comparative transcriptome analysis to elucidate the molecular features of PGR-induced dwarfing in pomegranates. Our results showed that all the three PGRs could significantly suppress auxin biosynthetic and metabolic processes, as well as auxin-mediated shoot development, which may be the main reason for the dwarfing. Besides, different PGRs were also found to induce dwarfing via specially mechanisms. Cellular response to strigolactone were downregulated by the application of paclobutrazol, while carbohydrate homeostasis and metabolism were specifically suppressed in conditions of either B9 or mannitol treatments. Furthermore, exogenous PGR application was supposed to causes adverse impacts on the normal physiological process of pomegranate seedlings, which may bring extra burden to stress adaptation of pomegranate plants. These novel findings unveiled the genetic basis underlying the dwarfing in pomegranates.

The expected increase of sustainable energy demand has shifted the attention towards bioenergy crops. Due to their know tolerance against abiotic stress and relatively low supply request, they have been proposed as election crops to be cultivated in marginal lands without disturbing the part of lands employed for agricultural purposes. Arundo donax L. is a promising bioenergy crop whose behaviour under water and salt stress has been recently studied at transcriptomic levels. As the anthropogenic activities produced in the last years a worrying increase of cadmium contamination worldwide, the aim of our work was to decipher the global transcriptomic response of A. donax leaf and root in the perspective of its cultivation in contaminated soil. In our study, RNA-seq libraries yielded a total of 416 million clean reads and 10.4 Gb per sample. De novo assembly of clean reads resulted in 378,521 transcripts and 126,668 unigenes with N50 length of 1812 bp and 1555 bp, respectively. Differential gene expression analysis revealed 5,303 deregulated transcripts (3,206 up- and 2,097 down regulated) specifically observed in the Cd-treated roots compared to Cd-treated leaves. Among them, we identified genes related to “Protein biosynthesis”, “Phytohormone action”, “Nutrient uptake”, “Cell wall organisation”, “Polyamine metabolism”, “Reactive oxygen species metabolism” and “Ion membrane transport”. Globally, our results indicate that ethylene biosynthesis and the downstream signal cascade are strongly induced by cadmium stress. In accordance to ethylene role in the interaction with the ROS generation and scavenging machinery, the transcription of several genes (NADPH oxidase 1, superoxide dismutase, ascorbate peroxidase, different glutathione S-transferases and catalase) devoted to cope the oxidative stress is strongly activated. Several small signal peptides belonging to ROTUNDIFOLIA, CLAVATA3, and C-TERMINALLY ENCODED PEPTIDE 1 (CEP) are also among the up-regulated genes in Cd-treated roots functioning as messenger molecules from root to shoot in order to communicate the stressful status to the upper part of the plants. Finally, the main finding of our work is that genes involved in cell wall remodelling and lignification are decisively up-regulated in giant reed roots this being a mechanism of cadmium avoidance adopted by giant cane and strongly supporting its cultivation in cadmium contaminated soils in a perspective to save agricultural soil for food and feed crops.

ngs2020_07_eauptic-eauptic one-How rapeseed transcriptome is affected by a short or a maintained water shortage and relationships betwenen genes expression and ionome variations .-Rapeseed not vernalized for a study at the vegetative stage. Brassica napusleaf blades samples which were grown at 80% of the field capacity (control) or during a moderate (50%) or a severe water shortage (25%), short (t1) or prolonged (t2).

Photo-inhibitory high-light stress induces damage to photosystems and changes a myriad of metabolic processes in plants. In Arabidopsis it leads to increased abundance of markers of protein degradation and transcriptional upregulation of proteases and proteolytic machinery, but proteostasis is largely maintained. To identify specific enzymes degrading at a faster rate under high light conditions, we developed a 13C partial labelling approach to measure rates of turnover of specific proteins in Arabidopsis rosettes. We identified 73 proteins with rates of protein degradation enhanced by high-light. In addition to the expected increase in degradation rate of the photosystem II (PSII) D1 subunit, we discovered significant increases in degradation rate for specific molecular chaperones, nitrate reductase, glyceraldehyde-3 phosphate dehydrogenase, and phosphoglycerate kinase. Significant increases in degradation of 65 other plastid, mitochondrial, peroxisomal, and cytosolic enzymes were also found, including factors involved in redox shuttles within and between organelles and the cytosol. Coupled analysis of protein degradation rate, transcriptional rate, and protein abundance revealed that 57% of the nuclear-encoded enzymes with higher degradation rates also had high light-induced transcriptional responses, ensuring proteostasis. In contrast, plastid-encoded proteins with enhanced turnover rates showed decreased transcript abundances and must maintain protein abundance by other processes. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of PSII D1 subunit and the function of PSII, to replace key protein degradation targets in plants and ensure proteostasis under high-light stress.

By mining public co-expression databases, we have identified FBN6 as a photosynthesis-associated gene. FBN6 is located in thylakoids and plastoglobules, and its knock-out results in stunted plants characterized by slightly reduced chlorophyll contents, shorter roots and late flowering under long-day conditions. The delayed growth phenotype of fbn6-1 cannot be attributed to altered basic photosynthesis parameters or a reduced CO2 assimilation rate. FBN6 is also co-expressed with redox/ROS-associated genes, and we show that under moderate light stress, the primary leaves of fbn6 plants begin to bleach and contain enlarged plastoglobules. Furthermore, anthocyanin accumulation is reduced in fbn6 mutants. RNA-Seq and metabolomics analyses point to an altered sulfate assimilation leading to accumulation of reduced glutathione which in turn confers cadmium tolerance of fbn6 seedlings.

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants.In the present study, we examined the gene expression pattern in Chlamydomonas reinhardtii GY-D55 cells at different time points, from early stage (2-24 h) to late stage (up to 96 h).

Results: We mapped about 3 million sequence reads per sample to the G. uralensis transcriptome. A total of 35,831 genes in all samples of G. uralensis were identified and quantified by transcriptions, among which 3608 DEGs were identified. There are 1589, 623, 469 and 927 DEGs in S vs CK, CK+B vs CK, S+B vs S and S+B vs CK+B comparisons, respectively. Validation of expression levels for 12 randomly selected DEG candidates was carried out by quantitative real-time PCR (qRT-PCR). The results showed high congruence between RNA-Seq and qRT-PCR results (coefficient of determination R2 =0.9088) indicating the reliability of RNA-Seq quantification of gene expression.Conclusions: Our study help to better understand the underlying molecular mechanisms of G2 improve the salt tolerance of G. uralensis.

Purpose: We aimed to compare transcriptomic changes after high concentration melatonin treatment in Arabidopsis；Methods: A total amount of 3 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).；Results:In total, eight samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis revealed different networks which were modulated by melatonin and IAA in Arabidopsis seedlings

Purpose: We aimed to dissect heat response of bermudagrass and identify heat stress responsive genes.；Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).；Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified genes modulated by short term heat (2h) and long term heat (12h) treatments.

Episodic drought stress negatively impacts the health of long-lived trees. Understanding the genetic and molecular mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. Here we aim to establish standardized drought stress protocols for transcriptome studies in poplar trees, to determine how hybrid poplars respond to prolonged and uniform exposure to drought; to determine if the responses to moderate and more severe growth-limiting drought stresses were qualitatively or quantitatively different; and, to determine how response to drought changes throughout the day. We established hybrid poplar trees (Populus x ’Okanese’) from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish three soil water contents reflecting well-watered, moderate, and severe growth-limiting drought conditions. Plants were rewatered as needed for three weeks to maintain the soil water conditions. The mild and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates and global transcriptomic changes. Notably, the time of day of sampling was strongest signal in the transcriptome data and it quantitatively and qualitatively affected drought responsive changes in gene expression. These analyses emphasize the complex nature of drought regulation in long-lived trees.

Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.

Results: The RNA-Seq data had high quality and reliable results were obtained from the transcriptome assembly. A high correlation between biological replicates was observed for all treatments, which indicated that the four biological replicates were reliable in this study. Based on the principal component analysis (PCA), a clear separation between the NaCl-treated group and controls could be observed. The Q30 percentage (sequences with sequencing error rate lower than 0.1%) was over 94%, and the average GC content of the RNA-seq reads was 55.46%. After removing the adaptor and low-quality sequence, each library received 68310810-83844286 clean reads. These clean reads were mapped to the reference genome with match ratios in the range of 93.6%-95.9%, and 120744 genes predicted from the genome were found to be expressed (with FPKM > 0), including 25180 annotated genes in wheat genome. 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings.；Conclusions: 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings.

Sago palm is an important agricultural starch producing plant which contributes to the economics of Malaysia where the trunk is the main plant part which the starch is stored. However, there are sago palms that planted on peat soil failed to develop its trunk even after 17 years been planted. This phenomenon is known as 'non-trunking', which eliminates the economic value of the plants. Numeral researches have been done to address the phenomenon but the molecular mechanisms of sago palm respond toward the responsible stresses are still lacking. Therefore, in this study we collected samples from Trunking (Normal) and Non-Trunking sago palm leaf samples which planted on peat soil for total RNA extraction followed by next generation sequencing using BGISEQ-500 platform. The raw reads were cleaned and de novo assembled using TRINITY software package. Total of 40.11 Gb bases were sequenced from the sago palm leaf samples and after assembled producing 102,447 unigenes, with N50 score 1,809 bp and GC ratio of 44.34%. Unigenes by aligning with 7 (NR, NT, GO, KOG, KEGG, SwissProt & InterPro) functional databases and 65,523 (63.96%) unigenes were annotated. Functional annotation results in the detection of 46,335 Coding DNA sequences by Transdecoder. 30,039 Simple-sequence repeats distributed on 21,676 Unigenes were detected using Primer3 software, and 2,355 Transcription Factor coding Unigenes were predicted using getorf and hmmseach software. A total of 492 up-regulated and 444 down-regulated at least two-fold differential expressed gene were detected using DESeq2 algorithm with 95% confidence.

We report the RNAseq technologies for high-throughput profiling of accessible chromatin regions and differentially expressed genes after cold treatment in Vitis amurensis, respectively. By combining the RNAseq results, we built putative transcriptional regulatory networks involving in cold responses in grape, and found some new transcription factors that may participate in cold responses in grape.

The nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, though it remains poorly characterized in plants. Here, we describe Arabidopsis homologues of the NuA4 scaffold proteins Enhancer of Polycomb-Like1 (EPL1) and Esa1-Associated Factor1 (EAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors suggesting that NuA4 activates nuclear plastidic genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished in Atepl1 genome-wide while another active chromatin mark H3K9ac is locally enhanced. Many chloroplast-related genes depend on NuA4 as they are downregulated with loss of H4ac and H2A.Z alone. Finally, we demonstrate that NuA4 promotes deposition of H2A.Z and by doing so prevents spurious activation of stress response genes.

ngs2020_16_carences-eauptic_carences- What are the molecular processes associated with macronutrient deficiencies in B. napus roots? What are metabolic pathway involved in root remobilization? -Root samples of N, Mg, P, S, K and Ca deprivations was harvested after 10 days of deprivations, and root samples of Cl, Mn and Co deprivations was havested after 22 days of deprivations.

SmD3 is a core protein of small nuclear ribonucleoproteins essential for pre-mRNA splicing. To assess the role of Arabidopsis SmD3-b in response to biotic stress we investigated sensitivity of the smd3-b mutant to Pseudomonas syringae pv. tomato DC3000 infection and its pathogenesis effectors flg22, elf18 and coronatine. We show that the mutant exhibits enhanced susceptibility to Pst accompanied with marked changes in the expression of key pathogenesis markers. mRNA levels of major biotic stress response factors were also altered upon treatment with Pseudomonas effectors. Our genome-wide transcriptome analysis of smd3-b mutant infected with Pst confirmed that lack of SmD3 protein deregulates defense to Pst DC3000 infection on the transcriptional level, including defects in splicing and altered pattern of alternative splicing. In addition, callose deposition, which is another marker of plant immunity, was strongly induced by elf18 and flg22 in the mutant, whereas production of reactive oxygen species triggered by flg22 was reduced. Finally, detection of phosphorylated forms of MPK3, MPK6 and MPK4/11 revealed higher activation of all MAPKs in the smd3-b mutant. All our data indicate that SmD3 contributes to plant immune response possibly via regulation of mRNA splicing of the key pathogenesis factors.

Melatonin, a natural phytohormone present in most plants, plays multiple roles in plant growth and stress responses. Although melatonin biosynthesis-related genes have been suggested to possess diverse biological functions, their roles and functional mechanisms in regulating rice grain yield remain largely unexplored. Here, we revealed that a rice caffeic acid O-methyltransferase (OsCOMT) gene is involved in melatonin biosynthesis through in vitro and in vivo evidences. Transgenic assays show OsCOMT significantly delays leaf senescence at the grain filling stage, and then improves photosynthesis efficiency. Further experimental and transcriptomic data suggest that OsCOMT inhibits the degradation of chlorophyll and chloroplast, which in turn delay leaf senescence. Histological analysis also reveals the role of OsCOMT in the development of vascular bundle system in rice. The levels of melatonin and cytokinin were significantly increased in the culm of OsCOMT-overexpression plant relative to those of the wild-type (WT). In the OsCOMT-overexpression line, the cytokinin-biosynthesizing genes were up-regulated and the cytokinin-degrading genes were down-regulated, thereby increasing the cytokinin levels compared with the WT. Thus, OsCOMT-mediated vascular patterning may result from the crosstalk between melatonin and cytokinin. More importantly, OsCOMT significantly increased grain number and yield production of rice in various background, including Nipponbare (NIP) and Suken118 (SK118). Our findings show novel insights into melatonin-mediated leaf senescence and vascular patterning, and provide a new strategy to enhance rice yield production.

Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.

CDK8 is a key subunit of Mediator complex, a large multiprotein complex that is a fundamental part of the conserved eukaryotic transcriptional machinery. However, the biological functions of CDK8 in plant abiotic stress responses remain largely unexplored. Here, we demonstrated CDK8 as a critical regulator in the abscisic acid (ABA) signaling and drought response pathways in Arabidopsis. Compared to wild-type, cdk8 mutants showed reduced sensitivity to ABA, impaired stomatal apertures and hypersensitivity to drought stress. Transcriptomic and chromatin immunoprecipitation analysis revealed that CDK8 positively regulates the transcription of several ABA-responsive genes, probably through promoting the recruitment of RNA polymerase II to their promoters. We discovered that both CDK8 and SnRK2.6 interact physically with an ERF/AP2 transcription factor RAP2.6, which can directly bind to the promoters of RD29A and COLD-REGULATED 15A (COR15A) with GCC or DRE elements, thereby promoting their expression. Importantly, we also showed that CDK8 is essential for the ABA-induced expression of RAP2.6 and RAP2.6-mediated upregulation of ABA-responsive genes, indicating that CDK8 could link the SnRK2.6-mediated ABA signaling to RNA polymerase II to promote immediate transcriptional response to ABA and drought signals. Overall, our data provide new insights into the roles of CDK8 in modulating ABA signaling and drought responses

We previously showed that increased levels of the tomato DELLA protein PROCERA (PRO) promoted ABA responses in guard cells, including ABA-induced stomatal closure and gene expression. Thus we aimed to identifiy DELLA-regulated genes in guard cells in order to study the molecular mechanism by which DELLA promotes stomatal closure.

In this study, blueberry transcriptomics and rhizosphere fungal diversity were analyzed by simulated potting method to treat blueberries with Cd stress, and the content of Fe, Mn, Cu, Zn and Cd in each tissue, soil and DGT of blueberries were determined. , Combined with transcriptomics for correlation analysis. A total of 84374 annotated genes were obtained in blueberry roots, stems, leaves and fruits, of which 3370 DEGs were found, and DEGs in the stem accounted for the highest proportion, totaling 2521. The annotation results show that these DEGs are mainly concentrated in a series of metabolic pathways related to signal transduction, defense and pathogenic response. Blueberries transfer excess Cd from the root to the stem for storage. The stem contains the highest Cd content, which is consistent with the transcriptomics analysis results, while the fruit contains the lowest Cd content. Correlation analysis between heavy metal content and transcriptomics results in each tissue was carried out, and a series of genes related to Cd regulation were screened. The blueberry root system relies on mycorrhiza to absorb nutrients in the soil. The intervention of Cd has severely affected the microflora structure of the blueberry rhizosphere soil. Coniochaetaceae, which is extremely tolerant, has gradually become the dominant population.

A cultivation facility that can assist users in controlling the soil water condition is needed for accurately phenotyping plants under drought stress in an artificial environment. Here we report the Internet of Things (IoT)-based pot system controlling optional treatment of soil water condition (iPOTs), an automatic irrigation system that mimics the drought condition in a growth chamber. The Wi-Fi-enabled iPOTs system allows water supply from the bottom of the pot, based on the soil water level set by the user, and automatically controls the soil water level at a desired depth. The iPOTs also allows users to monitor environmental parameters, such as soil temperature, air temperature, humidity, and light intensity, in each pot. To verify whether the iPOTs mimics the drought condition, we conducted a drought stress test on rice varieties and near-isogenic lines, with diverse root system architecture, using the iPOTs system installed in a growth chamber. Similar to the results of a previous drought stress field trial, the growth of shallow-rooted rice accessions was severely affected by drought stress compared with that of deep-rooted accessions. The microclimate data obtained using the iPOTs system increased the accuracy of plant growth evaluation. Transcriptome analysis revealed that pot positions in the growth chamber had little impact on plant growth. Together, these results suggest that the iPOTs system represents a reliable platform for phenotyping plants under drought stress.

Epigenetic changes in the DNA methylome are increasingly shown to play an integral role in regulating gene expression necessary for plants’ adaption to environmental stressors. Plants subjected to the novel environment of spaceflight onboard the International Space Station (ISS), show stress-related transcriptomic changes most notably associated with pathogen stress response. Here, we investigate how known terrestrial stress associated epigenetic modulations might play a role in spaceflight adaptation. To examine the role of 5mCyt in spaceflight adaptation, the APEX04-EPEX experiment conducted onboard the ISS evaluated the spaceflight altered genome wide methylation profiles of two methylation regulating gene mutants (methyltransferase 1 (met1-7) and elongator complex subunit 2 (elp2-5)) that are involved in pathogen defense response, along with a wild type Col-0 control. MethylSeq and RNAseq analyses were performed on both spaceflight grown samples and ground grown controls. In addition, the epigenetics effects that may contribute to the differential gene expression patterns observed between leaf and root tissues were also investigated in an organ-specific manner.

Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.

Purpose: We aimed to compare transcriptomic changes after melatonin (MT) and IAA treatments in Arabidopsis and dissected cross-talk between MT and IAA；Methods: A total amount of 1 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq2000 platform and paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).；Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified coregulated genes by melatonin and IAA in Arabidopsis seedlings

Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, miRNAs, and key miRNA-target pairs in M. ruthenica under drought and re-watering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed between the re-watering (RW) vs. drought (DS) comparison and control (CK) groups. The degradome sequencing analysis revealed that 348 miRNAs (37 novel and 311 conserved miRNAs) were identified with 6,912 target transcripts, forming 11,390 miRNA-target pairs in the three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21,18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour HL or HT treatment at the photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in HL- or HT-treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to HL and HT. We provide a systematic analysis of HL and HT responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.

We analyzed the transcriptomic profile of Col-0 and pif4-2 pif5-3 double mutant using 3-week-old plants. Two biological replicates were performed with the materials were treated at 42°C for 5 hours, and after 3 days of recovery growth, the 3rd and 4th rosette leaves which began to turn yellow at the edge were collected.

More than 40% of the world’s potentially arable lands are composed of acid soils, and the area exceeds 20 million hectares in China.Aluminum (Al) toxicity have become major factors threating crop production on acid soils. NTL proteins are a group of NAC transcription factors, and play an important role in the mechanisms of plant response to various abiotic stresses, such as drought, salt and cold stress. However, the underlying adaption mechanism of whether NTL is involved in regulating Al toxicity in plants remain poorly understood. Soybean is important grain and oil crop. Therefore, this study focused onanalyzing the function of GmNTLs in soybean adaptation to Al toxicity. Bioinformatics analysis and expression pattern analysis were performed on 15 members of the GmNTL family in the soybean. At the same time, we preliminary analyzed the function of some members in the adaptation mechanism of aluminum toxicity by overexpressing the genes in Arabidopsis thaliana.

Plants have evolved a sophisticated defense system to survive under natural drought conditions. MicroRNAs (miRNA) are small noncoding RNAs that act as a post-transcriptional regulator in the environmental stress response and developmental process. Although many studies have reported the involvement of the miRNAs in drought response, molecular mechanisms by which miRNAs confer drought tolerance remain elusive. Here, we show that MIR171f, a member of MIR171 gene family, is mainly expressed in response to drought stress and regulate transcript levels of SCARECROW-LIKE6-I (SCL6-I) and SCL6-II. The SCL6 genes are known to be involved in shoot branching and flag leaf morphology. The MIR171f-overexpressing (MIR171f-OE) transgenic plants showed reduced drought symptoms as compared with non-transgenic (NT) control plants under both field drought and PEG-mediated dehydration stress conditions. Transcriptome analysis using the MIR171f-OE and mir171f-K/O mutants revealed that MIR171f regulates the expression of flavonoid biosynthesis genes, consequently leading to drought tolerance. Flavonoid biosynthesis genes were up-regulated in MIR171f-OE plants as compared with NT control plants under both normal and drought conditions. Together, our findings demonstrated that MIR171f plays an important role in plant drought-tolerance mechanism by regulating transcript levels of SCL6-I and SCL6-II.

Larix kaempferi is important afforestation species in northeastern China and is one of the most drought-tolerant pine species.Larix kaempferi has a very complex genetic background and a large genome, and study on the molecular mechanisms of drought resistance is still lag behind. Four-month-old of L. kaempferi seedlings grown in the greenhouse into two groups, the drought treatment group was no watering for 14 d (D14), while normally watered seedlings were used as control group (CK). All plants harvested on the same day and at the same time for the upper part of seedling (circa 3 cm from the top), frozen in liquid nitrogen. We designed six samples (CK-1, CK-2, CK-3, D14-1, D14-2, and D14-3) in total for Illumina HiSeq.

Plants have evolved cell wall integrity signaling pathways to maintain cell wall homeostasis during rapid growth and in response to environmental stress. The cell wall leucine-rich repeat extensins LRX3/4/5, the RAPID ALKALINIZATION FACTOR (RALF) peptides RALF22/23, and FERONIA (FER) function as a module to regulate plant growth and salt stress responses via the sense of cell wall integrity. However, the intracellular signaling pathways that mediate the effects of the LRX3/4/5-RALF22/23-FER module are still largely unknown. Here, we report that jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) accumulate constitutively in lrx345 and fer mutants. Blocking JA pathway rescues the retarded growth phenotype of the lrx345 and fer-4 mutants, while disruption of ABA biosynthesis suppresses the salt-hypersensitivity of these mutants. Many salt stress-responsive genes display abnormal expression patterns in the lrx345 and fer-4 mutants, as well as in wild type plants treated with epigallocatechin gallate (EGCG), an inhibitor of pectin methylesterases, suggesting that the cell wall integrity is a critical factor that determines the expression of stress-responsive genes. Production of reactive oxygen species (ROS) is constitutively increased in the lrx345 and fer-4 mutants, and inhibition of ROS accumulation suppresses the salt-hypersensitivity of these mutants. Together, our results suggest that the LRX3/4/5-RALF22/23-FER module controls plant growth and salt stress responses by regulating hormonal homeostasis and ROS accumulation.

Perception and relay of cell wall signals is critical for plants to regulate growth and stress responses, but the mechanism underlying this biological process remains largely unknown. Here we report that RAPID ALKALINIZATION FACTOR (RALFs) peptides, Leucine-rich repeat extensins (LRXs) and FERONIA (FER) are physically associated in extracellular region. lrx345, fer-4, and transgenic plants overexpressing RALF22 or RALF23 all showed retarded growth, increased sensitivity to salt stress, and constitutively increased levels of ABA, JA, and SA. Salt treatment or chemical disruption of cell wall promotes the release of mature RALF peptides, which negatively regulate the function of FER by inducing its internalization. JA mutants coi1 and aos restore the retarded growth, and mutation of ABA2 suppresses the salt-sensitive phenotype of lrx345. Together, we propose that LRXs, RALFs, and FER function as a module to sense and transduce cell wall signals, thereby regulating growth and stress responses via hormones-mediated pathways.

MOP1-mediated regulation of gene expression of plant responses to early ABA induction has transcriptionally and physiologically relevant roles. Homozygous mop1-1 plants are compromised in their ability to recover from water deprivation.Purpose: Genome-wide identification of immediate and direct MOP1-dependent ABA transcriptional responsesMethods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 1 hour. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR.Results: we mapped ~33 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 1,856 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a log2FC ≥ 0.95 and FDR <0.05, 1,119 DEGs were found to be unique to one genotype/treatment comparison.Conclusions: MOP1-mediated regulation of gene expression in maize seedlings in the RdDM (mop1-1) mutant has relevant transcriptional and physiological roles in plants subjected to stress. Our study generated by RNA-seq technology identified genes and biological processes regulated by RdDM and ABA-mediated stress responses, including MOP1-dependent and immediate response genes (MIMs).

Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome was reported. A total of 967 PK genes were identified from pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by the phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 duplication events including 285 PK genes were found, and Ka/Ks ratio revealed they experienced strong negative selection. GO functional analysis indicated majority PKs involved in molecular functions and biological processes. The RNA-Seq data of PK genes in pecan were further analyzed at subfamily level, and different PK subfamilies performed various expression patterns across different conditions or treatments, suggesting PK genes in pecan involved in multiple biological functions and stress responses. Taken together, this study provided insight into the expansion, evolution and function of pecan PKs. Our findings regarding expansion, expression and co-expression analyses could lay a good foundation for future research to understand the roles of pecan PKs, and find the key candidate genes more efficiently.

Chromatin modifications play important roles in plant adaptation to abiotic stresses, but the precise function of histone H3 lysine 36 (H3K36) methylation in drought tolerance remains poorly evaluated. Here, we report that SDG708, a specific H3K36 methyltransferase, functions as a positive regulator of drought tolerance in rice.

Chromatin modifications play important roles in plant adaptation to abiotic stresses, but the precise function of histone H3 lysine 36 (H3K36) methylation in drought tolerance remains poorly evaluated. Here, we report that SDG708, a specific H3K36 methyltransferase, functions as a positive regulator of drought tolerance in rice.

In this project we are investigating the differential mechanism of tolerance in rice under combined stresses of salinity and partial submergence as encountered during saline water flooding by looking into expression profile of DEGs and uniquely expressed genes.

Heat stress is a great threat to plant growth because of their sessile lifestyle. Here, we show that histone methyltransferases SDG25 and ATX1 regulate gene expression and antagonize DNA remethylation under recovery stage after long-term high temperature treatment by catalyzing the methylation of histone H3K4 loci.

The periderm is a protective barrier crucial for land plants survival, but genetic factors involved in its regulation are fairly unknown. In a previous transcriptomic approach in the cork oak periderm (Quercus suber) we identified a RS2-INTERACTING KH PROTEIN (RIK) homolog, of unknown function and with a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. To gain insight into the function of RIK in periderm, the potato (Solanum tuberosum) tuber periderm was used as a model. The StRIK transcript profile showed ubiquitous accumulation in all vegetative tissues analyzed, including periderm and other suberized tissues such as root and wound-healing tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show evident effects in tuber periderm anatomy but unexpectedly unlike Wild type, the transgenic plants flowered. Nevertheless, the periderm of StRIK-RNAi lines did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis ortholog. Altogether those findings suggest that the potato StRIK might play roles in RNA maturation and stress response throughout diverse plant developmental processes such as flowering and periderm formation.

The current study has provided the first RNA-Seq dataset and comparative transcriptome profile of GRH responsive genes from Ilpum (GRH-susceptible rice cultivar) and a near isogenic line (NIL) carrying Grh1 gene introduced from Shingwang into Ilpum to investigate the possible transcriptional interaction with other defense related genes. In addition, RNA-Seq data and MapMan analysis revealed the activation of multiple regulatory pathways following GRH infestation. Furthermore, the observed differential transcriptome profile between Ilpum and NIL would suggest the existence of a possible interaction network between Grh1 and other defense related genes towards GRH resistance in rice.

Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicated that HDA6 and HDA19 function together with other components of the histone deacetylase complexes and co-regulate the expression of a number of genes. HDA6 and HDA19 have been thought to repress gene transcription by histone deacetylation. We found that the histone deacetylase complexes can also repress gene expression via certain histone-deacetylation-independent mechanisms. In the mutants of the histone deacetylase complexes, the expression of a number of stress-induced genes was up-regulated. Several mutants of the histone deacetylase complexes showed severe retardation in growth. Considering that the growth retardation is thought to be a trade-off for the increase of stress tolerance, we predict that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under non-stress conditions.

Plants have a large family of membrane receptor kinases (RKs) which sense extracellular signals to control plant growth, development, immunity, and stress response. The largest group of RKs contains an extracellular leucine-rich repeat (LRR) domain with over 200 members in Arabidopsis. However, the functional understanding of most of the LRR-RKs has been hampered by their genetic redundancy and the subtle phenotypes of RK overexpression. Here we show that the rapamycin-mediated heterodimerization of chimeric cytosolic kinase domains from receptor/co-receptor pairs in the plasma membrane can activate their downstream cellular signaling pathway, inducing the specific biological responses, including brassinosteroid, plant immunity, stomatal development, and lateral root development. This chemically controlled synthetic biology approach will be useful to investigate biological functions of LRR-RKs and their signaling pathways.

Sucrose Non-Fermenting1-Related Kinase1 (SnRK1) is an evolutionarily conserved protein kinase with key functions in energy management during stress responses in plants.To address a potential role of SnRK1 under non-stress conditions, we performed a metabolomic and transcriptomic characterization of 20 d-old rosettes of Arabidopsis SnRK1 gain- and loss-of-function mutants during the diurnal cycle.SnRK1 manipulation altered the slope of the correlation between sucrose and trehalose 6-phosphate (Tre6P). It also modulated the flux of carbon to the tricarboxylic acid cycle downstream of Tre6P-signalling. SnRK1 depletion modified expression of SnRK1-induced genes least at the end of the day (when Tre6P levels peak) and most at the end of the night (when Tre6P levels are lowest). Expression of a subset of these genes was attenuated by inducible Tre6P accumulation in a time-of-day dependent manner. Finally, transcriptional profiling uncovered a wide impact of SnRK1 on gene expression in non-stress conditions, establishing a clear connection with iron and sulfur metabolism.In conclusion, SnRK1 plays central functions in metabolic and transcriptional regulation in the absence of stress. SnRK1 is further involved in the reciprocal control of sucrose-driven Tre6P production and/or degradation and its activity is modulated by daily fluctuations in Tre6P levels.

We report the identification of RCI5, an Arabidopsis cold inducible gene encoding a FMO. RCI5 seems to participate in the biosynthesis of TMAO, a new plant methabolite. We also demonstrate that TMAO positevely controls Arabidopsis tolerance to low temperature, high salt in the soil and drough stress, by promoting a wide transcriptomic reprograming of stress-relate genes. Finally, we found that diferent crops also contain TMAO in their tissues, and that exogenous applications of TMAO also increases tomato tolerance to abiotic stress.

Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the devastating diseases causing significant losses to maize production worldwide. Although plant oxylipins have been widely reported as potent signals to activate diverse biotic stress responses, the roles of distinct oxylipin pathway branches initiated by either 9- or 13-lipoxygenases (LOXs) in defense against GSR remain unexplored. In this study, the functional analysis showed that disruption of ZmLOX5, a maize 9-LOX gene, resulted in increased susceptibility to GSR. To identify the key genes and metabolites associated with GSR resistance, we profiled transcriptome and oxylipins in the lox5 mutant and near-isogenic wild type. The results showed that JA biosynthetic pathway genes are highly up-regulated, whereas multiple 9-LOX pathway genes down-regulated in lox5-3 mutant in response to F. graminearum infection. Furthermore, oxylipin profiling of the mutant and corresponding wild type, B73, as well as a more resistant line, W438, uncovered significantly higher contents of JA-isoleucine (JA-Ile) and other jasmonates but relatively lower levels of 9-oxylipins in lox5-3 upon infection. By contrast, resistant line W438 and B73 displayed relatively lower levels of JAs, yet considerable increase of 9-oxylipins. Taken together, these results clearly indicated that the signaling pathways of 9-oxylipins and JAs antagonize each other, and that while ZmLOX5-produced 9-oxylipins contribute to resistance, JAs are likely to function as negative regulator in maize defense against GSR.

By using high through put Illumina based sequencing approach, we generated RNASEQ data for leaves and crowns of Alta and NCGR1363 at 0H and 42D exposure to temperature stress. We present the expression profile of 896 putative candidate genes identified within a QTL associated with freezing tolerance. Expression profiles revealed genotype specific cold responsive expression patterns in one group of candidates and expression differences between genotypes prior to treatment for many of the genes.

Fusarium head blight caused by Fusarium graminearum is a devastating disease of malting barley. Mycotoxins associated with contaminated grain can be transferred from malt to beer and pose a health risk to consumers. In western Canada, F. graminearum has undergone an adaptive shift from 15ADON constituency to dominance by virulent 3ADON-producers, likewise NIV-producers have established in regions of southern United States. Lack of adapted resistance sources with adequate malting quality has promoted the use of alternative breeding methodologies such as in vitro selection. We studied the low-deoxynivalenol characteristic of in vitro selected, two-row malting barley variety ‘Norman’ by RNAseq in contrast to its parental line ‘CDC Kendall’, when infected by 15ADON-, 3ADON- and NIV-producing isolates of F. graminearum. The current study documents higher mycotoxin accumulation by 3ADON isolates, thereby representing increased threat to barley production. At 72-96 hours post infection, significant alterations in transcription patterns were observed in both varieties with pronounced upregulation of the phenylpropanoid pathway and detoxification gene categories (UGT, GST, CyP450 and ABC) particularly in 3ADON treatment. Defense response was multi-tiered, where differential expression in ‘Norman’ associated with antimicrobial peptides (thionin 2.1, defensing, non-specific lipid-transfer protein) and stress-related proteins such as late embryogenesis abundant proteins, heat-shock, desiccation-related and a peroxidase (HvPrx5). Several gene targets identified in ‘Norman’ would be useful in application of breeding varieties with reduced deoxynivalenol content.

Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq.Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays.Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy.Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.

Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize in the Quiescent Center (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modeling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development.

Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. We find FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) to be specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by promoting histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.

To investigate the regulatory mechanisms of GmNFYA in salt stress, leaves and roots of transgenic plants and JACK plants were collected for RNA extraction and sequencing. Clean reads of RNA-sequencing were mapped to soybean genome and genes that had a 2 fold increase or 50% decrease, compared to JACK, were defined as differential expressed genes (DEGs).

The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long-term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and primary metabolome analyses were carried out on plant leaves collected from different physiological stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 46 metabolites were differentially regulated across stages. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post-transcriptional modification in metabolic reprogramming to prepare plants to desiccation and recovery upon rehydration. The integrative analysis of three -omics datasets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of fine regulations/changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. For example, maintenance of cyclic electron flow and photorespiration and switch from C3 to Crassulacean acid metabolism (CAM) photosynthesis may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. transcripts with a delayed translation, ATP-independent bypasses, alternative respiratory pathway and 4-aminobutyric acid (GABA) shunt may play a role in energy management, altogether conferring bioenergetic advantages to meet energy demands for survival during desiccation. This knowledge provides a high-resolution map of the changes occurring in the primary metabolism during dehydration and rehydration and enriches the current understanding of the molecular mechanisms underpinning plant desiccation tolerance. The datasets here provided will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.

Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and ultimately the formation of nitrogen-fixing root nodules. Here we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti, while conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of Early Nodulin 11 shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic, but not the osmotic, component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with Sinorhizobium meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggests that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, function to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.

In plants, smRNAs are often derived from long double-stranded RNA (dsRNA) molecules synthesized by one of the six genomically-encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding co-factors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their co-factors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDR clade proteins (RDR3 - 5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, 2, and 6) as well as the RDR2 co-factor RNA-DIRECTED DNA METHYLATION 12 (RDM12) and the RDR6 co-factor SUPRESSOR OF GENE SILENCING 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6, but that this protein seems to be a more general co-factor for the RDR family proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have higher survival rate under salt treatment in comparison to wild-type (Col-0). In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.

The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under growth limiting temperatures, time of day modulates the accumulation of polyadenylated mRNAs. In response to heat stress, plants will conserve energy and selectively translate mRNAs. How the clock and/or time of day regulates polyadenylated mRNAs bound by ribosomes in response to heat stress is unknown. In-depth analysis of Arabidopsis thaliana translating mRNAs found that time of day gates the response of approximately one-third of the circadian regulated heat responsive translatome. Specifically, time of day and heat stress interact to prioritize the pool of mRNAs in cue to be translated. For a subset of mRNAs, we observed a stronger gated response during the day, and preferentially before the peak of expression. We propose previously overlooked transcription factors (TFs) as regulatory nodes and show that the clock plays a role in the temperature response for select TFs. When the stress was removed, the redefined priorities for translation recovered within one-hour, though slower recovery was observed for abiotic stress regulators. Through hierarchical network connections between clock genes and prioritized TFs, our work provides a framework to target key nodes underlying heat stress tolerance throughout the day.

We sequenced mRNA of WT, p35S:AtBBD1 (OX) and atbbd1 (KO) plants. Plants were grown in soil for three weeks at 23 ℃ with 60% relative humidity. mRNA was isolated 6 hours after threating with 20% PEG.

We analyzed transcriptome changes in Arabidopsis between seed development (3 stages corresponding Heart (H), Bent (B) and mature (MS) embryo stages) at three growing conditions (23, 25 and 27°C)

The protein content determines the cell state. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are still unknown. We quantified 47,535 mRNAs and 3,742 proteins in filling grain of wheat under two thermal environments. The impact of mRNA abundance and sequence features implicated in protein translation and degradation on protein expression were evaluated by regression analysis. Transcription, codon usage and amino acid frequency mainly affect protein expression, and their combined contribution explains 58.2% and 66.4% of protein abundance variation in two types of heat stresses. Of which, transcription contributes more to the protein expression under severe heat stress (31%) than to mild stress (6%). Codon usage plays a stable and powerful role in protein expression under heat stress, even surpassing transcription. What’s more, the usage of AAG is a key factor regulating rapid protein expression under heat stress. This study revealed the main factors affecting the changes of protein abundance in the early stage of heat stress, and explained the mystery that plants can express protein rapidly under heat stress.

Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses. Key results: Soybean plants were not visibly nutrient or water stressed. We identified 55 consistently down-regulated genes in weedy plots. Many of the down-regulated genes were heat shock genes. Fourteen genes were consistently up-regulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the up-regulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. Main conclusion: The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

Purpose: To determine candidate genes involved in the increased susceptibility of ros1 plants to imazethapyr.；Results: Our study reveled that that imazethapyr up-regulated genes related to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis and epigenetic processes. We identified 31 candidate genes as putative involved in herbicide detoxification, some of this genes are under epigenetic regulation of ROS1.

In this work, we describe a TDNA insertion mutant for Mediator complex subunit 8 (MED8) that regulates the oxidative stress responses. Wild-type Col-0 and med8 seedlings were growth under control condition or oxidative stress (induced by methyl viologen treatment) and were subjected to RNA-seq profiling. Total mRNA fractions were isolated and subjected to signle-end deep sequencing (approx.30M reads/sample) to reveal differential expression between genotypes and conditions.

Results: We identified a small number of genes that were differentially expressed in both years. More importantly, gene set enrichment analysis of the data determined that weeds, when present through the critical weed free period impacted phytochrome signaling, defense responses, photosynthetic processes, oxidative stress responses, and various hormone signaling processes. When weeds were removed at V4 and the plants allowed to recover until V8, the weeds still imprinted impacts on phytochrome signaling, oxidative stress, and defense responses. Thus, it appears that weeds presence through the early portion of the critical weed free period, even after removal, induced processes that reduce corn growth and yield that lasted at least through V8.；Conclusions: This study represents the first investigation of the impact of the lasting effects of weeds during the early critical weed free period on the transcriptome of corn, and provides additional data on the impact of weeds through the critical weed free period that augments and confirms much of what was observed in similar microarray studies.

Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.

This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of heat stress on maize alternative splicing we used a controlled environment facility called the Enviratron to simulate field conditions. For our experiments, maize plants were subjected to conditions simulating normal diurnal rhythms of light and temperature, with increasing maximal daily temperature (MDT). Maize plants were grown continuously under four different temperature regimes with simulated morning temperatures ramped up over 6 hr to the MDT of 31°C, 33°C, 35°C or 37°C and simulated evening/night time temperatures ramped down over 8 hr to 10°C below the MDT. We tracked the alternative splicing events of maize W22 seedlings grow under different temperatures (MDT of 31°C, 33°C, 35°C or 37°C) to evaluate how different MDTs affect the program of gene alternative splicing in maize. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of V4 and V5 W22 plants (at 20 and 27 DAG, respectively). Plants were sampled in triplicates.

Results: Here we perform Hi-C, ATAC-seq and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including of HS-related genes, consistent with observed higher HS tolerance in this cultivar.；Conclusions: Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.

Predicting how climate change affects biotic interactions and their evolution poses a challenge. Plant-insect herbivore interactions are particularly sensitive to climate change, as climate-induced changes in plant quality cascade into the performance of insect herbivores. Whereas the immediate survival of herbivore individuals depends on plastic responses to climate change induced nutritional stress, long-term population persistence via evolutionary adaptation requires genetic variation for these responses. In order to assess the prospects for population persistence under climate change, it is therefore crucial to characterise response mechanisms to climate change induced stressors, and quantify their variability in natural populations. Here, we test developmental and transcriptomic responses to water limitation induced host plant quality change in a Glanville fritillary butterfly (Melitaea cinxia) metapopulation. We combine nuclear magnetic resonance spectroscopy on the plant metabolome, larval developmental assays and an RNA seq analysis of the larval transcriptome. We observed that responses to feeding on water limited plants, in which amino acids and aromatic compounds are enriched, showed marked intrapopulation variation, with individuals of some families performing better on control and others on water limited plants. The transcriptomic responses were concordant with the developmental responses: Families exhibiting opposite developmental responses also produced opposite transcriptomic responses, e.g. in growth associated intracellular signalling. The opposite developmental and transcriptomic responses are associated with between families differences in organic compound catabolism and storage protein production. The results reveal heritable intrapopulation variability in plasticity, suggesting potential for evolutionary responses to drought-induced changes in host plant quality in the Finnish M. cinxia metapopulation.

Although some mechanisms are known how plant growth beneficial bacteria help plants to grow under stressful conditions, we still know little how the metabolism of host plants and bacteria is coordinated during the establishment of functional interaction. In the present work, using single and dual transcriptomics, we studied the reprograming of metabolic and signaling pathways of Enterobacter sp. SA187 with Arabidopsis thaliana during the change from free-living to endophytic host-microbe interaction. We could identify major changes in primary and secondary metabolic pathways in both the host and bacteria upon interaction, with an important role of the sulfur metabolism and retrograde signaling in mediating plant resistance to salt stress. Also, we studied the effect of SA187 endogenous compounds and its role on sulfur metabolism and consequently salt tolerance. These data should help future research in the field of beneficial plant-microbe interactions for developing sophisticated strategies to improve agriculture of crops under adverse environmental conditions.transcriptome of Arabidopsis thaliana organs with beneficial microbe, beneficial microbe endogenous compound, and ethylene precursor

Recently we published a set of tobacco lines, expressing the Dacucus carota (carrot) DcLCYB1 gene, with accelerated development, increased carotenoid content, and plant yield. Due to this, expression of DcLCYB1 might be of general interest in crop species as a strategy to accelerate plant development and increase biomass production under adverse field conditions. However, to follow this path, a better understanding of the molecular basis of this phenotype is essential. Here, we combine OMICs (RNAseq, proteomics, metabolomics, and lipidomics) and stress experiments to advance our understanding on the broader effect of the LCYB expression on the tobacco genome and metabolism.

Aluminum (Al) is the most common metal in the Earth’s crust and Al toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. The first symptom of Al toxicity is the reduction of root growth, resulting in decreased water and nutrients uptake, plant growth retardation, and finally, yield reduction. Barley (Hordeum vulgare L.), which is the fourth cereal crop in regards to cultivation area and production tonnage, belongs to crops most sensitive to toxic aluminum ions in low pH soils. We present the RNA-seq transcriptome analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 µM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. Interestingly, in the short-term experiment, more genes were differentially expressed between root meristems grown at pH=6.0 and pH=4.0, than between those grown at pH=4.0 with and without Al treatment. The upregulated genes that were overrepresented at conditions of low pH, compared to optimal pH, were associated with response to oxidative stress, cell wall organization, and iron ion binding. Among genes downregulated by low pH were mainly those related to chromatin organization. These results show that low pH itself is a severe stress for barley plants. Among genes upregulated by short Al treatment, overrepresented were those related to response to stress condition and calcium ion binding. After 7 days of hydroponics, the number of DEGs between hydroponics at pH=4.0 and 6.0 were still high but lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 day Al treatment caused massive changes in the transcriptome profile compared to the condition of low pH alone. Over 4 000 genes were upregulated and almost 2 000 genes were downregulated by long-term Al stress. These DEGs were related to e.g. stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants.Additionally, we phenotyped in detail the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH=6.0, pH=4.0, and pH=4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress facor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be underlined that in the acidic arable lands, plants are exposed simultaneously to both of these stresses (low pH and Al), as Al becomes soluble at pH below 5.5. The presented transcriptome analysis may help to find potential targets for breeding barley plants more tolerant to such conditions.

Results Shoot transcriptome analysis revealed that bicarbonate quickly (3 h) induced Fe-deficiency related genes in T6(c-) leaves, while in A1 (c+) main initial changes were found in receptor-like proteins (RPL), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolate (GS), Sulphur starvation, starch degradation, and cell cycle.Conclusions: Our results suggest that leaves of carbonate tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with the ability to translocate more iron to aerial parts, producing a higher biomass and maintaining silique production. In leaves of A1(c+) plants, the activation of other genes related to apoplastic stress perception, signal transduction, GS, sulphur acquisition, and cell cycle regu-lation precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress

To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.

BACKGROUND: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Currently, the only effective strategies for controlling the diseases associated with this pathogen involve regular pesticide applications to manage psyllid population density. However, such practices are unsustainable and will eventually lead to widespread pesticide resistance in psyllids. Therefore, new control strategies must be developed to increase host-plant resistance to insect vectors. For example, expression of constitutive and inducible plant defenses can be improved through selection. Currently, it is still unknown whether psyllid infestation has any lasting consequences on tomato plant defense or tomato plant gene expression in general. RESULTS: To characterize the genes putatively involved in tomato defense against psyllid infestation, RNA was extracted from psyllid-infested and uninfested tomato leaves (Moneymaker) three weeks post-infestation. Transcriptome analysis identified 362 differentially expressed genes. These differentially expressed genes were primarily associated with defense responses to abiotic/biotic stress, transcription/translation, cellular signaling/transport, and photosynthesis. These gene expression changes suggested that tomato plants underwent a reduction in plant growth/health in exchange for improved defense against stress that was observable three weeks after psyllid infestation. Consistent with these observations, tomato plant growth experiments determined that the plants were shorter three weeks after psyllid infestation. Furthermore, psyllid nymphs had lower survival rates on tomato plants that had been previously psyllid infested. CONCLUSION: These results suggested that psyllid infestation has lasting consequences for tomato gene expression, defense, and growth.

Pierce's disease (PD) in grapevine (Vitis vinifera) is caused by the bacterial pathogen Xylella fastidiosa. X. fastidiosa is limited to the xylem tissue and following infection induces extensive plant‐derived xylem blockages, primarily in the form of tyloses. Tylose‐mediated vessel occlusions are a hallmark of PD, particularly in susceptible V. vinifera. We temporally monitored tylose development over the course of the disease to link symptom severity to the level of tylose occlusion and the presence/absence of the bacterial pathogen at fine‐scale resolution. The majority of vessels containing tyloses were devoid of bacterial cells, indicating that direct, localized perception of X. fastidiosa was not a primary cause of tylose formation. In addition, we used X‐ray computed microtomography and machine‐learning to determine that X. fastidiosa induces significant starch depletion in xylem ray parenchyma cells. This suggests that a signalling mechanism emanating from the vessels colonized by bacteria enables a systemic response to X. fastidiosa infection. To understand the transcriptional changes underlying these phenotypes, we integrated global transcriptomics into the phenotypes we tracked over the disease spectrum. Differential gene expression analysis revealed that considerable transcriptomic reprogramming occurred during early PD before symptom appearance. Specifically, we determined that many genes associated with tylose formation (ethylene signalling and cell wall biogenesis) and drought stress were up‐regulated during both Phase I and Phase II of PD. On the contrary, several genes related to photosynthesis and carbon fixation were down‐regulated during both phases. These responses correlate with significant starch depletion observed in ray cells and tylose synthesis in vessels.

This study is the first transcriptome study for Cd and melatonin treatment in lettuce, both transcriptomes and the expression profile would provide the foundation for further exploring the molecular mechanism of Cd accumulation, and develop breeding strategies aimed at decreasing Cd in crop plants.

Plants are primary producers of food and oxygen on Earth and will likewise be indispensable to the establishment of large-scale sustainable ecosystems and human survival in space. To contribute to the understanding of how plants respond to spaceflight stresses, we examined the relevance of the unfolded protein response (UPR), a conserved signaling cascade that responds to a number of unfavorable environmental stresses, in the model plant species Arabidopsis thaliana. To do so, we compared the transcriptional responses of wild type and UPR-defective seedlings to spaceflight during the SpaceX-CRS12 mission to the International Space Station. We established that orbital culture substantially altered the expression of hundreds of stress related genes compared to ground control conditions. Although many of these genes were differentially regulated in the UPR mutants in the ground control conditions compared to wild type, their expression was largely equalized in all genotypes by flight. Our results have yielded new information on how plants respond to growth in orbit and support the hypothesis that spaceflight induces the activation of signaling pathways that compensate for the loss of UPR regulators in the control of downstream transcriptional regulatory networks.

Here, we adopt a method that combines tRNA-seq and cp-RNA-seq to identify and quantify tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncovers complex tRFs repertoire and the dynamic expressions of tRNA genes in plants.

Purpose: Nonstructural carbohydrates has a major impact on trees response to meteorological conditions. The goals of this study were to define which changes in gene expression are linked to possible mechanisms used by the plant to buffer the decline in carbon source during gradual soil drying, an intensive abrupt heat wave, and recovery from drought?Methods: We combined measurements of nonstructural carbohydrates (NSC), tree physiology and expression of genes encoding starch metabolism enzymes. The experiment was conducted on potted olive (Olea europaea) trees, half of them under 28 days of soil drought.Results: We identified the gene family members relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase’s and starch synthase’s family members were identified, with some members upregulated throughout drought while other members in recovery. The daily starch metabolism machinery was different from the stress-mode starch metabolism machinery when some genes are unique to the stress-mode response.

During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures and identify hubs associated with desiccation tolerance, longevity, germination under water stress and dormancy.

Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.

Results: Transcriptome analysis has revealed that the tolerant genotype had increased photosynthesis in saline conditions while the susceptible genotype acted in a contrasting way. The chlorophyll content measurements have backed up this result with increase in tolerant and decrease in susceptible genotype. Transcriptome also displayed a more active carbon and amino acid metabolism for the tolerant genotype as well. Analysis of primary metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism with the accumulation of glutamate and asparagine and hinted a lowered photorespiration level for the tolerant one. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response pathway. According to ion content comparison, the tolerant genotype managed to block accumulation of Na+ in the leaves while accumulating significantly less Na+ in the roots compared to susceptible genotype. K+ levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn+2 and Mn+2 levels were also dropped in the tolerant roots, while Mo+2 levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype.Conclusion:The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance mainly in common bean, but for all crops.

A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.

We analysed transcriptome changes between seed devlopement (4 stages corresponding at before (S1) and after (S2) desiccation tolerance acquisition and before (S3) and after (S4) longevity acquisition) in dissected seed tissues (embryo, E; Endosperm Eo and Seed Coat SC)

Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting crop performance and yield. While the response of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, we hardly know anything about the response of its relative, the important oil crop plant Brassica napus. Here, we analyzed the molecular response of leaves of rapeseed seedlings to full submergence under illumination. RNAseq experiments revealed a strong carbon starvation response under submergence, but no indication for a low-oxygen response. We used two cultivars in this study, one Asian flooding-tolerant cultivar and one European hybrid cultivar, but those genotypes did not show strong differences in their responses to submergence.

We examined the transcriptome induced by GmNAC81 overexpression and leaf senescence and showed that GmNAC81 further modulates leaf senescence by regulating an extensive repertoire of functionally characterized senescence-associated genes (SAGs). GmNAC81 overexpression also uncovered the regulation of typical drought-responsive genes. Key regulators and effectors of ABA signaling were suppressed by GmNAC81 overexpression.

Heat stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, which however is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. Loss of H1 caused activation of pericentromeric GYPSY elements upon heat treatment, despite that these elements remained highly methylated. In contrast, non-pericentromeric COPIA elements became activated concomitantly with loss of DNA methylation. The same COPIA elements became activated in heat-treated chromomethylase2 (cmt2) mutants, indicating that H1 represses COPIA elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1 deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both, H1 and DNA methylation redundantly suppress the plant response to heat stress.

aap_bap_nitropath_2014-botrytisxn - impact of nitrogen nutrition on the response of plants to biotic stress-Comparison of Arabidopsis responses to Botrytis infection in relation to nitrogen nutrition (sufficient vs limited).

Illumina HiSeq technology was used to generate mRNA profiles from Helianthemum almeriense in three different conditions: non-mycorrhizal plant, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. Paired-end reads of 75 bp were generated and aligned to a de novo transcriptome assembly from H. almeriense, which was performed using Megahit version 1.1.3 and transcripts from each condition were mapped onto the de novo transcriptome with Bowtie2 version 2.3.0.

Illumina HiSeq technology was used to generate mRNA profiles from Terfezia claveryi in three different conditions: free living mycellium, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. Paired-end reads of 75 bp were generated and aligned to Terfezia claveryi reference transcripts using CLC Genomics Workbench 11.

Pomegranate (Punica granatum L.) is sensitive to drought stress, which largely affects its transplantation survival rate, fruit yield and quality. Abscisic acid (ABA) treatment can reduce the drought-induced adverse impacts on plants. However, no studies have ever applied ABA as an exogenous supply to alleviate the drought stress on pomegranates. In this study, we performed comparative transcriptome analysis between the ABA-treated and untreated pomegranates to reveal the ABA-induced mechanisms in response to drought-stress. Our results showed that exogenous ABA application substantially enhanced pomegranate drought resistance by strengthening metabolic pathways, such as BRs synthesis, peroxisome biogenesis, photosynthesis and hemicelluloses synthesis. Furthermore, treatments with different ABA concentrations may provoke different transcriptional responses and, once the concentration exceeds the optimal (60 μM), it might induce some potential adverse impacts on plant growth and stress resistance.

Global warming and heat stress belong to the most critical environmental challenges to agriculture worldwide, causing severe losses of major crop yields. In present study we report that the endophytic bacterium Enterobacter sp. SA187 protects Arabidopsis thaliana to heat stress. To understand the mechanisms at molecular level we performed RNA-seq

Jujube (Ziziphus jujuba Mill.) is an economically and agriculturally significant fruit crop and is widely cultivated throughout the world. Heat stress has recently become one of the major abiotic stresses limiting plant growth and productivity. However, there are few studies on the transcriptome profiling of jujube subjected to heat stress. In this study, we analyzed the physiological and transcriptomic changes of heat-resistant jujube cultivar ‘HR’ and heat-sensitive cultivar ‘HS’ caused by high temperature stress. We statistically determined 984, 1468, 1727 and 2098 differentially expressed genes (DEGs) between ‘HR’ and ‘HS’ after 0, 1, 3, 5 d of heat stress, respectively. Gene Ontology (GO) enrichment analysis indicated that Aa great deal of heat-responsive genes were identified in these DEGs by Gene Ontology (GO) enrichment analysis. It suggests the distinct molecular mechanism of jujube response to heat stress. Furthermore, we validated the expression profiles of 12 candidates using qRT-PCR to further confirm the accuracy of the RNA-seq data. These results will advance our knowledge of the genes involved in the complex regulatory networks of heat stress and provide genetic resources for further improving the heat tolerance in jujube.

The object of this study was to integrate physiological characteristics and genome-wide transcriptome analysis to understand the molecular basis of genetic variation in response to salt stress in melon. The comparison of transcriptome showed a number of variety-specific responsive genes were related to salt tolerance.

We characterized and compared the biological and molecular functions of HRE1α and HRE1β, two alternative splicing variants of HRE1, a AP2/ERF transcription factor in Arabidopsis. To compare the downstream regulatory mechanisms of HRE1α and HRE1β, Quant-Seq analysis was carried out. The experiment was designed to identify and compare differentially expressed genes (DEGs) between WT and HRE1α-overexpressing transgneic plants (OXs) and WT and HRE1β OXs grown for 14 days under SD conditions. We analyzed the biological process gene ontology (GO) annotation categories of the DEGs in HRE1α OXs and HRE1β OXs. The genes upregulated in HRE1α OXs, but not in HRE1β OXs, were enriched in the regulation of biological processes such as flower development, shoot system development, circadian rhythms, gene expression, response to gibberellin, nitrogen compound metabolic process, and aromatic compound biosynthetic processes. However, the genes up-regulated in HRE1β OXs, but not in HRE1α OXs, were enriched in the regulation of the following processes: response to toxic substances, secondary metabolic processes, response to biotic stimulus, glutathione metabolic process, response to reactive oxygen species, cell wall organization, DNA replication, response to salicylic acid, lipid localization, response to oxidative stress, carbohydrate metabolic process, photosynthesis, mitotic cell cycle process, response to osmotic stress, and response to abscisic acid. The genes upregulated in both HRE1α OXs and HRE1β OXs were enriched in biological processes involved in response to abiotic stimulus, response to light stimulus, response to endogenous stimulus, response to oxygen-containing compound, and response to lipid. In addition, we investigated the biological function of AtRH17, a DEAD-box RNA helicase gene in Arabidopsis, in salt stress response. To investigate the downstream regulatory mechanisms of AtRH17, Quant-Seq analysis was carried out. The experiment was designed to identify DEGs between WT and AtRH17 OXs grown for 14 days under SD conditions. GO annotation enrichment and KEGG pathway analysis showed that the upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4‐5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4‐5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition.

Hyperosmotic stress caused by drought and salinity is a significant environmental threat that limits plant growth and agricultural productivity. Osmotic stress induces diverse responses in plants including Ca2+ signaling, accumulation of the stress hormone abscisic acid (ABA), reprogramming of gene expression, and altering growth. Despite intensive investigation, no global regulators of all of these responses have been identified. Here, we show that the Ca2+-responsive phospholipid binding BONZAI (BON) proteins are critical for all of these osmotic stress responses. A Ca2+-imaging-based forward genetic screen identified a loss-of-function bon1 mutant with a reduced cytosolic Ca2+ signal in response to hyperosmotic stress. The loss-of-function mutants of the BON1 gene family, bon1bon2bon3, are impaired in the induction of gene expression and ABA accumulation in response to osmotic stress. In addition, the bon mutants are hypersensitive to osmotic stress in growth inhibition. BON genes have been shown to negatively regulate plant immune responses mediated by intracellular immune receptor NLR genes including SNC1. We found that the defects of the bon mutants in osmotic stress responses were suppressed by mutations in the NLR gene SNC1 or the immunity regulator PAD4. Our findings indicate that NLR signaling represses osmotic stress responses and that BON proteins suppress NLR signaling to enable global osmotic stress responses in plants.

Alterations of hydrogen peroxide (H2O2) levels have a profound impact on numerous signaling cascades orchestrating stress responses, plant growth and development, including programmed cell death. To expand the repertoire of known molecular mechanisms implicated in H2O2 signaling, we performed a forward chemical screen to identify small molecules that could alleviate the photorespiratory-induced cell death phenotype of Arabidopsis thaliana mutants lacking H2O2 scavenging capacity by peroxisomal CATALASE2. Here, we report the characterization of pakerine, a m-sulfamoyl benzamide from the sulfonamide family. Pakerine alleviates the cell death phenotype of cat2 mutants exposed to photorespiration-promoting conditions and delays dark-induced senescence in wild type Arabidopsis leaves. By using a combination of transcriptomics, metabolomics and affinity purification we identified ABNORMAL INFLORESCENCE MERISTEM 1 (AIM1) as a putative protein target of pakerine. AIM1 is a 3-hydroxyacyl-CoA dehydrogenase involved in β-fatty acid oxidation that contributes to jasmonic acid (JA) and salicylic acid (SA) biosynthesis. Whereas intact JA biosynthesis was not required for pakerine bioactivity, our results point towards a role for β-oxidation-dependent SA production in execution of H2O2-mediated cell death.

This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of heat stress on maize we used a controlled environment facility called the Enviratron to simulate field conditions. For our experiments, maize plants were subjected to conditions simulating normal diurnal rhythms of light and temperature, with increasing maximal daily temperature (MDT). Maize plants were grown continuously under four different temperature regimes with simulated morning temperatures ramped up over 6 hr to the MDT of 31°C, 33°C, 35°C or 37°C and simulated evening/night time temperatures ramped down over 8 hr to 10°C below the MDT. We tracked the gene expression events of maize W22 seedlings grow under different temperatures (MDT of 31°C, 33°C, 35°C or 37°C) to evaluate how different MDTs affect the program of gene expression in maize. At the same time, we analyzed the effects of temperature on gene expression in bzip60-2 and W22 V4 plants (20 DAG) and V5 plants (27 DAG) in the Enviratron as the temperature reached its MDT to investigate whether and how bZIP60 confers heat stress tolerance in maize. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of V4 and V5 W22 plants (at 20 and 27 DAG, respectively). Plants were sampled in triplicates.

MYB30 was found to regulate reactive oxygen species (ROS) - mediated systemic transcriptomics responses to light stress in Arabidopsis

We focused on Arabidopsis chloroplast ascorbate peroxidases (sAPX and tAPX) and proton gradient regulation 5 (PGR5) and used pgr5 single mutant, sapx tapx double mutant, and sapx tapx pgr5 triple mutant for RNA-seq analysis.

Salicylic acid (SA) and ethylene (ET) are two important plant hormones that regulate numerous plant growth, development, and stress response processes. Previous studies have suggested functional interplay of SA and ET in defense response, but precisely how these two hormones co-regulate plant growth and development processes remains unclear. The present findings reveal an antagonism between SA and ET in apical hook formation, a process that ensures successful soil emergence of dicotyledonous etiolated seedlings. Exogenous SA inhibited the ET-induced expression of HOOKLESS1 (HLS1) in a manner dependent on ETHYLENE INSENSITIVE3 (EIN3)/EIN3-LIKE1 (EIL1), the core transcription factors in the ET signaling pathway. We found that SA-activated NONEXPRESSER OF PR GENES1 (NPR1) physically interacted with EIN3 and interfered with the direct binding of EIN3 to target gene promoters, including the HLS1 promoter. Transcriptomic analysis further revealed that NPR1 and EIN3/EIL1 coordinately regulated subsets of genes that mediate plant growth and stress responses, suggesting that the interaction between NPR1 and EIN3/EIL1 might be an important mechanism for integrating the SA and ET signaling pathways in multiple physiological processes. Taken together, our findings shed light on the molecular mechanism underlying SA regulation of apical hook formation as well as the antagonism between SA and ET in early seedling establishment and possibly other physiological processes.

Methods: Leaf samples for RNA Seq analysis were collected from three independent plants at 7 hours after initiation of salt stress from control (CT2_1, CT2_2, CT2_3) and salt-stressed plants (TT2_1, TT2_2, TT2_3) were flash-frozen in liquid nitrogen for further analysis. Results: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq platform, and 150 bp paired-end reads were generated. Raw reads of fastq format were processed to obtain clean reads by removing the adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content, the clean data were calculated. Watermelon reference genome (cultivar Charleston Gray) and gene model annotation files were downloaded from CuGenDB (http://cucurbitgenomics.org/). Index of the reference genome was built using Bowtie v2.2.3, and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. : HTSeq v0.6.1 was used to count the reads mapped to each gene. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts. Differential expression analysis of control and drought stressed conditions (three biological replicates per tissue per treatment) was performed using the DESeq R package (1.18.0) (Anders and Huber, 2010). Genes with P-value < 0.05 found by DESeq were assigned as differentially expressed.

C4 photosynthesis was evolved from ancestral C3 photosynthesis by recruited pre-existed genes to perform new functions. Enzymes and transporters required for C4 metabolic pathway has been well documented, however, transcriptional factors (TFs) that regulate those C4 metabolic genes is poorly understood, in particular, how the TF regulatory network of C4 metabolic genes was re-wired, and the involved metabolic functions of those TFs along the evolution of C4 photosynthesis remained unknown. Here, by using RNA-Seq data from growth condition that reported to have effect on C4 photosynthesis, we constructed the TF regulatory network for four evolutionarily closely related species in the genus Flaveria, which represent different stages of the evolution of C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that four TFs are conserved along the evolution whose function either relate to stress response or light response. TFs regulating C4 core genes in C3 species involved in functions belong to RNA regulation and nitrogen metabolism, and that in both intermediate species and C4 species involved in photosynthesis and light responsiveness. Moreover, the TF-network of C4 core metabolic genes has the highest network density in type I C3-C4 species and C4 species when consider the fragment of TF-regulatory network that up-regulated under low CO2, suggesting that TFs regulating C4 genes were recruited to photosynthesis at type I C3-C4 both in involved functions and network density. Our results provide a valuable resource for studying molecular regulatory mechanisms underlying C4 metabolic process.

C4 photosynthesis was evolved from ancestral C3 photosynthesis by recruited pre-existed genes to perform new functions. Enzymes and transporters required for C4 metabolic pathway has been well documented, however, transcriptional factors (TFs) that regulate those C4 metabolic genes is poorly understood, in particular, how the TF regulatory network of C4 metabolic genes was re-wired, and the involved metabolic functions of those TFs along the evolution of C4 photosynthesis remained unknown. Here, by using RNA-Seq data from growth condition that reported to have effect on C4 photosynthesis, we constructed the TF regulatory network for four evolutionarily closely related species in the genus Flaveria, which represent different stages of the evolution of C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that four TFs are conserved along the evolution whose function either relate to stress response or light response. TFs regulating C4 core genes in C3 species involved in functions belong to RNA regulation and nitrogen metabolism, and that in both intermediate species and C4 species involved in photosynthesis and light responsiveness. Moreover, the TF-network of C4 core metabolic genes has the highest network density in type I C3-C4 species and C4 species when consider the fragment of TF-regulatory network that up-regulated under low CO2, suggesting that TFs regulating C4 genes were recruited to photosynthesis at type I C3-C4 both in involved functions and network density. Our results provide a valuable resource for studying molecular regulatory mechanisms underlying C4 metabolic process.

C4 photosynthesis was evolved from ancestral C3 photosynthesis by recruited pre-existed genes to perform new functions. Enzymes and transporters required for C4 metabolic pathway has been well documented, however, transcriptional factors (TFs) that regulate those C4 metabolic genes is poorly understood, in particular, how the TF regulatory network of C4 metabolic genes was re-wired, and the involved metabolic functions of those TFs along the evolution of C4 photosynthesis remained unknown. Here, by using RNA-Seq data from growth condition that reported to have effect on C4 photosynthesis, we constructed the TF regulatory network for four evolutionarily closely related species in the genus Flaveria, which represent different stages of the evolution of C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that four TFs are conserved along the evolution whose function either relate to stress response or light response. TFs regulating C4 core genes in C3 species involved in functions belong to RNA regulation and nitrogen metabolism, and that in both intermediate species and C4 species involved in photosynthesis and light responsiveness. Moreover, the TF-network of C4 core metabolic genes has the highest network density in type I C3-C4 species and C4 species when consider the fragment of TF-regulatory network that up-regulated under low CO2, suggesting that TFs regulating C4 genes were recruited to photosynthesis at type I C3-C4 both in involved functions and network density. Our results provide a valuable resource for studying molecular regulatory mechanisms underlying C4 metabolic process.

Programmed cell death (PCD) is essential for several aspects of plant life. We previously identified the mips1 mutant of Arabidopsis thaliana, which is deficient for the enzyme catalyzing myo-inositol synthesis, that displays light-dependent formation of lesions on leaves due to Salicylic Acid (SA) over-accumulation. Rationale of this work was to identify novel regulators of plant PCD using a genetic approach.A screen for secondary mutations that abolish the mips1 PCD phenotype identified a mutation in the BIG gene, encoding a factor of unknown molecular function that was previously shown to play pleiotropic roles in plant development and defence. Physiological analyses showed that BIG is required for lesion formation in mips1 via SA-dependant signalling. big mutations partly rescued transcriptomic and metabolomics perturbations as stress-related phytohormones homeostasis.In addition, since loss of function of the ceramide synthase LOH2 was not able to abolish cell death induction in mips1, we show that PCD induction is not fully dependent of sphingolipid accumulation as previously suggested.Our results provide further insights into the role of the BIG protein in the control of MIPS1-dependent cell death and also into the impact of sphingolipid homeostasis in this pathway.

The accumulation of misfolded proteins in the endoplasmic reticulum (ER) defines a condition called ER stress that induces the unfolded protein response (UPR). The UPR in mammalian cells attenuates protein synthesis initiation, which prevents the piling up of misfolded proteins in the ER. Mammalian cells rely on Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK) phosphorylation of eIF2alpha to arrest protein synthesis, however, plants do not have a PERK homolog, so the question is whether plants control translation in response to ER stress. We compared changes in RNA levels in the transcriptome to the RNA levels protected by ribosomes and found a decline in translation efficiency, including many UPR genes, in response to ER stress. The decline in translation efficiency is due to the fact that many mRNAs are not loaded onto polyribosomes (polysomes) in proportion to their increase in total RNA, instead some of the transcripts accumulate in stress granules (SGs). The RNAs that populate SGs are not derived from the disassembly of polysomes because protein synthesis remains steady during stress. Thus, the surge in transcription of UPR genes in response to ER stress is accompanied by the formation of SGs, and the sequestration of mRNAs in SGs may serve to temporarily relieve the translation load during ER stress

Little is known of the consequences of genetic pyramiding of abiotic stress tolerance loci in crops. In rice (Oryza sativa L.), ANAEROBIC GERMINATION1 (AG1) encodes TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 (OsTPP7) that enhances mobilization of endosperm reserves to the embryo, promoting formation of a highly elongated hollow coleoptile in seeds sown directly into shallow paddies. This trait reduces labor costs and herbicide use. SUBMERGENCE1 (SUB1) includes the ethylene-responsive transcription factor SUB1A that confers tolerance to complete submergence by dampening shoot elongation of vegetative-phase plants and enhancing regrowth upon desubmergence. As OsTPP7 and SUB1A-1 mRNAs simultaneously accumulate in shoots, we evaluated the independent contribution and interactions between these loci in rice seeded under complete submergence until the four-leaf stage (14 d). Evaluating growth, carbohydrates, and the transcriptome of shoot tissue of four near-isogenic genotypes uncovered independent and interacting effects including: (a) early enhanced coleoptile elongation by IR64(AG1); (b) precocious transition to phototrophy followed by limited elongation by IR64(SUB1); and (c) delayed phototrophy by IR64(AG1, SUB1). mRNA-sequencing highlighted time-dependent and genotype-specific regulation of mRNAs associated with energy sensing, carbohydrate catabolism, photomorphogenesis, elongation, and defense responses. Although SUB1A did not antagonize AG1 in direct seeding, seedling establishment could be negatively impacted if submergence escape does not occur before the transition to photoautotrophy, due to antithetical regulation of carbohydrate catabolism by AG1 and SUB1.

Ozone (O3) is a phytotoxic air pollutant that enters the plant through stomata and activates cell death programs leading to development of lesions in sensitive plant species. Exposure to O3 provokes the formation of reactive oxygen species (ROS) in the apoplast of plant cells. Imbalanced ROS homeostasis has deleterious toxic effects on DNA, proteins, lipids, and carbohydrates. However, ROS are not merely damaging molecules, as they also initiate signaling events that help plants acclimate to stress. Like under most abiotic and biotic stresses, apoplastic ROS signaling triggered by O3 induces massive changes in gene expression, enzyme activities and metabolic profiles. Thus, O3 is a very useful tool to study general mechanisms of ROS signaling and regulation of gene expression. Here we used a combination of transcriptome analysis and cell death assays to identify molecular mechanism initiated by apoplastic ROS signaling involved in the regulation of defense signaling and cell death in Arabidopsis thaliana.

We applied the Illumina HiSeq™ 2000 platform and analyzed differentially expressed genes (DEGs) from untopped and topped plants to study the global changes in gene expression in response to topping. We found that the number of DEGs varied from 7609 to 18,770 based on the reads per kilobase per million mapped reads (RPKM) values. The Gene Ontology (GO) enrichment analysis revealed that the cellular carbohydrate metabolic process and the disaccharide metabolic process, which may contribute to starch accumulation and stress/defense, were overrepresented terms for the DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that many DEGs were involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and plant hormone signal transduction, among other processes. The knowledge gained will improve our understanding of the processes of axillary shoot formation and enlargement at the transcriptional level. This study lays a solid foundation for future studies on molecular mechanisms underlying the growth of axillary shoots.

Transcriptome profiling (RNA-seq) of local and systemic tissue of Arabidopsis Col plants exposed to a local treatment of high light, heat stress and a combination of high light and heat stress on the same leafs or in different leaves

We analysed the effect of cold priming on cold and high light regulation of gene expression. 5 days after the first cold treatment the primary stress response was widely reset. Then, a second (triggering) cold stimulus (24 h 4 °C) and a triggering high-light stimulus (2 h 800 µmol quanta m-2 s-1), which regulate many stress responsive genes in the same direction in naïve plants, caused widely specific and even inverse regulation of priming-responsive genes.

Lamin proteins in animals are implicated in many nuclear functions, including chromatin organization, signaling transduction, gene regulation, and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown. In this work, we report that OsNMCP1 positively regulates root growth and drought resistance through modulating chromatin state and expression levels of many genes functioning in root growth and stress resistance. OsNMCP1 is localized at the nuclear periphery and induced by drought stress. Overexpression of OsNMCP1 resulted in a deeper and thicker root system and enhanced drought resistance compared to the wild-type control. Assay for transposase accessible chromatin with sequencing (ATAC-seq) analysis revealed that OsNMCP1-overexpression altered chromatin accessibility in many genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, and OsMSR15. Interestingly, OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complex OsSWI3C. The reported drought resistance or root growth related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C, and OsSWI3C overexpression led to decreased drought resistance. We propose that the interaction between OsNMCP1 and OsSWI3C may lead to release of OsSWI3C from the gene silencing complexes SWI/SNF under drought condition thus changing the chromatin accessibility in genes related to root growth and drought resistance.

Plants form callus and regenerate new organs when incubated on phytohormone-containing media. While accumulating evidence suggests that these regenerative processes are governed by transcriptional networks orchestrating stress responses and developmental transitions, it remains unknown if post-translational regulatory mechanisms are involved in this process. Here, we find that SIZ1, which encodes an E3 ligase catalyzing attachment of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to proteins, regulates wound-induced signal transduction and organ regeneration. We show that loss-of-function mutants for SIZ1 exhibit over-production of shoot meristems under in vitro tissue culture conditions, while this defect is rescued in a complementation line expressing pSIZ1::SIZ1. RNA-sequencing analysis revealed that siz1-2 mutant exhibits enhanced transcriptional responses to wound stress, resulting in the hyper-induction of over 500 genes immediately after wounding. Among them, we show that elevated level of WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) and WIND2 contribute to enhanced shoot regeneration observed in siz1 mutants, as the dominant-negative WIND1-SRDX partly rescues this phenotype in siz1-3. Although compromised SIZ1 function does not modify transcription of genes implicated in auxin-induced callus formation and/or pluripotency acquisition, it does lead to enhanced induction of cytokinin-induced shoot meristem regulators like WUSCHEL (WUS), promoting the formation of WUS-expressing foci in explants. This study thus suggests that SIZ1 negatively regulates shoot regeneration in part by repressing wound-induced cellular reprogramming.

Environmental stresses such as drought, heat and salinity limit plant development and agricultural productivity. While individual stresses have been studied extensively, much less is known about the molecular interaction of responses to multiple stresses. To address this problem, we investigated molecular responses of Arabidopsis thaliana to single, double, and triple combinations of salt, osmotic, and heat stresses. A metabolite profiling analysis indicated the production of specific compatible solutes depending on the nature of the stress applied. We found that in combination with other stresses, heat has a dominant effect on global gene expression and metabolites level patterns. Treatments that include heat stress lead to strongly reduced transcription of genes coding for abundant photosynthetic proteins and proteins regulating the cell life cycle, while genes involved in protein degradation are upregulated. Under combined stress conditions, the plants shifted their metabolism to a survival state characterized by low productivity. Our work provides molecular evidence for the dangers for plant productivity and future world food security posed by heat waves resulting from global warming. We highlight candidate genes, many of which are functionally uncharacterized, for engineering plant abiotic stress tolerance.

Transcription factors (TFs) are important regulators of plant growth and development and responses to stresses. TFs themselves are also susceptible to multiple post-translational modifications (PTMs). Relatively, redox-mediated PTM of TFs in plants is not well elucidated. Here, we found that NON-RIPENING (NOR), a master TF regulating tomato fruit ripening, is a target of SlMsrE4 or SlMsrB2, the methionine sulfoxide reductase A and B in tomato, respectively. Methionine oxidation in NOR, i.e. sulfoxidation, or mimicking sulfoxidation by mutating Met138 to glutamine, leads to the decreased DNA-binding capacity and transcriptional regulatory activity in vitro. On the other hand, SlMsrE4 and SlMsrB2 can partially repair oxidized-NOR and restore its DNA-binding capacity. Genetic transformation of the nor mutant with NOR genomic DNA almost completely rescues the ripening phenotype. However, transformation of nor with NOR-M138Q, the mimicked methionine sulfoxidation, inhibits the restore of fruit ripening phenotype, and this is associated with the decreased DNA-binding and transcriptional activation of numerous ripening-related genes. Taken together, these findings uncover a novel mechanism by which Msr-mediated redox modification of NOR regulates the expression of ripening-related genes, thereby influencing tomato fruit ripening. To our knowledge, this is the first report that redox modification of TF regulates fruit ripening.nor is a NOR mutant, the phenotype is obstructed by maturity; NOR-12 is a rotational NOR in NOR mutant, the phenotype is a mature inhibition phenotype that basically restores nor mutant; Nor-18 is a rotation of NOR-M138Q in nor mutant, phenotype with the effect of restoring maturity, but the recovery efficiency is lower than the swing NOR.

Methods: Leaf samples for RNA Seq analysis were collected from three independent plants at 8 days after initiation of drought stress from control (CT1_1, CT1_2, CT1_3) and drought-stressed plants (DT_1, DT_2, DT_3) were flash-frozen in liquid nitrogen for further analysis. Results: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq platform, and 150 bp paired-end reads were generated. Raw reads of fastq format were processed to obtain clean reads by removing the adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content, the clean data were calculated. Watermelon reference genome (cultivar Charleston Gray) and gene model annotation files were downloaded from CuGenDB (http://cucurbitgenomics.org/). Index of the reference genome was built using Bowtie v2.2.3, and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. : HTSeq v0.6.1 was used to count the reads mapped to each gene. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts. Differential expression analysis of control and drought-stressed conditions (three biological replicates per tissue per treatment) was performed using the DESeq R package (1.18.0) (Anders and Huber, 2010). Genes with P-value < 0.05 found by DESeq were assigned as differentially expressed. Conclusions: The transcriptomic changes induced by drought stress in leaf tissue at 8DAT was used for RNA-Seq analysis. A total of six libraries from leaf tissue (CT-1, CT-2, CT-3 for control and DT-1, DT-2, DT-3 for drought stress) were sequenced using the Illumina HiSeq platform. On average, 45.53 to 43.47 million raw reads were generated from leaf tissues in both treatments. Across all reads for both control and drought samples, the Q20 and Q30 percentage was more than 98 and 94%, respectively (sequencing error rate was less than 0.02%), and GC content for the libraries was ~45%. Among all the libraries, the ratio of total mapped reads was above 97%, of which ~92 % reads uniquely mapped to the reference watermelon genome for control and drought-stressed samples. The data generated from all libraries provided a foundation for quality analyses. The RNA-Seq analysis identified 3971 differentially expressed (p <0.05) genes in the leaf tissue of drought-stressed plants, of which a total of 1513 genes were upregulated and 2458 genes were downregulated.

Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops.

Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems.

Methods: The mRNA of rice plants cv. Ligeirinho was generated using deep sequencing, in duplicate, using Illumina Hi-Seq 2500, for the following treatments:I) control (C): plants received irrigation with water and nutrient solution throughout the experiment; II) vegetative (SV), plants were exposed to saline shock only at the vegetative stage; III) reproductive (SR) plants were exposed to saline shock only at the reproductive stage; and IV) vegetative + productive (SV+R), plants were exposed to saline shock at the vegetative stage (first shock event) and at the reproductive stage (recurrent event). The sequence reads that passed quality filters were analyzed at the transcript level using this method: Mapping using STAR and identification of differentially expressed genes (DEGs) was performed with the edgeR (false discovery rates - FDRs of <0.05). RT–qPCR validation was performed using SYBR Green assays.Results: Plants subjected to recurrent salt shock showed differences in differentially expressed genes (DEGs). Additionally, the mammalian target of rapamycin (mTOR) pathways, and carbohydrate and amino acid associated pathways were altered under all conditions. Memory genes can be classified according to their responses during the first event (+ or –) and the second shock event (+ or –), being possible to observe a larger number of transcripts for groups [+/–] and [–/+], genes characterised as "revised response."Conclusions: This is the first long-term transcriptional memory study in rice plants under salt shock, providing new insights into the process of plant memory acquisition.

In this work, identification of differentially expressed (DE) genes, including lncRNAs and mRNAs, in sea cucumber response to multiple environmental stress, such as thermal, hypoxic and the combined treatment.

Global warming has great impacts on plant growth and development. Heat shock transcription factors are the master regulators of heat stress response to alleviate protein misfolding in the cytosol in plants. However, how plants deal with accumulation of misfolded proteins in the endoplasmic reticulum (ER) under heat stress conditions is less understood, especially in crops such as in rice. Here we report a positive feed-back loop mediated by the membrane-associated transcription factors NTL3 and bZIP74 in heat stress response in rice. In response to heat stress, the ER-membrane-associated bZIP74 is activated and up-regulate the expression of NTL3 in rice; NTL3 encodes an ER-membrane-associated transcription factor that is activated and regulate downstream genes including bZIP74 involved in protein folding and reactive oxygen species scavenging. Loss-of-function mutations of NTL3 are sensitive to heat stress while inducible expression of the processed form of NTL3 increases heat stress tolerance in rice seedlings. Our work reveals the important role of NTL3 in ER stress response for heat stress tolerance in rice.

Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the differential expressed genes between GRF7OE and WT plants.

Singlet oxygen (1O2), the main ROS produced in chloroplasts, has long been recognized as a cytotoxin that inhibits photosynthesis and damages the cell. However, more recent findings have proposed 1O2 as a highly versatile signal that induces various stress responses. A signaling role for 1O2 was first documented in the conditional fluorescent (flu) mutant of Arabidopsis. Release of 1O2 in flu mutant induces bleach/die of young seedlings and growth inhibition of mature plants. However, all these drastic phenotypic changes can be suppressed by mutation of EXCUTER1 (EX1) gene. The Arabidopsis YDL1 was identified during a screen of revertant mutant from EMS mutagenized flu/ex1. Loss of function of SAFE1 leads to highly expression of 1O2-indluced genes in flu/ex1 mutant, mimicking the flu mutant. We found that YDL1 localized in the stroma of chloroplast, and suppressed 1O2-mediated stress responses via inhibiting 1O2-induced damage on the grana margins.

Plants balance their conflicting requirements for growth and stress tolerance via sophisticated pathways and unique genes that control responses to the external environment. We have identified a novel plant-specific gene, COST1(Constitutively Stressed 1), that affects plant growth and negatively regulates drought resistance by manipulating the autophagy pathway. An Arabidopsis cost1 mutant has decreased growth and increased drought tolerance, together with constitutive autophagy and increased expression of drought-response genes. The COST1 protein is degraded upon plant dehydration, and this degradation is blocked by treatment with inhibitors of the 26S proteasome or autophagy pathways. The cost1 mutant drought resistance is dependent on an active autophagy pathway, indicating that COST1 acts through manipulation of autophagy. COST1 co-localizes to autophagosomes with the autophagosome marker ATG8e and the autophagy adaptor NBR1, and physically interacts with ATG8e, indicating a pivotal role in direct regulation of autophagy. We propose a model in which COST1 represses autophagy under optimal conditions, thus allowing plant growth. During drought, COST1 is degraded, enabling activation of autophagy and suppressing growth to enhance drought tolerance.

C2H2-type zinc finger proteins are classic and extensively studied members of the zinc finger family. C2H2-type zinc finger proteins participate in plant growth, development and stress responses. In this study, 99 C2H2-type zinc finger protein genes were identified and classified into four groups, and many functionally related cis-elements were identified. Differential C2H2-ZFP gene expression and specific responses were analyzed under drought, cold, salt and pathogen stresses based on RNA-Seq data. Thirty-two C2H2 genes were identified in response to multiple stresses. Seven, 3, 5, and 8 genes were specifically expressed under drought, cold, salt and pathogenic stresses, respectively. Five glycometabolism and sphingolipid-related, pathways and the endocytosis pathway were enriched by KEGG analysis. The results of this study represent a foundation for further study of the function of C2H2-type zinc finger proteins and will provide us with genetic resources for stress tolerance breeding.

Waterlogging stress (WS) in a dynamic environment seriously limits plant growth, development, and yield. The regulatory mechanism underlying WS conditions at an early stage in maize seedlings is largely unknown. In the present study, the primary root tips of B73 seedlings were sampled before (0 h) and after (2 h, 4 h, 6 h, 8 h, 10 h, and 12 h) WS and then subjected to transcriptome sequencing, resulting in the identification of differentially expressed protein-coding genes (DEpcGs) and long non-coding RNAs (DElncRs) in response to WS. These DEpcGs were classified into nine clusters, which were significantly enriched in several metabolic pathways, such as glycolysis and methionine metabolism. Several Transcription factor families, including AP2-EREBP, bZIP, NAC, bHLH, and MYB, were also significantly enriched. In total, 6099 lncRNAs were identified, of which 3190 were DElncRs. A co-expression analysis revealed lncRNAs to be involved in 11 transcription modules, 10 of which were significantly associated with WS. The DEpcGs in the four modules were enriched in the hypoxia response pathways, including phenylpropanoid biosynthesis, MAPK signaling, and carotenoid biosynthesis, in which 137 DElncRs were also co-expressed. Most of the co-expressed DElncRs were co-localized with previously identified quantitative trait loci associated with waterlogging tolerance. A quantitative RT-PCR analysis of DEpcG and DElncR expression among the 32 maize genotypes after 4 h of WS verified significant expression correlations between them as well as the significant correlation with phenotype of waterlogging tolerance. Moreover, the high proportion of hypoxia response elements in the promoter region increased the reliability of the DElncRs identified in this study. These results provide a comprehensive transcriptome in response to WS at an early stage of maize seedlings and expand our understanding of the regulatory network involved in hypoxia in plants.

After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6-methyladenosine, m6A). Both RNA secondary structure and m6A have been demonstrated to regulate mRNA stability and translation as well as have been independently linked to plant response to excess salt concentrations in the soil. However, the effect of m6A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure is highly dynamic during salt stress, which is independent of changes in RNA-protein interactions. Conversely, we find that m6A is anti-correlated with RNA secondary structure in a condition-specific manner, with salt-specific m6A resulting in a decrease in mRNA secondary structure during salt stress. Remarkably, we show that the combination of salt-specific m6A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability and translation of transcripts encoding proteins involved in responses to abiotic stresses. In total, our comprehensive analyses reveal an important epitranscriptome, secondary structure-mediated post-transcriptional regulatory mechanism involved in plant long-term salt stress response and adaptation.

Major latex proteins (MLPs) play critical roles in defense and stress responses in plants. However, the functions of MLPs from the apple (Malus × domestica) have not been clearly characterized. Here, we focused on the biological function of MdMLP423, which was previously identified as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis revealed that MdMLP423 was a protein with a `Gly-rich loop' (GXGGXG) domain and belonged to the Bet v_1 subclass. Gene expression profile revealed that MdMLP423 was predominantly expressed in the flower. Additionally, the expression of MdMLP423 was significantly inhibited by Macrophoma kawatsukai and Alternaria alternata apple pathotype (AAAP) infection. To verify the function of MdMLP423, we generated its overexpressing transgenic lines in apple callus. The MdMLP423-overexpressing callus exhibited lower resistance to Macrophoma kawatsukai and AAAP infection, as evidenced by the lower expression of resistance-related genes, higher degree and faster speed of the disease than those of non-transgenic callus. RNA-seq analysis for MdMLP423-overexpressing callus and non-transgenic callus was constructed, and the expression analysis indicated that MdMLP423 regulated the expression of a series of differential expression genes (DEGs) and transcription factors, including DEGs involved in phytohormone signaling pathways, cell wall reinforcement, defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein and ABI3. Taken together, our results demonstrate that MdMLP423 plays negative regulation on Macrophoma kawatsukai and AAAP resistance through inhibiting the expression of cooperating with defense- and stress-related genes and transcription factor.

Regulation of light absorption under variable light conditions is essential to optimize photosynthetic and acclimatory processes in plants. Light energy absorbed in excess has a damaging effect on chloroplasts and can lead to cell death. Therefore, plants have evolved protective mechanisms against excess excitation energy that include chloroplast accumulation and avoidance responses. One of the proteins involved in facilitating chloroplast movements in Arabidopsis thaliana is the J domain-containing protein required for chloroplast accumulation response 1 (JAC1). The function of JAC1 relates to the chloroplast actin filaments appearance and disappearance. So far, the role of JAC1 was studied mainly in terms of chloroplasts photorelocation. Here, we demonstrate that the function of JAC1 is more complex, since it influences the composition of photosynthetic pigments, the efficiency of photosynthesis, and the CO2 uptake rate. JAC1 has positive effect on water use efficiency (WUE) by reducing stomatal aperture and water vapor conductance. Importantly, we show that the stomatal aperture regulation is genetically coupled with JAC1 activity. In addition, our data demonstrate that JAC1 is involved in the fine-tuning of H2O2 foliar levels, antioxidant enzymes activities and cell death after UV-C photooxidative stress. This work uncovers a novel function for JAC1 in affecting photosynthesis, CO2 uptake, and photooxidative stress responses.

Phototropins are plasma membrane‐associated photoreceptors of blue light. Arabidopsis thaliana genome has two genes, PHOT1 and PHOT2, encoding two phototropins that mediate phototropism, chloroplast positioning and stomatal opening. They are well characterized in terms of photomorphogenetic processes, but so far little was known about their involvement in photosynthesis and response to stress factors triggering oxidative stress and cell death. This work fills the gap in our understanding of PHOT1 and PHOT2 involvement in these processes. We used UV-C treatment to promote oxidative stress and cell death in Arabidopsis thaliana wild-type (Col-0 gl1), phot1, phot2 and phot1/phot2 mutants. Using RNAseq we identified genes differentially expressed in phot mutants, in comparison to the wild-type, in both non-stress conditions and after UV-C stress.

ONAC127 and ONAC129 are NAC transcription factors that involved in abiotic stress response and play key regulatory roles in apoplasmic transportation during rice caryopsis filling. To reveal the transcription regulatory network of ONAC127 and ONAC129 in rice caryopsis, we identified significantly differentially expressed genes by RNA-Seq analysis using the caryopses of the CRISPR-mutants(CR) and overexpression lines(OX) of ONAC127 and ONAC129 under natural heat stress(H) and normal cultivation condition(N).

To investigate genome-wide Arabidopsis TE release, we sequenced the wild-type Col-0 transcriptome under Control, Heat and Recovery conditions

Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new glyphosate-tolerant varieties is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire otherglyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice. Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg•ml-1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L+1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L+1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1). Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate stress in rice.

Due to the broad climate adaptation of perennial trees, phenological traits (e.g. chilling requirement-CR, bloom date-BD) exhibit complex inheritance patterns. Conceptually, these are adaptive responses to abiotic stress. As production depends on traits like CR, breeders have developed varieties that are phenotypically/genotypically matched to particular geographic/temperature zones. These genotypes are ideal for study of gene networks governing these climate-critical traits. Using genetic approaches, genome-wide association analyses, functional and comparative genomics in fruit and forest trees, we identified a foundational network of genetic activity (phenylpropanoid pathway) linking winter cold stress response to control of the endodormancy-ecodormancy transition (EET) and seed stratification. Our goal is to examine during endodormancy the allelic effects of genes controlling the production of stress related metabolic intermediates that regulate seed stratification, thus linking these two cold temperature responses. Our objective is to use a transcriptome sequencing approach to characterize genotypic effects on the phenylpropanoid gene network transcriptome during endodormancy and the EET. These adaptive genes and gene networks will be targets for knowledge based breeding strategies of fruit and forest trees to sustain and improve these resources to meet the challenges of rapid environmental change

Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison.Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.

Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.

Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis.

Nitrogen (N) is an essential macronutrient for crops. Plants developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main N inorganic forms taken up by plants and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. To assess the physiological response to these nutrients the shoot and root growth, the leaf pigment content and the amino acid amount in root and shoot were assessed. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. NH4+ activates the response to stress, while NO3- acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while reduces biomass and chlorophyll and flavonoids accumulation. The profiles observed for hydrolysed and free amino acids highlighted common and distinct features in response to the two nitrogen forms.

Purpose: The goal of the study is to compare the transcriptomic differences of the panicle tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.

Arundo donax L. is one of the most promising bioenergy crop due to its high biomass yield and low irrigation requirement. The resistance to biotic and abiotic stress causes the high invasiveness of this plant, which can grow with very low management input (e.g., pesticides, fertilization, irrigation) even in marginal lands or in fields irrigated with waste or salty water. We report the leaf transcriptome sequencing, de novo assembly and annotation of a giant reed G34 genotype under salt stress. This genotype shows a different transcriptomic response to salinity compared to other A. donax genotypes. This finding was unexpected considering that the genetic variability of this species is supposed to be low due to its vegetative reproductive process. This study aims to direct future efforts towards the A. donax genetic improvement.

We utilized RNA-seq to identify transcriptome changes following knockdown of the Arabidopsis N-terminal acetyltransferase NAA50. Transgenic Arabidopsis plants carrying a dexamethasone-inducible amiRNA were used to study the effects of NAA50 knockdown. Significant changes occurred in the transcriptomes of NAA50 knockdown plants at 12 and 24 hours after dexamethasone treatment. These changes demonstrate that loss of NAA50 results in a reduction in signaling related to plant growth and development, as well as an increase in the expression of stress- and defense-related pathways.

Heat stress is a common stress for plants. Long heat stress can triger a series of biological responses. RNA-seq is a useful method to profile RNA dynamics in creatures. Here we profiles the RNA dynamics in heat stressed Arabidopsis. These data will help us understanding the stress response mechanism in plants.

Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding of the effect of waterlogging stress in barley, we carried out a genome-wide gene expression analysis in roots of Yerong and Deder2 barley genotypes under waterlogging and control (well-watered) conditions by RNA-Sequencing, using Illumina HiSeq™ 4000 platform.

Small interfering RNAs (siRNAs) are critical for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21-, 22-, or 24- nucleotides (nt), wherein the 21- and 24-nt siRNAs mediate mRNA cleavage and DNA methylation2,3, respectively. However, the biological functions of 22-nt siRNAs remain elusive. Here we report the identification and characterization of a group of endogenous 22-nt siRNAs generated from the action of DICER-LIKE 2 (DCL2). When cytoplasmic RNA decay and DCL4 are deficient, the massive accumulation of 22-nt siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defect, and pigmentation. Notably, two genes that encode nitrate reductases, NIA1 and NIA2, produce nearly half of the total of 22-nt siRNAs. Production of 22-nt siRNA triggers explosive self-amplification that leads to a small RNA storm, and induces dramatic translational repression both gene-specifically and globally. 22-nt siRNAs are also found to preferentially accumulate upon nitrogen deficiency, which acts to restrain plant growth and promote stress responses. Thus, our research uncovers the unique properties of 22-nt siRNAs, a previously unexplored class of plant siRNAs, and highlights the length of small RNA as a major functional determinant.

Purpose: In order to explore the detoxification mechanism of nitrogen against cadmium stress in plants;Methods:Cultivation and treatment for four months of P.yunnanensis seedlings by soil culture, in triplicate, qRT–PCR validation was performed using TaqMan and SYBR Green assays;Results:Exogenous nitrogen induced the expression of resistance genes;Conclusions: Our study represents that exogenous nitrogen addition under Cd stress induced more differential expressed TFs.

Ascorbic acid (AA) is known to play a vital role in plant growth and detoxification of reactive oxygen species, however little is known about the significance of AA oxidation in plant defence against pathogens. • The role of ascorbate oxidation in rice defence against root-knot nematodes, Meloidogyne graminicola, was tested with application of AA, ascorbate oxidase (AO), dehydroascorbic acid (DHA), biosynthesis inhibitors and use of mutants. Transcriptome analysis was done on AO treated plants, and hormone measurements were executed to confirm the results. Biochemical analyses were used to study oxidative stress markers, including accumulation of H2O2, , malondialdehyde and AA/DHA.

Results:We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant’s life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected.;Conclusions:This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.

Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes. As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified. Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.

Nitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify genes that are related to the alleviated phenotypes after introducing NO3- to Panax notoginseng roots under NH4+ stresses. Twelve RNA-seq profiles in four sample groups, i.e., control, samples treated with NH4+, samples treated with NO3- only, and treated with both NH4+ and NO3- were obtained and analyzed to identify deregulated genes in samples with different treatments. ACLA-3 gene is downregulated in NH4+ treated samples, but is upregulated in samples treated with NO3- and with both NH4+ and NO3-, which is further validated in another set of samples using qRT-PCR. Our results suggest that unbalanced metabolism of nitrogen and nitrogen is the main cause of ammonium poisoning in roots of Panax notoginseng, and NO3- may significantly upregulate the activity of ACLA-3 which subsequently enhances the citrate cycle and many other metabolic pathways in Panax notoginseng root. These potentially increase the integrity of the Panax notoginseng roots. Our results suggest that introducing NO3- fertilizer is an effective means to prevent the occurrence of toxic ammonium in Panax notoginseng root.

Flooding stress is a major environmental threat for many terrestrial plants. The detrimental effects of flooding stress, however, vary between different plant species. Whereas many crops are rather sensitive to flooding, some wild species from flood-prone areas are well adapted to excess water conditions. Morphological adaptations like adventitious roots and aerenchyma formation, or the ability to elongate rapidly the above-ground organs, allow these plants to thrive in water.The focus of this research is Nasturtium officinale, also known as watercress, which is an auto-tetraploid, dicotyledonous and stem-growing Brassicaceae species. Its natural habitat is near rivers and streams, but absent from stagnant water. Submergence induces underwater elongation of stems and growth suppression of petioles in Nasturtium officinale. By using the RNA sequencing technique, we aimed to uncover the underlying mechanisms for these contrasting responses. Combining submergence experiments with hormone manipulations revealed that ABA degradation is required for stem elongation.

To understand the role of STCH4 in cold-responsive gene regulation；14-day-old wild-type and stch4-1 seedlings grown on 1/2 MS medium (1/2 × MS salts, 2% sucrose, 0.6% agar, pH 5.7) were treated without or with 4 ℃ for 4 or 24 hours for total RNA extraction.

Background: Hazy weather significantly increase air pollution and affect light intensity which may also affect medicinal plants growth. Syringa oblata Lindl. (S. oblata), an effective anti-biofilm medicinal plants, is also vulnerable to changes in plant photoperiods and other abiotic stress responses. Rutin, one of the flavonoids, is the main bioactive ingredient in S. oblata that inhibits Streptococcus suis biofilm formation. Thus, the present study aims to explore the biosynthesis and molecular basis of flavonoids in S. oblata in response to different light intensity. Results: In this study, it was shown that compared with natural (Z0) and 25% ~ 35% (Z2) light intensities, the rutin content of S. oblata under 50% ~ 60% (Z1) light intensity increased significantly. In addition, an integrated analysis of metabolome and transcriptome was performed using light intensity stress from two kinds of light intensities which S. oblata was subjected to: Z0 and Z1. The results revealed that differential metabolites and genes were mainly related to the flavonoid biosynthetic pathway. We found out that 13 putative structural genes and a transcription factor bHLH were significantly up-regulated in Z1. Among them, integration analysis showed that 3 putative structural genes including 4CL1, CYP73A and CYP75B1 significantly up-regulated the rutin biosynthesis, suggesting that these putative genes may be involved in regulating the flavonoid biosynthetic pathway, thereby making them key target genes in the whole metabolic process. Conclusions: The present study provided helpful information to search for the novel putative genes that are potential targets for S. oblata in response to light intensity.

Transcriptomic analysis by RNAseq of Col leaves subjected to high light, heat stress and the combination of high light and heat stress

Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2 - 4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.

BLI tightly controls the protein kinase activity of IRE1A in plants,and IRE1A plays new roles in plant growth and development

APUM9 is a conserved PUF RNA-binding protein (RBP) and the expression of this protein is under complex epigenetic regulation. A transposable element (TE)-mediates this epigenetic regulation and thereby restricts its expression in Arabidopsis. Currently, little is known about the molecular function of the APUM protein family and the biological relevance of the TE-mediated epigenetic control of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunits of the decapping complex suggesting that APUM9-mediated mRNA decay predominantly occurs via the decapping-dependent exonucleolytic pathway. APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated epigenetic control of plant APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.

RNA sequencing was used to identify alternative splicing events and differentially expressed genes (DEG) in 35S:HIN1 stable transgenic line compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hours moderate severity low water potential (-0.7 MPa) treatment. RNA sequencing analysis found that overexpression of HIN1 in unstressed plants was sufficient to duplicate the effects of stress on nearly 40% of the genes where intron retention was normally suppressed by stress in wild type. Differentially expressed genes (DEGs) were also analyzed (P < 0.05 and fold change ≥ 1.5 used as cut off values for DEGs). Differentially expressed genes in 35S:HIN1has limited overlap of DEGs between 35S:HIN1and wild type. This indicated that HIN1 plays a lesser role in stress-regulated gene expression than in splicing regulation.

This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of drought stress and NF-Y transcription factors ZmNF-YA1 and ZmNF-YB16 on maize, leaves from wild-type (W22), zmnf-ya1 (m67) mutant, wild-type (B104) and ZmNF-YB16 overexpression (OE) plants grow under well-watered and drought stress conditions were collected and RNAseq was performed. We tracked the gene expression events of inbred maize lines W22 or B104 seedlings in response to drought stress to evaluate how drought stress affects the gene expression program in maize. At the same time, we analyzed the effects of drought stress on gene expression in zmnf-ya1 and ZmNF-YB16 OE plants to investigate whether and how ZmNF-YA1 and ZmNF-YB16 confer drought stress tolerance in maize. Maize plants were grown under well-watered conditions until the V4 stage (zmnf-ya1 and W22) or V9 stage (ZmNF-YB16 OE and B104), and then half of them were exposed to drought stress treatment. Water loss in the soil and the electrolyte leakage from leaf cells were used to assess drought stress in plants. Leaves from 3-4 plants were pooled for each sample, and two replicates were used. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of the plants.

Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. pennellii. Response to hypoxic conditions was measured by analyzing transcriptional and post-translational regulation in root tips of each species. This was achieved by the use of Nuclei Tagged in specific Cell Types (INTACT) and Translating Ribosome Affinity Purification to obtain chromatin and sub-populations of gene transcripts. (1) Chromatin accessibility was evaluated by coupling INTACT with ATAC-seq (assay for Transposon-Accessible Chromatin). (2) INTACT was used to capture nuclear RNA (nRNA). (3) Polyadenylated mRNA (polyA RNA) was obtained by standard oligo(dT) selection. (4) Ribosome-associated polyA mRNA (polyA RNA) was obtained by use of Translating Ribosome Affinity Purification (TRAP). Ribosome footprinting (Ribo-seq) was accomplished by using TRAP to capture ribosome protected fragments after RNAseI digestion. Samples evaluated include the apical root tip (four species) and shoot region (Solanum species only) under control conditions and after 2 h of submergence

Our study revealed that a number of ethylene-related transcription factors, as putative master regulators of cold responses, were upregulated in ERY providing promising candidates to confer tolerance to susceptible cultivars. Our results also suggest that the photosynthesis machinery might be a good target to improve cold tolerance in anthers. In summary, our study provides valuable candidates for further analysis and molecular breeding for cold-tolerant rice cultivars.

The ubiquitination pathway regulates growth, development, and stress responses in plants, and the U-box protein family of ubiquitin ligases has important roles in this pathway. Here, 64 putative U-box proteins were identified in the Medicago truncatula genome. In addition to the conserved U-box motif, other functional domains, such as the ARM, kinase, KAP, and WD40 domains, were also detected. Phylogenetic analysis of the M. truncatula U-box proteins grouped them into six subfamilies, and chromosomal mapping and synteny analyses indicated that tandem and segmental duplications may have contributed to the expansion and evolution of the U-box gene family in this species. Using RNA-seq data from M. truncatula seedlings subjected to three different abiotic stresses, we identified 33 stress-inducible plant U-box genes (MtPUBs). Specifically, 25 salinity-, 15 drought-, and 16 cold-regulated MtPUBs were detected. Among them, MtPUB10, MtPUB17, MtPUB18, MtPUB35, MtPUB42, and MtPUB44 responded to all three stress conditions. Expression profiling by real-time PCR was consistent with the RNA-seq data, and stress-related elements were identified in the promoter regions. The present findings strongly indicate that U-box proteins play critical roles in abiotic stress response in M. truncatula.

The plant vascular system is essential for the enlarged plant stature and successful colonizzation the land by delivering resources throughout the plants and providing mechanical support. Despite several regulators of vascular patterning have been reported, how vascular system mediates stress resistance remain largely unknown. Here we identified a CsIND transcription factor that is specifically expressed in the xylem and phloem tissues in cucumber. Knock down of CsIND by RNAi lead to dwarf plants with enlarged or disorganized vascular systems in all aerial organs. The content of both auxin and jasmonic acid were increased in the CsIND-RNAi lines. Transcriptome profiling by RNA-Seq hints CsIND-regulated gene networks for defense response and vascular development. Biochemical analyses verified that CsIND directly binds to well-known vascular regulators including CsCCR1, CsMYB116, CsYAB5, CsBP and CsAUX, and physically interacts with dorsiventral patterning genes CsKAN2 and CsYAB5. Further, CsIND-RNAi plants displayed significantly enhanced tolerance to nitrogen dificency and resistance to cucumber downy mildew. Therefore, CsIND regulates vascular formation and resistance to biotic and abiotic stresses in cucumber, through the combinarory interactions with well-known vascular regulaors and hormone metabolism and signaling pathways

we show that a short moderate heat stress during the tetrad stage of pollen development targets vital metabolic pathways ultimately leading to sterility and yield losses in maize.

By pairwise comparisons of the RNA-seq data, 33 genes were showed significant expression differences between PuHSFA4a-OE and WT (FDR adjusted P value < 0.01 including 17 genes under normal condition, 19 genes under excess Zn treatment. Altered expression of 17 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.Conclusions: Our study represents the detailed analysis of excess Zn response transcriptomes , with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that next generation sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

The goal of this study was to examine the transcriptional events occuring during stress-free Brachypodium distachyon root development via illumina paired-end RNA-seq. 4 time-points were chosen that capture the transition from rapid vegetative growth into slower reproductive growth. Abstract - Root systems are dynamic, adaptable organs that play critical roles in plant development. Roots, however, remain understudied and therefore present opportunities for trait improvement in food and bioenergy crops. A comprehensive growth stage-based root phenotyping integrated with molecular signatures is required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root biomass, length, branching, root-to-shoot ratio and Carbon-to-Nitrogen ratio during time. To provide insight into gene regulation that accompanies root development and biomass accumulation, we generated comprehensive transcript profiles of Brachypodium whole-root system at four initial developmental stages that capture the transition from vegetative to reproductive growth. Our stringent data analysis revealed that multiple biological processes and various families of transcription factors (TFs) were differentially expressed during root development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated, while ARFs and GRFs were downregulated in a time-dependent manner. Our results suggested particular TF families and biological processes including trehalose metabolism as important factors possibly involved in root biomass accumulation. We introduced several Brachypodium root biomass-promoting genes which can be employed by the genome editing approaches for improving biomass productivity in grasses.

The explant is likely the most essential parameter of plant tissue culture. The vast majority of tissue culture studies have focused almost exclusively on the use of explants as a tool for organogenesis or propagation, and there is limited information that documents the changes that occur in an explant in response to cutting during explant preparation just prior to culture. To better understand the molecular changes occurring during the wounding process that accompanies the preparation of an explant, this study examined the mRNA transcription profile of potato (Solanum tuberosum L. cv. Desirée) single-node segments. To achieve this, RNA-seq analysis was performed to identify significantly differentially expressed genes (DEGs) that existed between uncut in vitro plantlets and cut explants. DEGs were connected to cellular processes in the extracellular region, nucleus, and plasma membrane, and were associated with biosynthesis, carbohydrate metabolism and catabolism, cellular protein modification, growth and development, and response to stress. These results provide a novel perspective of the changes taking place within explants when they are cut and serve as a valuable basis for the study of explant-related stress in plant tissue culture in other plant species, and may provide an understanding of the success or failure of the tissue culture protocol and subsequent establishment of in vitro cultures.

Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.

Two homozygous atx1/atx3/atx4 triple T-DNA insertion mutants were isolated (TM1 and TM2). Both have the same T-DNA mutant alleles but come from different crosses so they may contain different background mutations. atx triple mutants display significant early flowering and significant early leaf senescence phenotypes. Previous phenotype analyses show that early leaf senescence was detected at day 33 in the triple mutants. RNA-seq was used to identify gene expression changes occurring at the time of bolting that might be promoting the onset of leaf senescence, thus coupling the early flowering phenotype to the early leaf senescence phenotype (see "Timeseries Design Infographic"). Triple Mutants bolting at the peak of triple mutant bolting (Days 24 and 25, see "Peak of Triple Mutant Bolting Info" for details) were pooled and then 1/4th of these bolting plants were harvested. Plants were then randomly selected for harvesting from this pool in two day increments, three times. Thus, harvesting days were 25, 27, 29, and 31 days after stratification. This strategy was used to ensure the TM plants harvested at each time point were developmentally similar. The sixth leaf to emerge was harvested from each plant. Three replicates were generated per line, per time point (4 time points), totaling to 12 cDNA libraries per genotype. The 36 cDNA libraries were prepared using the BrAD-seq protocol and were then sequenced at the University of California, Irvine Genome High-throughput Facility."Peak of Triple Mutant Bolting Info", "Timeseries Design Infographic", "BrAD-seq Info". These images were included to help understand the experimental design.

In this study, we reported the RNA-seq profiling of two contrasting genotypes under waterlogging and recovery.Overall design The plants were grown in pots and subjected to waterlogging treatment at the flowering stage for 36 h and subsequently, 12 h drainage. Root samples were collected in triplicate at 22 time points under waterlogging/drainage treatments and at 10 time points in the control condition.

Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.

We have analyzed the poly(A) usage between Arabidopsis control and fip1-2 mutant seedlings grown in normal medium. FIP1 is a subunit of the polyadenalation machinary and loss of function of FIP1 affects plant development and response to salt, ABA and cadmium.

We sought to investigate the scope of transcriptome analyses of peppers subjected to four major environment stresses (heat, cold, drought, and salinity). For this, at the six-true-leaf stage, plants were subjected to a temperature of 10°C or 40°C to mimic cold or heat stress, respectively. For salinity stress, plants were treated with 50 mL of a 400 mM NaCl solution; for osmotic stress, the peppers were treated with 50 mL of 400 mM mannitol. For RNA-seq library construction, the third or fourth leaves from four plants were harvested per replicate at 0, 3, 6, 12, 24, and 72 h after treatment. A total of 204.68 Gb of transcriptome data were generated using transcriptome analysis pipelines consisting of quality control, quantification, and differential gene expression analyses. A hierarchical clustering of gene expression data were used to infer the quality of the RNA-seq data and the characteristics of samples in each treatment. The extensive transcriptome data obtained will provide valuable information for future studies of crops exposed to abiotic stresses.

In view of the continuous salinization of arable lands world-wide, there is an urgent need to better understand the mechanisms underlying plant responses to salt stress at different stages of their development. We investigated the role of calmodulin (CaM)-binding transcription activator 6 (CAMTA6) under salinity stress during early germination in Arabidopsis. These analyses suggest that ABA signaling is involved in CAMTA6-dependent salt-responsive gene expression, consistent with the ABA hyper-tolerance phenotype and the lack of HKT1 response to ABA and NaCl in the camta6 mutants.

Growth in soil inoculated with plant growth promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate |(ACC) deaminase or expressing of the corresponding acdS in transgenic lines reduces the decline in shoot length, shoot weight and photosynthetic capacity triggered by salt stress in Camelina sativa. Reducing the levels of stress ethylene decreases the expression of salt stress-responsive genes, specifically genes involved in development, senescence, chlorosis and leaf abscission that are highly induced by salt to the levels that may have a less negative effect on growth and productivity. Moderate expression of acdS under the promoter of the rolD promoter or growing plants in soil treated with the PGPB Pseudomonas migulae 8R6, were more effective in eliminating the expression of the genes involved in ethylene production and/or signaling than expression under the more active Cauliflower Mosaic Virus 35S promoter.

We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using RNA sequencing. Transcriptomic analysis revealed that 8204 genes were differentially expressed in three treatment groups. Among these genes, 158 photosynthesis-related genes, 42 antioxidant enzyme genes, 318 plant hormone-related genes and 457 transcription factors (TFs) might play vital roles in regulating wheat response to ER stress.

Genetically engineering Nicotiana tabacum to express Isoprene Synthase (ISPS) leads to changes in expression of genes assoiated with many growth regulator signaling pathways and signaling networks involved in abiotic and biotic stress responses.

Genetically engineering Arabidopsis thaliana to express Isoprene Synthase (ISPS) leads to changes in expression of genes assoiated with many growth regulator signaling pathways and signaling networks involved in abiotic and biotic stress responses.

Sequencing of 24 small RNA libraries produced 55.2M reads while 404M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins.

Sequencing of 24 small RNA libraries produced 55.2M reads while 404M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins.

Transcripts libraries were prepared from three sugarcane genotypes with high-sugar (HS), medium-sugar (MS) or low-sugar (LS) content that were treated with ethylene or H2O. The libraries were sequenced with the Illumina paired-end HiSeq platform.Transcriptomic analyses have identified about 160,000 unigenes of which 86000 annotated genes were classified into functional groups associated with carbohydrate metabolism, signaling, localization, transport, hydrolysis, growth, catalytic activity, membrane and storage, suggesting the structural and functional specification, including sucrose accumulation, occurring in maturing internodes. About 25,000 genes were differentially expressed between all genotypes and treatments combined. Genotype had a dominant effect on differential gene expression than ethylene treatment. Sucrose and starch metabolism genes were more responsive to ethylene treatment in low-sugar genotype. Ethylene caused differential gene expression of many stress-related transcription factors, carbohydrate metabolism, hormone metabolism and epigenetic modification. Ethylene-induced expression of ethylene-responsive transcription factors, cytosolic acid- and cell wall-bound invertases, and ATPase was more pronounced in low- than in high-sugar genotype, suggesting an ethylene-stimulated sink activity and consequent increased sucrose accumulation in low-sugar genotype.

In Arabidopsis, CBFs transcription factors (CBF1, CBF2 and CBF3) play fundamental roles in plant cold tolerance, especially in cold-acclimation. By employing CRISPR/Cas9, we knocked out CBF1 and CBF2 simultaneously in cbf3 background and generated cbfs triple mutant. This mutant facilitated the discovery of CBF-regulated genes. In this study, Arabidopsis 14-d-old Col-0 and cbfs mutant were treated with cold stress (4 degree centigrade) for 0, 3 and 24 hours. The seedlings were harvested for total RNA extraction and sequencing.

This research was undertaken to investigate the global role of inositol phosphorylceramide synthase (IPCS) activity in plants and reveal its potential as a herbicide target. The non-mammalian enzyme is a key component in the plant sphingolipid biosynthetic pathway and is shown here to be a possible herbicide target. RNA-Seq analyses demonstrated that over-expression of inositol phosphorylceramide synthase isoforms AtIPCS1, 2 or 3 in Arabidopsis thaliana resulted in the down-regulation of genes involved in plant response to pathogens. In addition, genes associated with the abiotic stress response to salinity, cold and drought were found to be similarly down-regulated. Detailed analyses of transgenic lines over-expressing AtIPCS1-3 at various levels revealed that the degree of down-regulation is specifically correlated with the level of IPCS expression. Singular enrichment analysis of these down-regulated genes showed that AtIPCS1-3 expression affects biological signaling pathways involved in plant response to biotic and abiotic stress. The up-regulation of genes involved in photosynthesis and lipid localization was also observed in the over-expressing lines.

Viruses have different strategy to infect their hosts. Acute type infection is fast resulting in severe symptoms or in the death of the plant, while in persistent type of interaction the virus can survive within its host for a long period of time with mild symptoms. During our studies we investigated gene expression changes of virus infected Nicotiana benthamiana and Solanum lycopersicum after systemic spread of the virus by two different methods: microarray hybridization and RNA sequencing. Using these high throughput techniques we could easily differentiate between acute and persistent type of infection and validate key expression changes by Northern blot hybridization. We also demonstrated that in persistent infection not only drastic downregulation of important housekeeping genes, but induction of stress genes are missing, making possible for the virus to survive in its host for a long period of time. Symptoms of acute and persistent type virus infection differ markedly and according to our results the type of infection can be distinguished even at an early point by characterizing the photosynthetic activity of virus infected plants.

For environmental safety, the high concentration of heavy metals in the soil should be removed. Cadmium (Cd), one of the heavy metals polluting the soil while its concentration exceeds 3.4 mg/kg in soil. Potential use of cotton for remediating heavy Cd-polluted soils is available while its molecular mechanisms of Cd tolerance remains unclear in cotton. In this study, transcriptome analysis was used to identify the Cd tolerance genes and their potential mechanism in cotton. Finally 4,627 differentially expressed genes (DEGs) in the root, 3,022 DEGs in the stem and 3,854 DEGs in leaves were identified through RNA-Seq analysis, respectively. These genes contained heavy metal transporter genes (ABC, CDF, HMA, etc.), annexin genes, heat shock genes (HSP) amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The DEGs mainly enriched in two pathways, the influenza A and the pyruvate pathway. GhHMAD5 protein, containing a heavy-metal domain, was identified in the pathway to transport or to detoxify the heavy ion. GhHMAD5-overexpressed plants of Arabidopsis thaliana showed the longer roots compared with the control. Meanwhile, GhHMAD5-silenced cotton plants showed more sensitive to Cd stress compared with the control. The results indicated that GhHMAD5 gene is remarkably involved in Cd tolerance, which gives us a preliminary understanding of Cd tolerance mechanisms in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate the soil polluted with heavy metals.

microRNAs (miRNA’s) regulation target gene expression, often transcription factors and as such control entire transcriptional networks. This control is important for various developmental transitions and stress responses in a wide range of eukaryotic organisms. While miRNA-mediated gene regulation has been investigated over time (temporal) and in whole organs or tissues in multiple different organisms highlighting their importance, there has been a distinct lack of focus on spatial resolution of miRNA biology. Here we present at cell-type specific resolution, miRNA loading and miRNA action within the Arabidopsis root. Our results for the first time demonstrate the multiple novel modes of miRNA action and illustrate the widespread nature of miRNA movement, at a genome scale within a complex eukaryotic organ.

Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.

we report the application of high throughput sequencing technology for digital gene expression profiling of the gene expression pattern in Arabidopsis root tips treated with 0.5 µM narciclasine at 2 and 12 hr.Compared with controls, 236 genes were upregulated and 54 genes were downregulated with 2 hrs of narciclasine treatment, while 968 genes were upregulated and 835 genes were down-regulated with 12 hrs of treatment. The Gene Ontology analysis revealed that the differentially expressed genes were highly enriched during oxidative stress, including those involved in the 'regulation of transcription', 'response to oxidative stress', 'plant-pathogen interaction', 'ribonucleotide binding', 'plant cell wall organization', and 'ribosome biogenesis'. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway enrichment statistics suggested that carbohydrate metabolism, amino acid metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of phenylpropanoid and secondary metabolites were significantly inhibited by 12 hrs of narciclasine exposure.

The Unfolded Protein Response (UPR) is activated in plants in response to ER stress and plays an important role in mitigating stress damage. We have analyzed an ire1a ire1b bzip17 triple mutant in Arabidopsis with defects in stress signaling and found that the mutant is also impaired in vegetative plant growth under conditions without externally applied stress. This raises the question as to whether the UPR functions in plant development in same manner as it does in responding to stress. bZIP17 is an ER-associated membrane transcription factor that is mobilized to the nucleus in response to stress. Through the analysis of a mobilization defective bZIP17 mutant, we found that bZIP17 must be capable of mobilization to support normal plant development. Likewise, through the analysis of ire1 mutants, we found that protein kinase and ribonuclease activities of IRE1 must be functional to support normal development. These findings demonstrate that the UPR is active, albeit at low levels, during unstressed conditions, and that these activities are required for normal development.

Brachypodium distachyon as an annual species that colonises broken ground is a highly appropriate model to define drought tolerance mechanisms. We have previously identified accessions exhibiting drought tolerance, high susceptibility and intermediate tolerance to drought; respectively, ABR8, KOZ1 and ABR4, from a screen of 138 genotypes. To define the mechanisms of tolerance, the responses to drought were assessed using transcriptomic and metabolomic approaches. Analysis of RNA-seq before and following drought suggested relatively few differentially expressed genes in ABR8. Linking these to gene ontology (GO) terms revealed an enrichment for biological processes related to “regulated stress response”, “plant cell wall” and “oxidative stress”. Interestingly, drought tolerance also appeared to correlate with pre-existing differences in gene expression linked to GO terms associated with the cell wall. These included glycoside hydrolases involved in cell wall remodelling, pectin methylesterases, expansins and a pectin acetylesterase. Metabolomic assessments of the same samples also indicated few statistically significant changes in ABR8 with drought. Instead, pre-existing differences in the cell-wall associated metabolites appeared to correlate with drought tolerance. Our data suggests two different modes/levels at which cell wall characteristics can play a role in conferring drought tolerance: (i) an active response mode/level which involves stress induced changes in cell wall features to help the plant cope with drought and (ii) an intrinsic mode in which innate differences in cell wall composition and architecture between genotypes are important in determining tolerance to drought stress. Both modes seem to contribute to the drought tolerance of ABR8. Identification of the exact mechanisms through which the cell wall confers drought tolerance will be important to fully exploit the contribution of the cell wall in the development of drought tolerant cereals and other grasses.

Verticillium wilt which is caused by Verticillium dahliae causes massive annual losses of cotton yield. Control by conventional mechanisms is not possible due to wide host range and longevity of dormant fungi in the soil in case of absence of a suitable host. Plants have developed various mechanisms to boost their immunity against various diseases, and one of which is through the induction of various genes. In this research work, carried out of RNA sequencing and identified the members of the ABC genes are critical in enhancing resistance to V. dahliae infection. A total of 166 ABC genes were identified in Gossypium raimondii with varying physiochemical properties. A novel ABC gene, Gorai.007G244600 was found to be highly upregulated, its homolog in the tetraploid cotton Gh_D11G3432, was then silenced through virus induced gene silencing (VIGS) in tetraploid cotton, the mutant cotton seedlings that have the ability to tolerate V. dahliae infection were significantly reduced. Evaluation of oxidant, hydrogen peroxide (H2O2) and malondialdehyde (MDA) were found to have increased levels in the leaves of the mutant compared to the wild types. In addition, antioxidant enzymes, peroxidase (POD), catalase (CAT) and superoxide dismutase (SOD) concentration levels were significantly reduced in the mutant cotton compared to the wild types. Moreover, expression levels of the biotic stress genes, cotton polyamine oxidase (GhPAO), cotton ribosomal protein L18(GhRPL18) and cotton polygalacturonase-inhibiting protein-1 (GhPGIP1) were all downregulated in the mutant but highly upregulated in the wild cotton tissues. The outcome of this research has shown that ABC genes could be playing an important role in enhancing immunity of cotton to V. dahliae infection and can be explored in developing more resilient cotton genotypes with improved resistance to V. dahliae infection.

Although the ubiquitous bacterial secondary messenger cyclic diguanylate (c-di-GMP) plays important roles in various cellular functions including the formation of biofilm in a wide range of bacteria, its function in model plant pathogen Pseudomonas syringae is largely elusive. In order to test this in P. syringae, we overexpressed a diguanylate cyclase (YedQ) and a phosphodiesterase (YhjH) that are originally from Escherichia coli, resulting in high and low c-di-GMP levels in P. syringae, respectively. Through performing genome-wide RNA sequencing of these two strains, we found that c-di-GMP regulates (i) fliN, fliE and flhA genes, which are associated with flagellar assembly, (ii) alg8 and alg44, which are related to exopolysaccaride biosynthesis pathway, (iii) pvdE, pvdP and pvsA genes, related to siderophore biosynthesis pathway, and (iv) sodA, which is a superoxide dismutase. In particular, we identified five genes sensitive to elevated c-di-GMP level and constructed five luciferase-based reporters that effectively respond to intracellular level of c-di-GMP in P. syringae, which can be used to measure c-di-GMP levels in vivo in the future. Based on the RNA-seq results, phenotypic assays confirmed that c-di-GMP regulated many important biological pathways in P. syringae, such as negative regulation of type III secretion system (T3SS) and motility as well as positive regulation of EPS production, siderophore production and oxidative stress resistance. Taken together, the present study demonstrated that c-di-GMP is closely related to virulence and stress response in P. syringae, suggesting that tuning its level can be a new strategy to protect plants from the attack of this pathogen in the future.

Here, we apply this approach to A. thaliana root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single-cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution

The functions of AP2/ERF family transcription factors in stress responses are well documented, but their roles in the brassinosteroid (BR)-regulated growth and stress responses have not been established. Here we show that stress-inducible AP2/ERF family transcription factor TINY inhibits BR-regulated growth while promoting drought response. TINY overexpression plants have stunted growth, increased sensitivity to BR biosynthesis inhibitors and compromised BR-responsive gene expression. In contrast, a tiny tiny2 tiny3 triple mutant has increased BR-regulated growth and BR-responsive gene expression. TINY positively regulates drought response by activating drought responsive genes and promoting abscisic acid-mediated stomatal closure. Global gene expression studies revealed that TINY and BRs oppositely regulate genes involved in plant growth and stress response. TINY interacts with and antagonizes BES1 in the regulation of these genes. The GSK3-like protein kinase BIN2, a negative regulator in the BR pathway, phosphorylates and stabilizes TINY, providing a mechanism for BR-mediated down-regulation of TINY to prevent activation of stress response under optimal growth conditions. Taken together, our results demonstrate that TINY is negatively regulated by BR signaling through BIN2 phosphorylation and positively regulates drought response, as well as inhibits BR-mediated plant growth through TINY-BES1 antagonistic interactions. Our results thus provide insight into the coordination of BR-regulated growth and drought responses.

Iron (Fe) and phosphorus (P) are essential nutrients for plants growth. Despite their abundance in soils, they are barely available for plants. In order to overcome these nutritional stresses, plants have evolved strategies including physiological, biochemical and morphological adaptations. Biosynthesis and release of low molecular weight compounds from the roots play a crucial role in P and Fe mobilization. White lupin (Lupinus albus L.) is considered a model plant for studying root exudates and for P-deficient adaptation. White lupin is able to markedly modify its root architecture by forming special structures called cluster roots, and modifies the rhizospheric soil characteristics by biosynthesising and releasing great amounts of exudates. These phenomena are quite well described in response to P deficiency, but there is few information on the adaptation of a cluster-root producing plant species to Fe deficiency. This prompted this work, aimed to characterize the physiological and transcriptomic responses of white lupin plants to Fe deficiency. Occurrence of Strategy I components and interactions with P nutrition has been also investigated in this work. Results showed a physiological and transcriptional link between the responses to Fe and P deficiency in white lupin roots. Phosphorus-deficient plants activated the Strategy I Fe acquisition mechanisms that lead to an enhanced Fe mobilization and translocation and that might help the P acquisition process. On the other hand, also the Fe deficiency enhanced the phosphate acquisition and some P-deficient-responsive genes were overexpressed.

Drought stress can cause huge crop production losses. Drought resistance consists of complex traits, and is regulated by arrays of unclear networks at the molecular level. A stress-responsive NAC transcription factor gene SNAC1 has been reported for its function in the positive regulation of drought resistance in rice, and several downstream SNAC1 targets have been identified. However, a complete regulatory network mediated by SNAC1 in drought response remains unknown. In this study, we performed Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq of SNAC1-overexpression transgenic rice (SNAC1-OE) lines and wild-type under normal and moderate drought stress conditions, to identify all SNAC1 target genes at a genome-wide scale by RNA-Seq analyses. We detected 980 differentially expressed genes (DEGs) in the SNAC1-OE lines compared to the wild-type control under drought stress conditions. By ChIP-Seq analyses, we identified 4,339 SNAC1-binding genes under drought stress conditions (SNAC1BGDs). By combining the DEGs and SNAC1BGDs, we identified 93 SNAC1-targeted genes involved in drought responses (SNAC1TGDs). Most SNAC1TGDs are involved in transcriptional regulation, response to water loss, and other processes related to stress responses. Moreover, the major motifs in the SNAC1BGDs promoters include a NAC recognition sequence (NACRS) and an ABA responsive element (ABRE). SNAC1-OE lines are more sensitive to ABA than wild-type. SNAC1 can bind to the OsbZIP23 promoter, an important ABA signaling regulator, and positively regulate the expression of several ABA signaling genes.

In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37°C) and moderate cold (10°C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis.

Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.

To better understand the molecular mechanisms of the response of arbuscular mycorrhizal S. cannabina to salt stress, the transcriptional profile in both mycorrhizal and non-mycorrhizal Sesbania cannabina subjected to 3 and 27 hours NaCl treatment respectively were performed using the Illumina HiSeq™ 2000 sequencing platform (Illumina Inc., San Diego, CA, USA). Bioinformatic analysis of transcriptome data was performed to allow identification and functional annotation of differentially expressed genes (DEGs). By comparing the different genes appeared in control and treatment groups, we can learn more about the species-specific responses employed by S. cannabina and find novel associated genes or strategies in mycorrhizal plant under salt stress.

RESULTS: Using RNA-Seq, transcriptome changes were monitored in Arabidopsis seedlings during the first 24 h of exposure (at 1, 3, 6, 12 and 24 h) to 21 μM t-chalcone (I50 dose), examining effects on roots and shoots separately. Expression of 892 and 1000 genes was affected in roots and shoots, respectively. According to biological function, many of the affected genes were transcription factors and genes associated with oxidative stress, heat shock proteins, xenobiotic detoxification, ABA and auxin biosynthesis, and primary metabolic processess. These are secondary effects found with most phytotoxins. Potent phytotoxins usually act by inhibiting enzymes of primary metabolism. KEGG pathway analysis of transcriptome results from the first 3 h of t-chalcone expsoure indicated several potential primary metabolism target sites for t-chalcone. Of these, p-hydroxyphenylpyruvate dioxygenase (HPPD) and tyrosine amino transferase were consistent with the bleaching effect of the phytotoxin. Supplementation studies with Lemna paucicostata and Arabidiopsis supported HPPD as the target, although in vitro enzyme inhibition was not found.CONCLUSIONS: t-Chalcone is possibly a protoxin that is converted to a HPPD inhibitor in vivo.

Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research we focused on plants from Fabaceae family, which have a unique ability for establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We present the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results prove a decrease in the efficiency of nitrogen fixation as well as extensive changes in plant and bacterial transcriptomes shortly after watering cessation. We show for the first time that not only symbiotic plant component, but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrate that both M. truncatula and L. japonicus root nodules are susceptible to water deprivation, they indicate significant differences in plant and bacterial response to drought between tested species, which may be related to various type of root nodules formed by these species.

Arundo donax L. is one of the most promising bioenergy crop due to its high biomass yield and low irrigation requirement. The resistance to biotic and abiotic stress causes the high invasiveness of this plant which can grow with very low management input (e.g., pesticides, fertilization, irrigation) even in marginal lands or in fields irrigated with waste or salty water. Despite its economic importance, the A. donax genomic resources are still limited. In particular, no information on its transcriptional response to salt stress is available.We report the leaf transcriptome sequencing, de novo assembly and annotation of a giant reed genotype under two levels of salt stress. The study will be useful for providing insight into the molecular mechanism underlying its extreme adaptability also offering a platform for directing future efforts towards the genetic improvement of this species.

We report the role of SmE1 protein in the control of Arabidopsis development and tolerance to abiotic stresses. SmE1 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieve over selected transcripts depending on the stimulus nature.

Plants from temperate regions can be primed by exposure to low, non-freezing temperatures resulting in improved freezing tolerance. Whereas the molecular and metabolic basis of cold priming has been investigated in detail, hardly anything is known about memory of a previous cold event under warm conditions and a following low temperature triggering event. We show that three days of cold priming at 4°C, a seven-day lag phase at 20°C and a triggering treatment of 4°C improved the freezing tolerance of Arabidopsis Col-0 and other accessions compared to plants that were not primed before. Transcripts, metabolites and lipids as possible molecular determinants of this increase in freezing tolerance were investigated in Arabidopsis accessions Col-0 and N14 after priming, memory phase and triggering by Illumina-based RNA-Seq, GC-MS metabolite profiling and UPLC FT-MS-based lipidomics. Comparing primed and triggered with only triggered samples 93 and 128 unique differentially expressed genes could be identified in Col-0 and N14, together with three and six significantly changed lipids and one metabolite in N14. Possible functions of these candidates will be discussed. This work identified for the first time molecular and metabolic changes accompanying cold stress memory and triggering by a second cold stress.

In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . We mapped over 71 billion nucleotides to Populus genome. Our data demonstrates that with the current sequence depth ~ 19 % of Populus genome undergoes antisense transcription subjected to drought regulation. All in all we have identified that in root tissues 524 differentially expressed antisense genes and 247 drought-responsive SA gene pairs which are significantly regulated by drought (padj <0.05). Taken all data from both drought treatments, we have identified 1185 unique drought-responsive antisense gene loci and 606 drought-responsive SA gene pairs (padj <0.05).

Water availability is a key determinant of terrestrial plant productivity. Many climate models predict that water stress will increasingly challenge agricultural yields and exacerbate projected food deficits. To ensure food security and increase agricultural efficiency, crop water productivity must be increased. Research over past decades has established that the phytohormone abscisic acid (ABA) is a central regulator of water use and directly regulates stomatal opening and transpiration. In this study, we investigated whether the water productivity of wheat could be improved by increasing its ABA sensitivity. We show that overexpression of a wheat ABA receptor increases wheat ABA sensitivity, which significantly lowers a plant’s lifetime water consumption. Physiological analyses demonstrated that this water-saving trait is a consequence of reduced transpiration and a concomitant increase in photosynthetic activity, which together boost grain production per liter of water and protect productivity during water deficit. Our findings provide a general strategy for increasing water productivity that should be applicable to other crops because of the high conservation of the ABA signaling pathway.

Results: To investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over 2 billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first public release of degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7,000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1,000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 hours of the cold stress response in Brachypodium.Conclusions: Knowledge gained from this study provides considerable insight into the degradomes and the breadth of miRNA target conservation among these three species. Additionally associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which will aid researchers in developing stress tolerant transgenic crops.

To identify genes that are drought-responsive we conducted drought (soil water depletion) experiments on 3-month-old *P*. *trichocarpa *clonal plants. The plants undergo five different stages based on the appearance of their shoots and leaves during the drought experiments. Stage I: The shoot and leaves are green, and the leaves are well-spread. Stage II: The leaves are droopy. Stage III: The shoot is droopy, and the leaves are partially dry. Stage IV: The leaves are brown and totally dry. Stage V: The shoot is brown. With fully irrigation, the soil water content is 74% and the xylem water content is 80.6%. Plants in Stage III (Day 5) are under a mild drought state. The soil and xylem water content in Stage III dropped to 33% and 75.3%, respectively. Stage IV (Day 6-10) is a severe drought state where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively in Day 7. The stressed plants from Stage I-IV could all recover in 3 days after rehydration, but the plants in Stage V could not recover after rehydration.

Drought is a major abiotic stress that threatens global food security. Circular RNAs (circRNAs) are endogenous RNAs. How these molecules influence plant stress responses remains elusive. Here, a large scale circRNA profiling identified 2174 and 1354 high-confidence circRNAs in maize and Arabidopsis, respectively, and most were differentially expressed in response to drought. A substantial number of drought-associated circRNA hosting genes were involved in conserved or species-specific pathways in drought responses. Comparative analysis revealed that circRNA biogenesis was more complex in maize than in Arabidopsis. In most cases, maize circRNAs were negatively correlated with sRNA accumulation. In 368 maize inbred lines, the circRNA-hosting genes were enriched for SNPs associated with circRNA expression and drought tolerance, implying either important roles of circRNAs in maize drought responses or their potential use as biomarkers for breeding drought-tolerant maize. Additionally, the expression levels of circRNAs derived from drought-responsible genes encoding calcium-dependent protein kinase and cytokinin oxidase/dehydrogenase were significantly associated with drought tolerance of maize seedlings. Specifically, Arabidopsis plants overexpressing circGORK (Guard cell outward-rectifying K+-channel) were hypersensitive to ABA, but insensitive to drought, suggesting a positive role of circGORK in drought tolerance. We report the transcriptomic profiling and transgenic studies of circRNAs in plant drought responses, and provide evidences highlighting the universal molecular mechanisms involved in plant drought tolerance.

We conducted a genome-wide transcriptomic analysis in soybean leaves treated with a short-term (24 h) Pi-deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for both Pi-sufficient leaves (PSL) and Pi-deficient leaves (PDL), and therefore a total of four libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified short-term Pi-stress responsive genes. Some DEGs potentially involved in Pi sensing, signaling, and homeostasis were up-regulated by Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation, and cell wall modification were affected at the early stage of Pi deprivation. At least thirty-one transcription factor genes belonging to 10 diverse families were found to be responsive to Pi starvation.

Transcriptome profiling (RNA-seq) of local and systemic leaves of Arabidopsis Col treated with 50 mM DPI and exposed to a local treatment of high light.To inhibit the propagation of the ROS wave from the local to the systemic leaf, a drop of 0.3% agarose-containing water or 50 mM DPI, was placed at the midpoint between the local and systemic leaves of 4– to 5-week-old Col-0 plants. Local tissue was then subjected to light stress for 8 min and both local and systemic leaves were used for RNA-Seq.

Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite directionof protein-coding genes often positively correlates with and is required for theexpression of their cognate sense genes. We further characterized MAS, a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 (MAF4) locus.MAS is induced by cold and indispensable for the activation of MAF4 transcriptionand suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes

N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.

N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.

Strophostyles helvola is a close relative to common bean (Phaseolus vulgaris) and inhabits both coastal and non-coastal regions in North America. However, the mechanism of saline adaptation in S. helvola remains unclear. A transcriptome profiling would facilitate dissecting the underlying molecular mechanisms in salinity-adapted S. helvola. In this study, we reported the RNAseq analyses of two genotypes (a salt-tolerant beach genotype and a salt-sensitive inland genotype) of S. helvola stressed with salt. S. helvola plants were grown in pots and treated with half lethal-guided dose of NaCl solution for 3h, 24h, and 7d. The plants supplied with the same amount of water were used as controls. The whole roots sampled from the three time points were equally pooled as one biological replicate, and three replicates were used for library construction and transcriptome sequencing on Illumina Hiseq 2500. The comparative analyses of root transcriptomes presented here provides a valuable resource for discovery of genes and networks involved in salt tolerance in S. helvola.

To investigate the downstream genes of VaWRKY14 during drought stress response in Arabidopsis, RNA-Seq was carried out on two biological replicates of wild-type and 3 transgenic Arabidopsis lines mixture under normal and drought treatment conditions

Water shortage is a major factor that harms agriculture and ecosystems worldwide. Plants display various levels of tolerance to water deficit, but only resurrection plants can survive full desiccation of their vegetative tissues. Haberlea rhodopensis, an endemic plant of the Balkans, is one of the few resurrection plants found in Europe. We performed transcriptomic analyses of this species under slight, severe and full dehydration and recovery to investigate the dynamics of gene expression and associate them with existing physiological and metabolomics data.De novo assembly yielded a total of 142,479 unigenes with an average sequence length of 1,034 nt. Among them, 18,110 unigenes were differentially expressed. Hierarchical clustering of all differentially expressed genes resulted in seven clusters of dynamic expression patterns. The most significant expression changes, involving more than 15,000 genes, started at severe dehydration (~20% relative water content) and were partially maintained at full desiccation (<10% relative water content). More than a hundred pathways were enriched and functionally organized in a GO/pathway network at the severe dehydration stage. Transcriptomic changes in key pathways were analyzed and discussed in relation to metabolic processes, signal transduction, quality control of protein and DNA repair in this plant during dehydration and rehydration.Reprograming of the transcriptome occurs during severe dehydration, resulting in a profound alteration of metabolism toward alternative energy supply, hormone signal transduction, and prevention of DNA/protein damage under very low cellular water content, underlying the observed physiological and metabolic responses and the resurrection behavior of H. rhodopensis.

To impose the heat treatment similar to the Structure-seq experiment, we applied RNA-seq to 14-day-old rice (Oryza sativa) shoot tissue to investigate the effect of heat stress (42°C) as compared to control condition (22°C).

In order to gain insight into stability of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

In order to gain insight into abundance of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

Alternative splicing (AS) plays key roles in plant development and responses to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from alternative splicing) in plant accessions and its contributions to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0, and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing (RNA-seq). We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that SNPs influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.

MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNA sequences. Here, we investigated the contribution of OsDCL1 to innate immunity in rice. Activation-tagged dcl1a mutants (dcl1a-Ac) showed enhanced susceptibility to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi. Susceptibility to pathogen infection in dcl1a-Ac plants was associated with weaker induction of defence gene expression. Plant growth and development were not affected in dcl1a-Ac plants in the absence of pathogen challenge. To analyse the impact of OsDCL1a activation on the host transcriptome, we compared the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants. OsDCL1a activation misregulated genes involved in detoxification of reactive oxygen species (ROS) and accumulation of O2•- in leaves. Consequently, dcl1a-Ac plants were more sensitive to oxidative stress caused by methyl viologen treatment. Notably, transcriptome analysis revealed downregulation of diterpenoid phytoalexin biosynthetic genes in dcl1a-Ac, the expression of these genes also being weakly induced during pathogen infection in these plants. Finally, OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. Our findings support that OsDCL1a plays an important role in regulating innate immunity in rice.

Abstract: Drought is the primary cause of global agricultural losses and represents a major threat to worldwide food security. Currently, plant biotechnology stands out as the most promising strategy to increase crop growth in rain-fed conditions. The main mechanisms underlying drought resistance have been uncovered by studies of plant physiology and by engineering crops with drought-resistant genes. However, plants with enhanced drought resistance usually display lower levels of growth, highlighting the need to search for novel strategies capable of uncoupling drought resistance from growth. Here, we show that the brassinosteroid family of receptors, in addition to promoting growth, guides phenotypic adaptation to a great variety of drought stress traits analyzed herein. Whilst mutations in the ubiquitously localized BRI1 receptor pathway show an enhanced drought resistance at the expense of plant growth, we found that vascular-enriched BRL3 receptors confer drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress the BRL3 receptor pathway triggers the synthesis and mobilization of osmoprotectant metabolites, mainly proline and sugars. This preferentially occurs in the vascular tissues of the roots and favors overall plant growth. Altogether, our results uncover a new role for the spatial control of BR signaling in drought tolerance, and offer a novel strategy to address food security issues in an increasingly water-limited climate.

We sequenced mRNA from leaves of Arabidopsis under the control (CK), warming (W) and heat (H) treatments using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for different response patterns under prolonged warming versus rapid-onset heat stress in Arabidopsis.

Transcriptome analysis of cold-treated leaves (unifoliates) of soybean seedlings were performed. RNAseq analysis was performed using two lanes on a Illumina HiSeq2000 and sequenced on a 100bp, paired-end run.

Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expression of alkali-responsive genes in rice has not previously investigated. In this study, the transcriptomic data were compared between an alkaline-tolerant [WD20342 (WD)] and an alkaline-sensitive [Caidao (CD)] rice cultivar under control and alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis suggested the enrichment of IAR genes involved in response to various stimuli or stresses. According to KEGG pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.

We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.We treated the seedlings under the stress conditions, including cold, drought, heat, high-salt, and high-light. Also, we choose two tissues, roots and panicles for RNA sequencing.

The control of genome integrity throughout cellular generations is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is STRUCTURAL MAINTAINANCE OF CHROMOSOME 5/6 (SMC5/6) complex, related to cohesin and condensin complexes. Here, we analyzed mRNA abundance changes in the partial loss of function mutant of NON-SMC ELEMENT 4A (nse4a-2 mutant allele), a subunit of SMC5/6 complex, in Arabidopsis.

WRKY transcriptional factors play important roles in response to various abiotic stresses. In this study, we demonstrate that inserting a copy of soybean WRKY54 driven by a constitutive promoter of CMP (cestrum yellow leaf curling virus) or a drought induced promoter of RD29a, improves drought tolerance in transgenic soybean plants. GmWRKY54 is a transcriptional activator and regulates expressions of large numbers of stress-related genes. Using a GO enrichment toolkit, we found that GmWRKY54 up-regulated GO terms related to transcriptional regulator and gene expression and down-regulated GO terms related to photosynthesis and membrane. Using a co-expression network analysis, we find that dozens of genes are negatively co-expressing with photosynthetic genes. These genes are related to ABA signaling pathway, Ca2+ signaling pathway and transcriptional factors. Transgenic plants confer drought tolerance through improving stomatal closure, reducing transpiration rate and reducing membrane damage during water deficit. GmWRKY54 activates expression of these ABA or Ca2+ signaling-related genes, which finally regulates stomatal aperture. GmWRKY54 binds to the promoter regions of genes encoding an ABA receptor (PYL8-1), two calcium dependent protein kinase (CPK3-1 and CPK3-2), a CBL (Calcineurin B-like protein) interacting protein kinase (CIPK11-2), a SnRK family protein kinase and a ferritin, suggesting that they are the direct targets of GmWRKY54. Our study reveals that GmWRKY54 significantly improves drought tolerance in soybean and regulates expression of large numbers of drought-related genes, suggesting that GmWRKy54 maybe a master regulator of drought response.

We tracked the gene expression events following treatment of maize seedlings with the endoplasmic reticulum (ER) stress agent tunicamycin. ER stress elicits the unfolded protein response (UPR) and when plants are faced with persistent stress, the UPR transitions from an adaptive or cell survival phase to programmed cell death.

We used Illumina-based RNA-seq to identify differentially expressed genes in wild-type Arbaidopsis or in transgenic plants over-expressing HSFA1b-RFP. These data were interescted with ChIP-seq experiments conducted under the same conditions. The aim of the combined analyses was to identify HSFA1b-regulated genes involved in growth to stress transitions.

Many Cactaceae species exhibit determinate growth of the primary root as a consequence of root apical meristem (RAM) exhaustion. The genetic regulation of this root growth pattern is unknown. We de novo assembled and annotated the root apex transcriptome of the Pachycereus pringlei primary root at three developmental stages with active or exhausted RAM. The assembled transcriptome was characterized and used to evaluate differential transcript expression, identify RT-qPCR reference genes, and infer a transcriptional regulatory network. We generated a robust and comprehensive transcriptome of the primary root apex of P. pringlei and identified putative orthologs of Arabidopsis regulators of RAM maintenance, as well as putative lineage-specific transcripts. Furthermore, the transcriptome contained putative orthologs of most proteins involved in housekeeping processes, hormone signaling, and metabolic pathways. Specific transcriptional programs operate in the root apex at specific developmental time points. The transcriptional state of the P. pringlei root apex as the RAM becomes exhausted is comparable to that of cells from the meristematic, elongation, and differentiation zones of Arabidopsis roots. We suggest that the genetic program underlying the drought stress response is induced during development of the Cactaceae root, and that lineage-specific transcripts could contribute to root apical meristem exhaustion in Cactaceae.

Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and the proteome. At the same time, pollen is largely heat sensitive, particularly at early developmental stages. To define the changes during development and the response of different stages to elevated temperatures we investigated the transcriptome and proteome of pollen at tetrad, post-meiotic and mature stage before and after application of elevated temperatures. We used Solanum lycopersicum as an economically important crop. We demonstrate that the number of transcripts declines from tetrad to mature stage, while the protein content shows the opposite trend. Comparison of the transcriptome and proteome led to the discovery of two translational modes assigned as direct translation – transcripts increased in a specific pollen stage lead to increased translation in the same stage – and delayed translation – transcripts are produced for translation in later stages. The response to elevated temperatures is with ~5% of all genes being upregulated comparable to general plant behavior. The alteration at proteome level marked the mature pollen as least responsive and the post-meiotic stages as most responsive with altered levels of 40% of the identified proteins. For a subset of the genes with direct translation we observed a downregulation of protein levels after heat stress, whereas some of the genes with delayed translation showed a shift from delayed to direct translation when heat stress is applied. Further, Hsps, proteasome subunits, ribosomal proteins as well as eukaryotic initiation factors are the most drastically affected groups. On the example of Hsps we document that the response at transcriptome and proteome levels in e.g. the post-meiotic and mature stage does not correlate. Moreover, while all stages respond to heat stress with regulation of transcript abundance of Hsps in a comparable manner, changes at proteome level are distinct. Thus, we demonstrate that the difference in heat stress response in different stages of pollen development is rather manifested by significant changes of protein than transcript abundance.

Floodings already have a nearly 60% share in the worldwide damage to crops provoked by natural disasters. Climate change will cause plants to be even more frequently exposed to oxygen limiting conditions (hypoxia) in the near future due to heavy precipitation and concomitant waterlogging or flooding events in large areas of the world. Although the homeostatic regulation of adaptive responses to low oxygen stress in plants is well described, it remained unknown by which initial trigger the molecular response to low-oxygen stress is activated. Here, we show that a hypoxia-induced decline of the ATP level of the cell reduces LONG-CHAIN ACYL-COA SYNTHETASE (LACS) activity, which leads to a shift in the composition of the acyl-CoA pool. High oleoyl-CoA levels release the transcription factor RELATED TO APETALA 2.12 (RAP2.12) from its interaction partner ACYL-COA BINDING PROTEIN (ACBP) at the plasma membrane to induce low oxygen-specific gene expression. We show that different acyl-CoAs provoke unique molecular responses revealing a novel role as cellular signalling component also in plants. In terms of hypoxia signalling, dynamic acyl-CoA levels integrate the cellular energy status into the oxygen signalling cascade with ACBP and RAP2.12 being the central hub. The conserved nature of the ACBP:RAP2.12 module in crops and the novel mechanistic understanding of how low-oxygen stress responses are initiated by oleoyl-CoA in plants provide useful leads for enhancing future food security.

To gain the possible direct or indirect targets of VaAQUILO, RNA-Seq was carried out on three biological replicates of wild-type and 3 transgenic Arabidopsis lines mixture (#1, #2 and #3) under normal and cold treatment conditions (Based on the distribution of samples in a first PCA plot, the two most similar replicates per condition were considered for further statistical analyses) .

We report about the effects of temperature increase on rice response to Xanthomonas oryzae pv. oryzae using high throughput sequencing (RNA-Seq). The time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartment by Xoo and heat stress in both susceptible (IR24) and the resistant (IRBB67). Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature to have its resistance enhanced. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plant cope with combined biotic and abiotic stresses. This study provides an understanding of how IRBB67 mediated resistance to Xoo under temperature get insight to cross talk in abiotic and biotic stress regulatory pathway.

Hydrogen peroxide (H2O2) is an important signaling molecule in plant developmental processes and stress responses. However, whether H2O2-mediated signaling can crosstalk with plant hormone signaling is largely unclear. Here, we show that H2O2 induces oxidation of the BRASSINAZOLE-RESISTANT1 (BZR1) transcription factor, which functions as a master regulator of Brassinosteroid (BR) signaling. Oxidative modification enhances BZR1 transcriptional activity by promoting its interaction with regulators of auxin- and light-signaling, including AUXIN RESPONSE FACTOR6 (ARF6) and PHYTOCHROME INTERACTING FACTOR4 (PIF4). Genome-wide analysis shows that H2O2-dependent regulation of BZR1 activity plays a major role in modifying gene expression related to several BR-mediated biological processes. Furthermore, we show that the thioredoxin TRXh5 can interact with, and catalyze reduction of, BZR1. We conclude that reversible oxidation of BZR1 connects H2O2- and thioredoxin-mediated redox signaling to BR signaling to regulate plant development

Plants have evolved to possess adaptation mechanism to cope with drought stress by reprograming transcriptional networks through drought responsive transcription factors, which in turn mediate morphological and physiological changes. NAM, ATAF1-2, and CUC2 (NAC) transcription factors are known to be associated with various developmental processes and stress tolerance. In this study, we functionally characterized the rice drought responsive NAC transcription factor OsNAC14. OsNAC14 was predominantly induced at meiosis stage, and induced by drought, high salinity, ABA and low temperature in leaves than roots. Overexpression of OsNAC14 resulted in drought tolerance at the vegetative growth stage and enhanced filling rate at vegetative growth. OsNAC14 overexpression elevated expression of genes related to DNA damage repair, defense response, strigolactone biosynthesis, which correlated with resistance to drought tolerance. Furthermore, OsNAC14 directly bound to the promoter of drought inducible OsRAD51A1, a key component in homologous recombination in DNA repair system. These results indicate that OsNAC14 mediate drought tolerance by recruiting factors involved in DNA damage repair and defense response to enable plant to protect from cellular damage caused by drought stress, thereby provide mechanism for drought tolerance.

We performed a transcriptomics analysis in the wild type and the mutant, and the expression levels of PEP-encoded genes, chloroplast development and heat-strss-related genes genes were affected inwlp2s mutant.

Salinity tolerance is a complex trait and, despite many efforts to obtain rice plants resistant to salt, few results have been achieved since a deeper understanding of the tolerance mechanisms is still needed. We used imaging of photosynthetic parameters, ion analysis and transcriptomic approaches to unveil differences between two rice varieties differing in salt sensitivity. Moreover, we analysed H2O2 production in roots, using a fluorescent probe, and the ensuing gene regulation. Transcriptomic analyses conducted in tolerant plants supported the set-up of an adaptive program consisting of allocating sodium preferentially to roots, restricting it to the oldest leaves and activating regulatory mechanisms of photosynthesis in new leaves. As a consequence, plants resumed growth even under prolonged salt stress. By contrast, in the susceptible variety, RNA profiling unveiled a mis-targeted response, leading to senescence and cell death. In roots of tolerant plants, an increase in H2O2 was observed as early as 5 minutes after treatment. Consequently, the expression of genes involved in perception, signal transduction and response to salt were induced at earlier times when compared to susceptible plant roots. Our results demonstrate that a prompt H2O2 signalling in roots participates to a coordinated response resulting in adaptation instead of senescence in salt treated rice plants.

Purpose: We aimed to dissect heat response of tall fescue and possible roles of melatonin and 24-epibrassinolide during thermotolerance.Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified genes modulated by short term heat (2h) and long term heat (12h) treatments.

Several nucleoporins in the nuclear pore complex (NPC) have been reported to be involved in abiotic stress responses in plants. However, the molecular mechanism of how NPC regulates abiotic stress responses, especially the expression of stress responsive genes remains poorly understood. From a forward genetics screen using an abiotic stress-responsive luciferase reporter (RD29A-LUC) in the sickle-1 (sic-1) mutant background, we identified a suppressor caused by a mutation in NUCLEOPORIN 85 (NUP85), which exhibited reduced expression of RD29A-LUC in response to ABA and salt stress. Consistently, the ABA and salinity induced expression of several stress responsive genes such as RD29A, COR15A and COR47 was significantly compromised in nup85 mutants and other nucleoporin mutants such as nup160 and hos1. Subsequently, Immunoprecipitation and mass spectrometry analysis revealed that NUP85 is potentially associated with HOS1 and other nucleoporins within the nup107-160 complex, along with several mediator subunits. We further showed that there is a direct physical interaction between MED18 and NUP85. Similar to NUP85 mutations, MED18 mutation was also found to attenuate expression of stress responsive genes. Taken together, we not only revealed the involvement of NUP85 and other nucleoporins in regulating ABA and salt stress responses, but also uncovered a potential relation between NPC and mediator complex in modulating the gene expression in plants.

Jasmonates (JA) and abscisic acid (ABA) are phytohormones known to play important roles in plant response and adaptation to various abiotic stresses including salinity, drought, wounding, and cold. JAZ (JASMONATE ZIM-domain) proteins have been reported to play negative roles in JA signaling. However, direct evidence is still lacking that JAZ proteins regulate drought resistance. In this study, OsJAZ1 was investigated for its role in drought resistance in rice. Expression of OsJAZ1 was strongly responsive to JA treatment, and it was slightly responsive to ABA, salicylic acid, and abiotic stresses including drought, salinity, and cold. The OsJAZ1-overexpression rice plants were more sensitive to drought stress treatment than the wild-type rice Zhonghua 11 (ZH11) at both the seedling and reproductive stages, while the jaz1 T-DNA insertion mutant plants showed increased drought tolerance compared to the wild-type plants. The OsJAZ1-overexpression plants were hyposensitive to MeJA and ABA, whereas the jaz1 mutant plants were hypersensitive to MeJA and ABA. In addition, there were significant differences in shoot and root length between the OsJAZ1 transgenic and wild-type plants under the MeJA and ABA treatments. A subcellular localization assay indicated that OsJAZ1 was localized in both the nucleus and cytoplasm. Transcriptome profiling analysis by RNA-seq revealed that the expression levels of many genes in the ABA and JA signaling pathways exhibited significant differences between the OsJAZ1-overexpression plants and wild-type ZH11 under drought stress treatment. Quantitative real-time PCR confirmed the expression profiles of some of the differentially expressed genes, including OsNCED4, OsLEA3, RAB21, OsbHLH006, OsbHLH148, OsDREB1A, OsDREB1B, SNAC1, and OsCCD1. These results together suggest that OsJAZ1 plays a role in regulating the drought resistance of rice partially via the ABA and JA pathways.

Recent studies have shown that several plant species require microbial associations for stress tolerance and survival. In this work, we show that the desert endophytic bacterium Enterobacter sp. SA187 enhances yield and biomass of alfalfa in field trials, revealing a high potential for improving desert agriculture. To understand the underlying molecular mechanisms, we studied SA187 interaction with Arabidopsis thaliana. SA187 colonized surface and inner tissues of Arabidopsis roots and shoots and conferred tolerance to salt and osmotic stresses. Transcriptome, genetic and pharmacological studies revealed that the ethylene signaling pathway plays a key role in mediating SA187-triggered abiotic stress tolerance to plants. While plant ethylene production is not required, our data suggest that SA187 induces abiotic stress tolerance by bacterial production of 2-keto-4-methylthiobutyric acid (KMBA), known be converted into ethylene in planta. These results reveal a part of the complex molecular communication process during beneficial plant-microbe interactions and unravel an important role of ethylene in protecting plants under abiotic stress conditions.

Cereal cyst nematode (Heterodera avenae) can be attracted by wheat roots before infestation, while largely is unknown underlying this phenomenon. Here, we examined the transcriptional responses of both wheat roots and nematodes during the attraction stage by mRNA sequencing analysis (with and without reference genome, respectively). We found that consistent with their respective mobility, the immobile host wheat root only had 93 DEGs (27 up-regulated and 66 down-regulated), while the mobile plant parasitic nematode H. avenae reacted much more actively with 879 DEGs (867 up-regulated and 12 down-regulated). Among the DEGs, a number of wheat DEGs (most down-regulated) were involved in biotic stress pathways, while several putative effector genes (up-regulated) were found in the nematode DEGs. Results of the experiments demonstrated that nematode responds more actively than wheat during the attraction stage of parasitism, and the parasite responses mainly involved up-regulation whereas the host responses mainly involved down-regulation.

RNA polymerase II C-terminal domain (CTD) phosphorylation regulates transcription of both protein-coding mRNAs and non-coding RNAs (ncRNAs). However, understanding about CTD-phosphoregulation in plant ncRNA transcription is still obscure. Here we used Arabidopsis CTD phosphatase-like 4 knock-down lines (CPL4RNAi) and show that CPL4 functions in a genome-wide, conditional 3'-extensions of small nuclear RNA (snRNA) and biogenesis of novel snR-DPGs, which are protein-coding snRNA-mRNA fusion transcripts (snR-Downstream Protein-coding Gene). Production of snR-DPG is dependent on pol II snRNA promoter (PIIsnR), and CPL4RNAi promotes readthrough of snRNA 3’-end processing signal and pol II transcription downstream of snRNA. Also discovered was a novel unstable ncRNASSP14, which is driven by a PIIsnR and is conditionally 3'-extended to produce mRNA. In wild type, the snRNA-to-snR-DPG switching is induced by salt stress, and is associated with alteration of CTD phosphorylation status in the transcribing pol II complex. The snR-DPG transcripts occur widely in plants, suggesting that the transcriptional snRNA-to-snR-DPG switching is a previously unknown mechanism ubiquitous in plants to regulate gene expression in response to environmental stresses.

Drought is one of the main climate threats for crop plant production limitation. Climate change models predict constant global warming accompanied by strong reduction in water availability, especially for agricultural needs. Potato belongs to crop plants that are considered as sensitive to water shortage. Global estimation analyses show that drought may decrease potato yield by 18-32% in the period of 2040-2069 (Hijmans, 2003, Obidiegwu et al. 2015, Front in Plant science). Crop models predict that potato yields may reduce by ~30% as a result of water deficit in Poland (http://www.climateadaptation.eu/poland/agriculture-and-horticulture/). Genetic variability between potato cultivars has been described regarding their tolerance to drought (Soltys-Kalina et al. 2016). To diminish the effect of forecasted potato harvest losses, it is crucial to identify as many as possible potato plant strategies to withstand long drought periods during vegetative season. For this reason, we decided to analyse the expression differences in transcriptomes independently in two selected pairs of potato cultivars, Gwiazda/Oberon and Tajfun/Owacja. Cultivars in each pair are closely related to each other (having one parent in common or one grandparent in common, respectively) but differ in their sensitivity to drought conditions. In this paper, we identified at least 24 top selected genes whose expression profiles differ significantly during drought period when closely related studied cultivars are compared.Moreover, all but one of selected potato genes have their homologues in Arabidopsis plant genome. We found that A. thaliana mutants with mostly downregulated expression of seven selected homologous genes differ in their response to drought. To our knowledge, all of these genes were until now not reported as drought-related. Thus, our original approach and obtained results allowed to identify new players in plant response to drought.

Temperature has a major role in plant growth and survival, for example wheat yields decrease by about 6% for every 1°C rise in global temperature [1]. High temperatures induce the expression of protective chaperones and modulate growth responses. Key players in the heat protection response are transcription factors of the HEAT SHOCK FACTOR A1 (HSFA1) family [2]. However the pathways that activate the HSFA1 class TFs, and how these perceive temperature and integrate it with other environmental signals are not clear. Plants are exposed to considerable diurnal temperature variation, and have evolved pathways to anticipate likely future conditions. For example, the cold response pathway is gated by the circadian clock, enabling the degree of responsiveness to cold to be controlled in the context of the environment [3, 4] and genes promoting elongation growth and flowering in response to warm temperature are induced during the night via thermosensory phytochromes [5 ,6]. It is not known in Arabidopsis if the warm temperature protective pathways are gated. In this study we find that there is strong diurnal variation in the heat stress response of Arabidopsis, and we show that this correlates with the expression of HSP70 in the day night cycle. The dark to light transition is in fact sufficient to robustly induce expression of warm temperature protective genes such as HSP70. A forward genetic screen with a HSP70-Luciferase reporter line revealed genes necessary for controlling this process and identified a central role for chloroplast signalling in the warm temperature response that accounts for diurnal variation in thermotolerance.

Plant homeodomain (PHD) finger proteins are ‘histone code readers’. They recognize and bind to epigenetically modified histone H3 ‘tail’. Here we reported that an Alfin1-like soybean protein, GmPHD6, read H3K4me0/1/2 but not H3K4me3 with the N-terminal instead of the PHD finger. GmPHD6 does not possess transcriptional regulatory ability. Through the PHD finger, GmPHD6 interacts with its co-activator, LHP1-1/2. Using a transgenic hairy root system, we demonstrated that over-expression of GmPHD6 improved stress tolerance in transgenic soybean composites. Perhaps due to the excessive amount of LHP1 compared to that of GmPHD6, over-expression of LHP1-1/2 failed to do so. The integrity of the complex is essential in stress response, for the abrogation of DNA binding activity of GmPHD6 or the decrease of LHP1 content leads to stress sensitivity in soybean. GmPHD6 influences expression of dozens of stress-related genes to confer stress tolerance. Among these genes, we identified three direct targets of GmPHD6, ASR (ABA-stress-ripening induced), CYP71A22 (cytochrome P450) and CYP82C4. Our study reveals significant findings in stress response. GmPHD6 and LHP1 are recruited to H3K4me0/1/2 marks, where several stress-related genes may locate in, to form a transcriptional activation complex. GmPHD6 locates target sites through recognizing the G-rich elements in their promoters; LHP1 enhances expression levels of these targets. Genetically engineering of GmPHD6/LHP1 complex should improve stress tolerance in crop plants.

Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 hours induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense and stress responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.

The Texas Potato breeding program has been succesful at bringing several potato variety including somaclonal selection made in the field. This genetic diversity is in part due to somaclonal variability that appears within potato selections for which tubers are used as seeds. However, nogenetic or molecular evidences were identified so far. In this investigation, we used RNA-seq, which allows genome-wide gene expression analysis to compare the transcriptomes of the subclonal Russet Norkotah selection TXNS278 with standard Russet Norkotah grown in commercial fields. Among the selections, TXNS278 appeared in a multi- year analysis as a top No 1 yielding variety. Russet Norkotah and TXNS278 leaf and root transcriptomes were compared at two time points. Results indicated that yield differences between Russet Norkotah and TXNS278 might possibly be linked to differences in responses to biotic and abiotic stresses and hormonal signaling

Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute a large gene family in plants. These known PPR proteins have been identified to play important roles in organellar RNA metabolism and plant development in Arabidopsis and rice. However, functions of PPR genes in woody species remain still largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the poplar genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships, gene duplication. Transcriptomic analyses identified that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), wounding, cold and salinity. Quantitative RT-PCR analysis further confirmed the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a more comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.Purpose: The goal of this study is to compare the PPR genes profile in Wild Type with biotic and abiotic treatment of P. trichocarpa. Treatment including M. brunnea, SA and MeJA, wound, low temperature, and salinity. Plant material treatment: Hormone treatments: SA (5 mM in water) and MeJA [1mM in 0.1% (v/v) ethanol] were applied at the different concentrations as 5 ml droplets on each plant. The treated plants were immediately covered with a transparent lid. Fungal inoculation: The leaves were collected after 24 h. Leaves of three-month-old plants were inoculated with M. brunnea f.sp. multigermtubi. Mycelial plugs (6 mm) were placed on excised leaves (at least three leaves for each plant). These leaves were incubated in Petri dishes with humid filter paper in a humid chamber for 3 d. Low temperature stress: The healthy, well-hydrated plants were transferred to a growth chamber at 4°C under the same light and photoperiodic conditions for 1 h. After cold treatment, plants were allowed to recover at 20°C for 1 h. Wounding stress: For the wounding treatment, the young leaves of poplar plants were harvested after being punctured with sterile needles and placed at 20°C for 2 h. Salinity stress: The four-week-old seedlings were subjected to salt stress. Saline treatments had the NaCl concentrations of 100 mM added to full-strength Hoagland’s solution for 2 d. Wild type plant were grown in a greenhouse at 25°C under a 14/10 h light/dark cycle. Additionally, the leaves applied for all stress treatments, pathogen infection, CK and DGE analysis were excised from the second and third internodes.

Background: Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the “landscape” of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis and a tremendous amount of WGBS data has been generated by the research community. However, methods for the systematic comparison of DNA methylation profiles to identify novel regulatory mechanisms have yet to be established.Results: Here we developed a standardized pipeline and re-analyzed over three hundred publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments. In total this collection included more than 3,700 Gb (Giga base-pairs) of sequencing data and a large number of wild-type controls. This enabled us to identify “high-confidence Differentially Methylated Regions” (hcDMRs) with high reliability by comparing each ‘test’ library to each of the 54 controls. We adopted two statistical methods, Statistical Measurements on Overlapping of DMRs (S-MOD) followed by Quantitative Measurements on Overlapping of DMRs (Q-MOD), to compare and cluster libraries based on their impacts on DNA methylation. In addition to confirming existing relationships using this unbiased approach, we revealed novel connections between methylation pathways. For instance, MET1 and CMT3 were found to be required for maintenance of asymmetric CHH methylation at non-overlapping regions of CMT2 targeted heterochromatin.Conclusions: Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes, and can also be adopted for other omics datasets. Together, the results demonstrate the effectiveness of data-driven, hypothesis-generating epigenetic research.

We conducted transcriptome comparison between control and salt treatment to identify potential regulatory components involved in F. tataricum salt responses. A total of 53.15 million clean reads from control and salt-treated libraries were produced via an llumina sequencing approach. Then we de novo assembled these reads into a transcriptome dataset containing 57921 unigenes with N50 length of 1400 bp and total length of 44.5 Mb. A total of 36688 unigenes could find matches in public databases. GO, KEGG and KOG classification suggested the enrichment of these unigenes in 56 sub-categories, 25 KOG, and 273 pathways, respectively. Comparison of the transcriptome expression patterns between control and salt treatment unveiled 455 differentially expressed genes (DEGs). Further, we found the genes encoding for protein kinases, phosphatases, heat shock proteins (HSPs), ATP-binding cassette (ABC) transporters, Glutathione S-transferases (GSTs), abiotic-related transcription factors and circadian clock might be relevant to the salinity adaption of this species. Thus, this study offers an insight into the salt tolerance mechanisms, and will serve as useful genetic information for tolerant elites breeding programs in future.

Background: Plant disease is a major challenge to agriculture worldwide, and it is often exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress increases host susceptibility, a tendency which could spell disaster in light of the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the molecular mechanisms that cause it. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants infected with Xanthomonas oryzae (Xo), an economically important bacterial pathogen of rice, during high temperature stress.Results: Using RNA-Seq technology, 8,499 differentially expressed genes were identified as temperature responsive in one rice cultivar, IRBB61, experiencing susceptible and resistant interactions with Xo across three time points. Many genes with gene ontology terms associated with stress response were identified. Notably, genes in the plant hormone abscisic acid (ABA) biosynthesis and response pathways were identified as upregulated by high temperature in both mock-treated plants and plants in the susceptible interaction and suppressed by high temperature in plants in the resistant interaction. A DNA sequence motif similar to known ABA-responsive cis-regulatory elements was identified in the promoter region upstream of genes upregulated in susceptible but downregulated in resistant interactions.Conclusions: The results of our study suggest that the plant hormone ABA is an important node for cross-talk between plant transcriptional response pathways to high temperature stress and pathogen attack. Genes in this pathway represent an important focus for future study to determine how plants evolved to deal with simultaneous abiotic and biotic stresses.

The AP2/ERF family is one of the plant-specific transcription factors (TFs) whose members have been associated with various developmental processes and stress tolerance. Here, we functionally characterized the drought-inducible OsERF48, a group Ib member of the rice ERF family that contains four conserved motifs, CMI-1, 2, 3 and 4. Transactivation assay in yeast revealed that the CMI-1 at the C-terminal end was essential for its transcriptional activity. When the OsERF48 was overexpressed in an either root-specific (ROXOsERF48) or whole-body (OXOsERF48) expression manner, both transgenic plants showed a longer and denser root phenotype than the nontransgenic (NT) controls. When plants were grown on a 40% PEG-infused medium, an in vitro drought condition, ROXOsERF48 plants showed a more vigorous root growth over OXOsERF48 and NT plants. In addition, the ROXOsERF48 plants exhibited higher grain yield under field-drought conditions than OXOsERF48 and NT plants. We constructed a putative regulatory network of OsERF48 by cross-referencing of RNA-seq data of ROXOsERF48 roots with a co-expression network database, revealing an involvement of 20 drought-related genes. These include genes for stress signaling, carbohydrate metabolism, cell-wall proteins, and drought-response. More importantly, OsCML16, a key gene for calcium signaling during abiotic stress, was identified to be the direct target of OsERF48 by the ChIP-qPCR and the protoplast transient assay. Thus, our results demonstrated that OsERF48 regulates OsCML16, a calmodulin-like protein gene that enhance root growth and drought tolerance.

By analyzing the transcriptome of WT/ΔpcrR/ΔpcrK strains in the presence of 2iP and comparing gene expression level between them, we report genes with different expression levels between WT and ΔpcrR/ΔpcrK strains in the presence of plant cytokinin 2iP.

Analysis of the impact of plant growth regulators on submergence tolerance of rice at gene expression level. The hypothesis tested in the present study was that the submergence-tolerance was improved by foliar application of paclobutrazol under sumergence stress conditions.

Improving plant stress response holds great agricultural potential. One promising, yet speculative, possibility is the formation of plant stress memory facilitating enhanced responses to recurring stress. One possibility is the involvement of environmentally-induced variation in reversible chromatin marks, such as DNA methylation, leading to the altered regulation of underlying genetic elements that promote enhanced stress tolerance. Such potential has spurred numerous investigations yielding conflicting results, thus it remains unclear whether robust stress-induced chromatin variation can encode plant stress memory conveying enhanced stress tolerance. Herein we investigate for the possibility of stress-induced alterations in DNA methylation to convey stress memory, both on mitotic and transgenerational timescales, such that previously stressed plants show improved stress tolerance with correlated alterations in DNA methylation at stress-responsive loci. We find that although the experience of stress may be stored mitotically, it does not appear to be transmitted meiotically and is independent of DNA methylation changes. Overall, the DNA methylome appears to be robust against stress-induced variation and is unlikely to contribute to any form of stress memory.

Wounding is a primary trigger of organ regeneration but how wound stress reactivates cell proliferation and promotes cellular reprogramming remains elusive. In this study we combined the transcriptome analysis with quantitative hormonal analysis to investigate how wounding induces callus formation in Arabidopsis thaliana. Our time-course RNA-seq analysis revealed that wounding induces dynamic transcriptional changes that can be categorized into five clusters with distinct temporal patterns. Gene ontology analyses uncovered that wounding modifies the expression of hormone biosynthesis and response genes, and quantitative analysis of endogenous plant hormones revealed accumulation of cytokinin prior to callus formation. Mutants defective in cytokinin synthesis and signalling display reduced efficiency in callus formation, indicating that de novo synthesis of cytokinin has major contribution in wound-induced callus formation. We further demonstrate that type-A ARABIDOPSIS RESPONSE REGULATOR (ARR)-mediated cytokinin signalling regulates the expression of CYCLIN D3;1 (CYCD3;1) and mutations in CYCD3;1 and its homologs CYCD3;2-3 cause defects in callus formation. Our transcriptome data, in addition, showed that wounding activates multiple developmental regulators, and we found novel roles of ETHYLENE RESPONSE FACTOR 115 (ERF115) and PLETHORA3 (PLT3), PLT5, PLT7 in wound-induced callus formation. Together, this study provides novel mechanistic insights into how wounding reactivates cell proliferation during callus formation.

The roots of halophytes such as mangroves provide the first line of defense against the constant salt stress they experience. Such adaptation should include major reprogramming of the gene expression profiles. Using RNA-sequencing approach we identified 101,446 ‘all-unigenes’ from the seedling roots of the mangrove tree Avicennia officinalis. From the data 6618 genes were identified to be differentially regulated by salt when two-month-old greenhouse-grown seedlings without prior exposure to sea water were subjected to 24 h of 500 mM NaCl treatment. About 1,404 genes were significantly up-regulated, while 5214 genes were down-regulated. Based on Gene Ontology analysis, they could be classified under various categories, including metabolic processes, stress and defense response, signal transduction, transcription-related and transporters. Our analysis provides the baseline information towards understanding salt balance in mangroves and hence mechanism of salt tolerance in plants.

Gene expression patterns in roots of Camelina sativa with enhanced salinity tolerance arising from growth in soil treated with plant growth promoting bacteria producing 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) or from expression of the corresponding acdS gene in transgenic lines.Salinity stress negatively affects crop production. However in camelina, grown in soils treated with PGPB producing 1-aminocyclopropane-1-carboxylate deaminase (acdS ) or transgenic lines expressing acdS exhibited increased salinity tolerance. AcdS reducing the level of stress ethylene to below the point where it is inhibitory to growth. Gene expression patterns in roots responding to salt stress was affected by the expression of acdS under the control of CaMV 35S or root-specific (rolD) promoters in transgenic lines, or by growth in soils treated with endophytic PGPB producing acdS indicate that the number of the genes were differentially expressed were more assigned to genome III in transgenic plants however in PGPB treated plants the number of the genes were differentially expressed were almost equally assigned to all three genomes. Different promoter may induce different set or even different homeologues genes in camelina with probably the same function in response to salt stress. Though root is not a photosynthetic tissue reduction of the ethylene in root cells has positive effect on plant photosynthetic machinery. The expression of the genes involved in minor CHO metabolism was up-regulated mainly in roots of acdS contain plants during salt stress. Moderate reduction in ethylene production has positive effect on root growth during salt stress but reduction of the ethylene higher than a certain level has negative effect on root growth due to reduction of the expression of the genes involved in root cell elongation. AcdS gene modulating the level of ROS in cells in the level that induce ROS signaling but preventing cellular damage by make a balance on up and down-regulation of the genes involved in oxidation-reduction process in root cells under salinity stress. The acdS containing PGPB (8R6) were mostly effected the ethylene signaling and ABA biosynthesis and signaling in positive way but transgenic line depends to the promoter affecting Auxin, JA and BR signaling or biosynthesis.

We used RNA-Seq to perform a whole transcriptome analysis in roots of Azucena (tropical japonica), IR64 (indica), and the near-isogenic lines AZU[IR64121] and IR64[AZU12.1] in control conditions and treated with 80 μM Al3+ activity for 4 hours

In this study genome-wide gene expression profiling was used to analyze mechanisms of drought tolerance in Brassica rapa. Using an Illumina Mi-Seq platform we sequenced RNA from shoot tissues of drought tolerant and drought sensitive B. rapa genotypes in control conditions and after application of osmotic stress. Differentially expressed genes between the different conditions and genotypes were used to identify drought relevant gene networks.

Submergence induces hypoxia in plants; exposure to oxygen following submergence, termed reoxygenation, produces a burst of reactive oxygen species. The mechanisms of hypoxia sensing and signaling in plants have been well studied, but how plants respond to reoxygenation remains unclear. Here, we show that reoxygenation in Arabidopsis thaliana involves rapid accumulation of jasmonates (JAs) and increased transcript levels of JA biosynthesis genes. Application of exogenous methyl jasmonate improved tolerance to reoxygenation in wild-type Arabidopsis; also, mutants deficient in JA biosynthesis and signaling were very sensitive to reoxygenation. Moreover, overexpression of the transcription factor gene MYC2 enhanced tolerance to post-hypoxic stress and myc2 knockout mutants showed increased sensitivity to reoxygenation, indicating that MYC2 functions as a key regulator in the JA-mediated reoxygenation response. MYC2 transcriptionally activates members of the VITAMIN C DEFECTIVE (VTC) and GLUTATHIONE SYNTHETASE (GSH) gene families, which encode rate-limiting enzymes in the ascorbate and glutathione synthesis pathways. Overexpression of VTC1 and GSH1 in the myc2-2 mutant suppressed the post-hypoxic hypersensitive phenotype. The JA-inducible accumulation of antioxidants may alleviate oxidative damage caused by reoxygenation, improving plant survival after submergence. Taken together, our findings demonstrate that JA signaling interacts with the antioxidant pathway to regulate reoxygenation responses in Arabidopsis.

The temporal control of gene expression leads to time of day effects on metabolism and physiology. To identify early transcript level changes occurring in the Brassica rapa oil-type variety R500 during initial drought perception we performed an RNA-seq time course experiment. Leaf tissue was collected from well-watered and drought treated 18 day old plants grown under 14h light at 22°C/10h dark at 18°C every 4h over 2 days with 2 biological replicates at every time point. We collected physiology measurements at every time point and observed dynamic time of day changes in photosynthetic rate, stomatal conductance, non-structural carbohydrates and PSII efficiency. Using a co-expression network approach, phase dependent gene modules were correlated with the physiology data to reveal temporally regulated drought responses. This study provides insight into the transcriptome level responses occurring in the plant in the early stages of drought perception before visible signs of stress occur.

Soil salinity presents a notable challenge to agriculture and to increasing the use marginal lands for farming. Here we provide a detailed analysis of the physiology, chemistry and gene expression patterns in roots and shoots of Camelina sativa in response to salt stress. Salt treatment reduced shoot, but not root length. Root and shoot weight were affected by salt, as was photosynthetic capacity. Salt treatment did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels. Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt. Genes encoding proteins involved in chelation and storage were highly up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots. In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated, probably to improve desiccation tolerance. Partial genome expression partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa genomes. Genome I and II were involved in the response to salinity stress to about the same degree, while about 10 % more differentially-expressed genes were associated with Genome III. This study has provided valuable information and insight into the response of camelina to salt stress. Examination of this data and comparison to similar studies in more halophytic species will allow development of even more salt-tolerant varieties of this emerging industrial crop.

Drought is one of the major abiotic stresses threatening rice (Oryza sativa) production worldwide. Drought resistance is controlled by multiple genes, and therefore, a multi-gene genetic engineering strategy is theoretically useful for improving drought resistance. However, the experimental evidence for such a strategy is still lacking. In this study, a few drought-responsive genes from rice were assembled by a multiple-round site-specific assembly (MISSA) system, and the constructs were introduced into the rice cultivar KY131 via Agrobacterium-mediated transformation. The transgenic lines of the multi-gene and corresponding single-gene constructs were pre-evaluated for drought resistance. We found that the co-overexpression of two genes, encoding a constitutively active form of a bZIP transcription factor (OsbZIP46CA1) and a protein kinase (SAPK6) involved in the abscisic acid (ABA) signaling pathway, showed significantly enhanced drought resistance compared with the single-gene transgenic lines and the negative transgenic plants. Single-copy lines of this bi-gene combination (named XL22) and the corresponding single-gene lines were further evaluated for drought resistance in the field using agronomical traits. The results showed that XL22 exhibited greater yield, biomass, spikelet number, and grain number under moderate drought stress conditions. The seedling survival rate of XL22 and the single-gene overexpressors after drought stress treatment also supported the drought resistance results. Furthermore, expression profiling by RNA-Seq revealed that many genes involved in the stress response were specifically up-regulated in the drought-treated XL22 lines and some of the stress-related genes activated in CA1-OE and SAPK6-OE were distinct, which could partially explain the different performances of these lines with respect to drought resistance. In addition, the XL22 seedlings showed improved tolerance to heat and cold stresses. Our results demonstrate that the multi-gene assembly in an appropriate combination may be a promising approach in the genetic improvement of drought resistance.

Analysis of gene expression data from four genetically diverse wild soybean accessions helps reveal both sensitive and resistant responses of the plants to increased ozone levels. Results help characterize genetic response of wild soybean to ozone stress and could help provide information on genetic resources for creating ozone-tolerant soybean breeding lines.

The present study identified and characterized miRNAs, which may play a major role in stress resistance. we applied high-throughput sequencing to investigate the alterations of miRNAs expression of sea cucumber under hypoxia stress(DO2_1,DO2_2,DO2_3),slight hypoxia stress(DO4_1,DO4_2,DO4_3) and normal condition(DO8_1,DO8_2,DO8_3). These results will provide a basis for future studies of miRNA regulation in sea cucumbers under hypoxia stress.

MicroRNAs (miRNAs) play an important role as regulators of gene expression. In plants they affect a wide variety of biological process like growth, development and response to biotic and abiotic stress. Glycine max is one of the most important crop worldwide due to its rich protein and oil content. Drought and salt stress are the main abiotic stresses that affect soybean. Salt stress impacts the fisiology of the plants due to the damage in the photosynthetic rate, growth and development. This work aim to identify salt-stress responsive miRNAs and their respective targets in Glycine max using high-throughput RNA sequencing technology.

OsNAC6 is a stress responsive NAC transcription factor in rice known as a regulator for the transcriptional networks of the drought tolerance mechanisms. However, little is known about the associated molecular mechanisms for drought tolerance. Here, we identified OsNAC6-mediated root structural adaptation such as increased root number and root diameter that was sufficient to confer drought tolerance. Multiyear (5 years) drought field tests clearly demonstrated that OsNAC6 overexpression in roots produced higher grain yield under drought conditions. Genome-wide analyses revealed that OsNAC6 directly up-regulated 13 genes. Taken together, OsNAC6 is a valuable candidate for genetic engineering of drought-tolerant high-yielding crops.

One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affecting normal plant growth and causing agricultural losses worldwide. The advent of state-of-the-art technologies such as high throughput mRNA sequencing (RNA-Seq) has revolutionized whole-transcriptome analysis by allowing, with high precision, to measure changes in gene expression. In this work, we used tissue-specific RNA-Seq to gain insight into the Petunia hybrida transcriptional responses under sodium chloride (NaCl) stress using a controlled hydroponic system. Roots and leaves samples were taken from a continuum of 48 hours of acute 150 mM NaCl. This analysis revealed a set of tissue- and- time point specific differentially expressed genes, such as genes related to transport, signal transduction, ion homeostasis as well as novel and undescribed genes, such as Peaxi162Scf00003g04130 and Peaxi162Scf00589g00323 expressed only in roots under salt stress. In this work, we identified early and late expressed genes in response to salt stress while providing a core of differentially express genes across all time points and tissues, including the trehalose-6-phosphate synthase 1 (TPS1), a glycosyltransferase reported in salt tolerance in other species. To test the function of the novel petunia TPS1 allele, we cloned and showed that TPS1 is a functional plant gene capable of complementing the trehalose biosynthesis pathway in mutants (tps1) yeast. The list of candidate genes to enhance salt tolerance provided in this work constitutes a major effort to better understand the detrimental effects of salinity in petunia with direct implications for other economically important Solanaceous species

Results:In total, eight samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis revealed that 1777 genes were transcriptionally affected by AtZAT18 trasngene or drought treatment. The results showed that overexpression of AtZAT18 modulated expression level changes of 423 and 561genes under control and drought stress conditions, respectively. Drought stress treatment changed expression of 971 genes with 768 up-regulated and 203 down-regulated.

To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from four-week-old rice seedlings grown in soil that had been subjected o drought conditions for 2 to 3 d. From the upregulated genes, we found a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates plant’s degree of tolerance to water deficiencies through its control of ascorbate peroxidase and catalase mediating ROS processing machinery besides the control of total leaf area and stomatal density as previously reported.

UV-B radiation affects leaf growth in a wide range of species. In this work, we demonstrate that UV-B levels present in solar radiation inhibits maize leaf growth without causing any other visible stress symptoms, including accumulation of DNA damage. We conducted kinematic analyses of cell division and expansion to understand the impact of UV-B radiation on these cellular processes. Our results demonstrate that the decrease in leaf growth is a consequence of a reduction in cell production, and a shortened growth zone (GZ) in UV-B irradiated leaves. To determine the molecular pathways involved in UV-B inhibition of leaf growth, we performed RNA sequencing on isolated GZ tissues of control and UV-B exposed plants. Our results show a link between the observed leaf growth inhibition and the expression of specific cell cycle and developmental genes, including Growth Regulating Factors (GRFs) and transcripts for proteins participating in different hormone pathways.

We report the role of LSM2-8 complex in the Arabidopsis tolerance to abiotic stresses. LSM2-8 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieved over selected transcripts depending on stress nature.Transcriptomic profiling through RNA-seq of Col-0 and lsm8-1 plants exposed to low temperatures (4ºC, 24h) or high salt conditions (150 mM NaCl, 10h).

Drought stress is the main environmental factor influencing hemp growth and yield. However, little is known about the response mechanism of hemp to drought stress. A total of 44.10 M tags and 8.91G bases were sequenced in the control hemp (CK) and drought stress hemp (DS) libraries. A total of 1292 differentially expressed genes (DEGs), including 883 up-regulated genes and 409 down-regulated genes, were identified. These results may contribute toward improving our understanding about the drought stress regulatory mechanism of hemp, and improving its drought tolerance ability.

We report global gene expression profilies of Brassinosteroid related Arabidopsis mutants in response to dehydration and fixed-carbon starvation stresses by RNA-seq.Arabidopsis plants of listed genotypes were grown for 4 weeks under long day (16 hour light) conditions before being subjected to control, 4 hour dehydration, or 5 day fixed carbon starvation treatments.

Elevated temperature occurring at reproductive stage has great impact on gametophyte development and therefore ultimate fruit or seed set in plants, the underlying molecular mechanisms are less understood. We investigated the effect of elevated temperature stress on reproductive development in Arabidopsis with tissue-specific transcriptome profiling and observed distinct response patterns between vegetative and reproductive tissues. Heat stress exposure affected reproductive developmental programs including early phases of anther/ovule development and meiosis process, and genes participating in the unfolded protein response (UPR) were enriched among the heat up-regulated reproductive tissue-specific genes. We found that the bzip28bzip60 double mutant defective in UPR were sensitive to elevated temperature stress in terms of reduced silique length and fertility comparing to the wild-type plants. Comparison of heat responsiveness between the wild-type and bzip28zip60 plants identified 521 genes that were regulated by bZIP28 and bZIP60 upon heat stress at reproductive stage, most of which were non-canonical UPR genes. Further ChIP-Seq data revealed 133 direct targets of bZIP28 in Arabidopsis seedlings subjected to heat stress, of which 39 target genes were up-regulated by heat stress at reproductive stage. Our results provide novel insights into heat responsiveness in reproductive tissues and demonstrate the protective roles of UPR for maintaining fertility upon heat stress in plants.

Heat stress is one of the primary abiotic stresses that limit crop production . Grape is a popular cultivated fruit with high economic value throughout the world, and whose growth and development is often influenced by high temperature. Alternative splicing (AS) is a widespread mechanism increasing transcriptome complexity and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed proteomic and transcriptomic （especially AS）changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature. Intron retention (IR), exon skipping (ES) and alternative donor/acceptor sites were markedly induced under different high temperatures. IR was the most abundant up- and down-regulated AS event; moreover, IR events at 40 and 45oC were far higher than those at 35oC. These results indicated AS, especially IR, is an important posttranscriptional regulatory during grape leaf responses to high temperature. Proteomic analysis showed that protein levels of the RNA binding proteins SR45, SR30, and SR34, and the nuclear ribonucleic protein U1A in grape leaves gradually rose as ambient temperature increased. The results also revealed why AS events occurred more frequently under high temperature in grape leaves. After integrating transcriptomic and proteomic data, we found that HSPs and some important transcript factors such as MBF1c and HSFA2 were mainly involved in heat tolerance in grape through up-regulating transcriptional and translational levels, and were especially modulated by AS. The results provide the first simultaneous evidence for grape leaf responses to high temperature at transcriptional, posttranscriptional and translational levels.

To investigate how JA regulates Al-induced inhibition of root growth, a transcriptional analysis through RNAseq was performed by comparing the coi1-2 mutant and WT plants in the presence or absence of Al. In the absence of Al, 149 and 147 genes were up- and down-regulated, respectively, at least 2-fold in the roots of the coi1-2 mutant and WT plants. In the presence of Al, 1747 and 5838 genes were up- and down-regulated, respectively, in the roots of WT plants, while 1449 and 3773 genes were up- and down-regulated, respectively in the coi1-2 mutant. While the comparison of the Al-exposed coi1-2 mutant and WT plants reveals that totally 1187 genes were up-regulated and only 197 genes were down-regulated at least 2-fold.

Limonium bicolor, a typical recretohalophyte living in saline land, excretes excessive salt to the environment through salt glands in the epidermis for avoiding salt stress. The aim of this study was to screen genes involved in salt secretion by high-throughput RNA sequencing. A model was established to illustrate the candidate genes regulating salt secretion of salt gland. These genes will shed light on molecular mechanism of salt secretion of salt gland in plant.Normalized cDNA libraries of L. bicolor were constructed using mature leaves treated with 200 mM NaCl (with the highest salt secretion) and the control. Illumina paired-end platform was utilized to yield 2×100 bp independent reads. After de novo assembly, unigenes were aligned to the non-redundant (Nr) protein database and differentially expressed genes were enriched by GO annotations. Candidate genes were further verified by L. bicolor mutants with abnormal salt secretion.19,498 genes were targeted in Nr database and 5,768 were differentially expressed mapping to Arabidopsis, 2,269 up-regulated and 3,519 down-regulated under NaCl treatment compared with the control. Genes related to ion transport, vesicle, reactive oxygengen species scavenging, abscisic acid-dependent signal pathway and transcription factors were found high expression under NaCl treatment, of which 55 genes were likely involved in salt secretion and also confirmed by salt-secretion mutants.The present report identified candidate genes which are highly associated with salt secretion of L. bicolor salt gland. A salt transporting pathway was illustrated to explain how Na+ excreted outside by salt gland in L. bicolor. This data provides a useful reference source for salt secretion study of recretohalophytes.

Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between between long and short day model species.

RNA-seq analyses of leaves from drought stressed rice plants was performed, producing differential expression profiles of genes containing coding RNAsand noncoding RNAs.

Drought is a major environmental stress that limits growth and development of cool-season annual grasses. Drought transcriptional profiles of resistant and susceptible lines were studied to understand the molecular mechanisms of drought tolerance in annual ryegrass (Lolium multiflorum L.). A total of 4,718 genes exhibited significant differential expression in two L. multiflorum lines. Additionally, up-regulated genes associated with drought response in the resistant lines were compared with susceptible lines. Gene ontology enrichment and pathway analyses revealed that genes partially encoding drought-responsive proteins as key regulators were significantly involved in carbon metabolism, lipid metabolism, and signal transduction. Comparable gene expression was used to identify the genes that contribute to the high drought tolerance in resistant lines of L. multiflorum.

Arbuscular mycorrhizal (AM) associations enhance the phosphorous and nitrogen nutrition of host plants, but little is known about their role in potassium (K+) nutrition. Medicago truncatula plants were co-cultured with the AM fungus Rhizophagus irregularis under high and low K+ regimes for six weeks. We determined how K+ deprivation affects plant development, mineral acquisition, and how these negative effects are tempered by the AM colonization. The transcriptional response of AM roots under K+ deficiency was analyzed by whole genome RNA-seq. K+ deprivation decreased root biomass, external K+ uptake, and modulated oxidative stress gene expression in M. truncatula roots. AM colonization induced specific transcriptional responses to K+ deprivation that seem to temper these negative effects. A gene network analysis revealed putative key regulators of these responses. This study confirmed that AM associations provide some tolerance to K+ deprivation to host plants, revealed that AM symbiosis modulates the expression of specific root genes to cope with this nutrient stress, and identified putative regulators participating in these tolerance mechanisms.

Samples were collected after 1 h of the heat treatment. Samples were collected for control and heat stressed plants.RNA-seq was performed for shoot (in triplicate for each condition) and root (in duplicate for each condition)

A large number of high-quality transcripts were fistly obtained by sequencing the pooled RNAs from trifoliate orange under different stress treatments (cold, salt, drought). Four cold-treated libraries were further mapped to the assembled transcriptome, leading to identification of more 5,000 DEGs. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were most significantly enriched in the DEGs. A total of 60 transcription factors were revealed to be cold responsive.n addition, a number of genes involved in catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were either up- or down-regulated under cold stress. These data provide valuable information for elucidating transcriptomic reprogramming and underlying mechanisms of trifoliate orange in response to cold and underpin exploitation of genes of interest in the future.

Methods: DeepSAGE, a tag based approach, was used to identify differentially expressed genes under cold and freeze treatments in seabuckthorn (Hippophae rhamnoides L.). The 30 days old plantlets, at six leaves stage, were subjected to cold stress (CS) at 4°C and freeze stress (FS) at -10°C treatment for 6 hr. The seedlings grown at 28°C were taken as control (CON). Total RNA from all the three samples was isolated. Illumina Gene Expression Sample Prep Kit and Solexa Sequencing Chip (Flowcell) were used for tag preparation and the main instruments used for sequencing included Illumina Cluster Station and Illumina HiSeqTM 2000 System. Bioinformatics analysis resulted in to high number of differentially expressed genes under cold and freeze stress.Results: 36.2 million raw tags including 13.9 million distinct tags were generated from three leaf tissue libraries (control, cold stress and freeze stress). After removing low quality tags, 35.5 million clean tags including 7 million distinct clean tags were obtained. In total, 11922 differentially expressed genes (DEGs) were identified including 6539 up regulated and 5383 down regulated genes.Conclusions: DeepSAGE data of seabuckthorn provided useful resource and reference dataset for further functional genomics analysis in seabuckthorn and other important crops. The present study implicated a large number of genes with different biological functions expressing differentially in response to cold and freeze stress treatment. Isolation and further characterization of these genes will help researchers in understanding their role in cold and freeze tolerance in seabuckthorn and may provide important gene resources to be exploited for the development of stress tolerant crop plants in future.

Alhagi sparsifolia Shap. is a perennial subshrub belonging to genus Alhagi, family Leguminosae. As a typical desert phreatophyte, this plant species has highly developed deep roots and displays a great capacity to withstand poor soil as well as extreme dry, cold and hot weather. A. sparsifolia is naturally distributed in the arid and salinized regions of northernwestern China and adjacent countries in Central Asia, and plays a fundamental role in maintaining the local ecosystem. In addition, this plant is usually used as a fodder for local animals due to its high protein content, and is important in the development of local livestock husbandry. Considering its great tolerance to harsh environments, A. sparsifolia represents an ideal species for deciphering the mechanism of plant adaption to abiotic stress, such as water deficit. However, understanding the stress adaption in this plant is limited. While a few studies were conducted on physiological responses of A. sparsifolia to water stress, research has never been done to explore the genomic basis for its drought-tolerance to date. In particular, as a non-model plant species, the genomic resource of A. sparsifolia is rather scarce, only one expressed sequence tag (EST) and one protein have been deposited in Genbank prior to Sept., 2014. In aim to explore the genetic basis underlying drought tolerance in this species, recently we took advantage of transcriptome sequencing to survey the water stress responsive genes in A. sparsifolia primary roots. Using Illumina HiSeq™ 2000 platform, we sequenced the primary root samples individually collected at four different time points (0, 6h, 24 and 30h) from A. sparsifolia seedlings during 24h of water stress following 6h of rehydration. The resulting 38,763,230, 67,511,150, 49,259,804 and 54,744,906 high quality reads were pooled and assembled into 33,255 unigenes with an average length of 1,057 bp. All-unigenes were subjected to functional annotation by searching against the public databases including NR, NT, Swiss-Prot, Pfamm, GO, KOG and KEGG. On the basis of the established transcriptome database, we evaluated the gene expression profiles in A. sparsifolia primary roots at 0, 6, 24 and 30h in the course of water stress and subsequent rehydration. An extensive repertoire of the differently expressed genes (DEGs) reflecting the early response to water stress (6h), the late response to water stress (24h) and the response to post stress rehydration (30h) were identified. In addition, to unravel the dynamic changes of gene expression during water stress and subsequent rehydration, we further captured the DEGs commonly or specifically regulated at 6, 24 and 30h. Functional categorization of the DEGs disclosed the activation of oxidoreductase system in A. sparsifolia primary roots upon water stress, and particularly emphasized the significance of the ‘Glutathione metabolism pathway’. To our knowledge, this is the first description of the genetic makeup of A. sparsifolia, thus providing a substantial contribution to the sequence resources for this species. The DEGs identified herein offers a deep insight into the molecular mechanism of A. sparsifolia in response to water stress, and merits further investigation.

Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.

Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.

We checked the difference of CB-1 and K326 by transcriptomic and metabolomic analysis and found some important genes related to cold stress

Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). Stress regulation of some TE-lincRNAs was observed in Arabidopsis. Our findings indicate that TE-associated lincRNAs potentially play important roles in plant abiotic stress responses. Moreover, in the Arabidopsis chromatin remodelling mutant ddm1 that has an altered chromatin state, novel lincRNAs including TE-lincRNAs were generated. The novel lincRNAs were inherited in the subsequent generations in the wild type background, suggesting that lincRNAs could act as an adaptive reservoir in eukaryotes.

Purpose: To elucidate the potential molecular mechanisms that are involved in drought tolerance of Haloxylon ammodendron.Method: Pathways and candidate genes drought-resistant genes were identified in shoots and roost of Haloxylon ammodendron under sorbitol treatment for 6 and 24h using RNA-seq and Digital Gene Expression.Results: 3,353 differently expressed genes in shoots and 4,564 in roots were successfully indentified.Conclusion: A detailed investigation of the pathways and candidate genes identified in this study promote the research on the molecular mechanisms of drought resistance in the xerophytic species, and lay a solid foundation for developing stress-tolerant forage and crop species by using excellent genes relevant to drought tolerance in Haloxylon. ammodendron.

To reveal how ARF10 and ARF16 regulate Al-induced root-growth inhibition, a transcriptome analysis was carried out by comparing without and with Al-exposed arf10/16 double mutant line and WT through RNA sequencing. The present transcriptomic analysis has revealed that many of the differentially transcribed genes associated with cell wall modification were regulated by transcription factors ARF10 and ARF16. The implication is that the auxin-regulated Al-induced inhibition of root growth arises from auxin signalling-regulated cell wall structure or component modification.

Transcriptome of plants exposed to 0, 20 and 60 sec light stress was analyzed using Illumina HiSeq2000. We found that mRNA accumulation of more than 700 transcripts in plants occurs as early as 20-60 sec following light stress application

Alternative splicing caused by exposure of pollen to high temperatures leads to the generation of transcripts with pre-mature termination codon targeted for degradation or mRNAs putatively coding for truncated proteins with altered functions thereby controlling important cellular pathways including transport and localization, heat stress response, gene expression and various biosynthetic processes.

We report that CBP20 phosphorylation can regulate root growth in ethylene. We examined the gene expression in roots and shoots of wild type (Col) and cbp20 mutant (in Col background).Ethylene is one of the most essential hormones for plant developmental processes and stress responses. EIN2 is a key factor in ethylene signaling pathway and its function is regulated by phosphorylation. However, the phosphorylation regulation in the ethylene signaling pathway is largely unknown. Here we report the phosphorylation of CBP20 is regulated by ethylene, and the phosphorylation is involved in root elongation. The constitutive phosphorylation format of CBP20 rescues the cbp20 root ethylene hyposensitive phenotype, while the constitutive de-phosphorylation format of CBP20 is unable to rescue the root phenotype of cbp20 in response to ethylene. Genome wide study on ethylene regulated gene expression and microRNA expression in the roots and shoots of both Col and cbp20, together with the result of genetics validation suggest that ethylene induced phosphorylation of CBP20 is involved in root growth and one pathway is through the regulation of microRNAs and their target genes in roots.

We examined changes in steady-state transcript level in leaves of Arabidopsis plants subjected to salinity, heat stress and their combination by a transcriptome analysis of leaves.

The photorespiratory pathway, short photorespiration, is an essential process in oxygenic photosynthetic organisms but also reduces the efficiency of photosynthetic carbon assimilation and is hence frequently considered as a wasteful process. By comparing the response of wild-type plants and mutants impaired in photorespiration to a shift in ambient CO2 concentrations, we demonstrate that photorespiration also plays a beneficial role during short-term acclimation to reduced CO2 availability. Wild-type plants responded with few differentially expressed genes, mostly involved in drought stress, which is likely a consequence of enhanced opening of stomata and concomitant water loss upon shift toward low CO2. In contrast, mutants with impaired activity of photorespiratory enzymes were highly stressed and not able to adjust stomatal conductance to reduced external CO2 availability. The mutants´ transcriptional response was congruent, indicating a general reprogramming to deal with the consequences of reduced CO2 availability, signaled by enhanced oxygenation of ribulose-1,5 bisphosphate and amplified by the artificially impaired photorespiratory metabolism. Central in this reprogramming was the pronounced reallocation of resources from growth processes to stress responses. In conclusion, we demonstrate that unrestricted photorespiratory metabolism is a prerequisite for rapid physiological acclimation to a reduction in CO2 availability.

Environmental stress is detrimental to plants viability and requires an adequate reprogramming of cellular activities to maximize plant survival. We present a global analysis of the adaptive stress response of Arabidopsis thaliana to prolonged heat stress. We combine deep sequencing of RNA and ribosome protected fragments to provide genome wide map of adaptation to heat stress on at transcriptional and translational level. Our analysis shows that the genes with the highest upregulation upon heat stress are known heat-responsive gene, chaperons and other genes involved in protein folding control. Majority of these genes exhibits increase on both transcriptional and translational level. No translational inhibition or ribosome stalling was observed, which can be observed in the early thermal stress response, indicating that plants alter their cellular composition in order to adapt to the prolonged exposure to increased temperatures.

In order to understand the mechanisms of Drought induced susceptibility (DIS) we’ve conducted a dual RNAseq experiment on rice infected tissues by Magnaporthe oryzae. At 4 days post inoculation tissues have been collected on mock inoculated and M. oryzae inoculated plants. Rice were conducted under two type of water regime: DIS Drought during three days before inoculation, NoDIS no drought before inoculation. RNAseq was conducted both on rice and fungal RNA.

Abiotic environmental stresses cause serious economic losses in agriculture. These stresses include temperature extremes, high salinity and drought. To isolate drought-responsive novel coding and noncoding genes, we used the next generation sequencing method from three rice cultivars (wild type nipponbare, nipponbare AP2 transgenic plants, wild type vandana). 36 NGS data of mRNA-seq, small RNA-seq, riboZero-seq were analyzed. For the analyses of these data we constructed a TF-TG (Transcription Factor-Target Gene) network and an ap2 rooted cascading tree. Using these networks and tress we isolated lincRNAs, differentially expressed miRNAs and their targets. We identified several drought stress-related novel/function unknown coding transcripts (transcription factors and functional genes) and non-coding transcripts (small noncoding transcripts such as microRNA and long noncoding transcripts) from these database analyses and have constructed databases of drought stress-related coding and noncoding transcripts

By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism. In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants. These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants – underline a defense mechanism in alfalfa against grazing stresses.

Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To unravel the molecular mechanisms that regulate the response towards an impact of increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2) and screened for second-site mutations that attenuate the Fv'/Fm' decrease and lesion formation linked to the cat2-2 phenotype. A mutation in the transcriptional regulator SHORT-ROOT (SHR) of the GRAS family rescued the cell death phenotype of cat2-2 plants under photorespiration-promoting conditions in a SCR-independent way, and provoked perturbation of photorespiratory metabolites. SHR deficiency boosted ascorbate levels and prevented the oxidation of the glutathione pool in cat2-2 background upon exposure to photorespiratory stress. These results reveal an unanticipated role for SHR as a regulator of cellular redox homeostasis.

With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.

In this study, we aim to present a global view of transcriptome dynamics during drought stress in different chickpea genotypes. We generated about 800 million high-quality reads from 14 libraries (control and stress samples for two chickpea genotypes for drought stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype.

Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-β-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance.

Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To unravel the molecular mechanisms that regulate the response towards an impact of increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2).

We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges.

We use Solanum dulcamara subjected to drought or flooding and damaged by Spodoptera exigua to analyze such interactions at multiple levels. Drought and herbivory caused comparable effects on S. dulcamara physiological response, which was reflected by a considerable overlap in S. dulcamara transcriptomic profiles. This included many defense responses and genes involved in biosynthesis of secondary metabolites that were induced by drought and herbivory but repressed by flooding. Furthermore, combination of drought and herbivory additively induced a part of these herbivore-induced responses suggesting that drought-stressed plants were more resistant. Our study provides concrete evidence of how abiotic stresses differentially affect the plant complex hormonal interactions to fine-tune plant responses to insects.

Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h) or long (12 h) durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina’s NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering along with Spearman correlation analysis identified that the differentially expressed genes segregated in two major clusters representing early (5-15 DAP) and late stages (20-30 DAP) of silique development. Further analysis led to the discovery of sub-clusters having similar patterns of gene expression. Two of the sub-clusters (one each from the early and late stages) comprised of genes that were inducible by both the durations of cold stress. Comparison of transcripts from these clusters led to identification of 283 transcripts that were commonly induced by cold stress, and were referred to as ‘core cold-inducible’ transcripts. Additionally, we found that 689 and 100 transcripts were specifically up regulated by cold stress in early and late stages, respectively. We further explored the expression patterns of gene families encoding for transcription factors (TFs), transcription regulators (TRs) and kinases, and found that cold stress induced protein kinases only during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold hardiness in B. juncea.

This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.

Results: the physiological measurements carried out confirmed the drought sensitivity of IS20351 and the drought tolerance of IS22330 previously studied. The expression of drought-related genes was more abundant in the sensitive genotype IS20351 compared to the tolerant IS22330. The Gene Ontology enrichment highlighted a massive increase in transcript abundance in “response to stress” and “abiotic stimulus”, “oxidation-reduction reaction” in the sensitive genotype IS20351 under drought stress. “Antioxidant” and “secondary metabolism”, “photosynthesis and carbon fixation process”, “lipids” and “carbon metabolism” were the pathways most affected by drought in the sensitive genotype IS20351. The sensitive genotype IS20351 showed under well-watered conditions a lower constitutive expression level of “secondary metabolic process” (GO:0019748) and “glutathione transferase activity” (GO:000004364).Conclusions: RNA-Seq analysis revealed to be a very useful tool to explore differences between sensitive and tolerant sorghum genotypes. The transcriptomic results supported all the physiological measurements and were crucial to clarify the tolerance of the two genotypes studied. The connection between the differential gene expression and the physiological response to drought states unequivocally the drought tolerance of the genotype IS22330 and the strategy adopted to cope with drought stress.

The soybean aphid, a plant sap sucking insect, is an important soybean pest in the USA causing significant yield losses. The Rag2 gene of soybean provides resistance to soybean aphid biotypes I and II. Transcriptomic analyses were performed on near isogenic lines (NILs) with the Rag2 allele for aphid resistance or rag2 for susceptibility at the Rag2 locus. Soybeans were infested with soybean aphids and leaves were collected at 0, 4, 8, 24, and 48 hours after infestation. RNA were extracted and a high throughput RNA-seq approach was used to examine mRNA expression in Rag2 and rag2 soybean leaves. The expression of ~43,000 genes was detected in both the Rag2 and rag2 leaves. Statistical analysis identified 2361 genes significantly regulated between the resistant and susceptible lines at different times after aphid infestation. Genes found up-regulated in the Rag2 line were annotated as involved in the cell wall, secondary and hormone metabolism, as well as in stress, signaling and transcriptional responses. Genes found up-regulated in the rag2 line were annotated as involved in photosynthesis and carbon metabolism. Interestingly, mRNAs of 2 genes (unknown and mitochondrial protease) located within the Rag2 locus were expressed significantly higher in the resistant genotype. The expression of the putative NBS-LRR resistant gene present in the Rag2 locus was not different between the two soybean lines. However, another NBL-LRR gene located just at the border of the Rag2 locus was and, therefore, may be involved in the differential resistance to aphid infestation exhibited by the two NIL genotypes analyzed.

Arabidopsis thaliana polyamine oxidase 5 gene (AtPAO5) functions as a thermospermine (T-Spm) oxidase. Aerial growth of its knock-out mutant (Atpao5-2) is significantly repressed by low dose(s) of T-Spm but not by other polyamines. Massive analysis of 3’-cDNA ends (MACE) was performed. Cell wall, lipid and secondary metabolisms were dramatically affected in low dose T-Spm-treated Atpao5-2. Intriguingly Fe-deficient responsive genes and drought stress-induced genes were up-regulated, suggesting that vascular system loses the function. Histological observation showed that vascular system of the joint part between stem and leaves was structurally destroyed. The results indicate that T-Spm homeostasis by a balance of synthesis and catabolism, catalysed by AtPAO5 in Arabidopsis, is important for maintaining vascular system. Phylogenetic analysis showed that PAOs from vascular plants are classified into four clades (I-IV) and AtPAO5 belongs to the clade III. Clade III members show high identity to metazoan PAOs and are not found in non-vascular plants. Furthermore, all the clade III genes are intron-less or contain a single intron whereas the other three clade genes usually contain 7 to 9 introns. The data suggest the occurrence of a horizontal gene transfer of ancestral clade III PAO gene(s) from primitive animals. Fine tuning of T-Spm metabolism is critical for vascular plants and its catabolic gene was acquired from a certain Metazoan to equip the vascular system.

Male reproductive tissues are more sensitive to heat stress compared to vegetative tissues, however the basis of this phenomenon is poorly understood. Heat stress transcription factors (Hsfs) regulate the transcriptional changes required for protection and recovery from heat stress. HsfA2 has been characterized as co-activator of HsfA1a in tomato and is considered as one of the major Hsfs accumulating in response to elevated temperatures. The role of HsfA2 in heat stress response of different tissues was examined by exploring the composition and structure of the tissue-specific regulatory networks in transgenic tomato plants with suppressed HsfA2 expression (A2AS). Transcriptome analysis revealed that HsfA2 acts in condition- and tissue-specific manner and that only a subset of heat stress induced genes require HsfA2 for higher expression. Remarkably, although HsfA2 is not essential for thermotolerance in seedlings and flowering plants, it is required for maintenance pollen viability under stress conditions. We show that the activation of Hsf networks is important for the developmentally regulated priming of heat stress response occurring at early stages of anther and pollen development. Thereby, HsfA2 is involved in pollen thermotolerance by directly regulating heat stress responsive genes but also by stimulating the synthesis of molecular chaperones under non-stress conditions.

Analysis of the maize alternative splicing landscape, including transcript discovery and quantification during development and drought

The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.

We report the role of LSM1-7 complex in the Arabidopsis tolerance to abiotic stresses. LSM1-7 controls gene expression reprogramming at the post-transcriptional level by promoting the decapping of mRNA. This function is selectively achieve over selected stress-induced transcripts depending on stress nature.

Results: Using RNA-Seq technology with the Trinity assembled method, we generated a seedling plant transcriptome at a sequencing size of 51.78Gb of Zea mays ssp. mexicana L. from pooled RNA samples which included control (CK), cold (4℃) and drought (PEG2000, 20%) stressed plant samples. A total of 414,232,462 high quality clean reads were used to conduct de novo assembly and annotation of genes without reference genome information. All of these reads were assembled into 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp). A total of 3,504 up-regulated and 1,220 down-regulated genes were detected under cold stress and 532 up-regulated and 82 down-regulated genes were detected under drought stress. A Venn diagram indicated that 208 genes were affected by both cold and drought stresses. 3 cold stress pathways and 5 drought related pathways showed significant KEGG pathways. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The ABA dependent pathway, trehalose synthetic pathway and CBF6 gene of ICE1-CBF pathway may play important roles in the DEGs co-up-regulated by both stresses of Zea mays ssp. mexicana L.Conclusions: We analyzed transcriptome data and gene expression profile information from seedlings of Zea mays ssp. mexicana L. under cold and drought stresses. Together these data provides the most comprehensive sequence study available for Zea mays ssp. mexicana L. and provides some important functional genes and molecular mechanism information for improving the quality characteristic of maize in the future.

Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments

Plants have developed complex mechanisms to respond and adapt to abiotic stresses, coupling elaborate modulation of gene expression together with the preservation of genome stability. Epigenetic mechanisms - DNA methylation, chromatin modifications and non coding RNAs - were shown to play a fundamental role in stress-induced gene regulation and may also result in genome destabilization, with the activation and/or the transcription of silenced transposons and retroelements, causing genome rearrangements and novel gene expression patterns. Maize leaf transcriptome was analyzed by total RNA-Seq in both B73 and rmr6 (PolIV mutant involved in siRNA biogenesis and in the RdDM pathway) after drought and salt stress application. Reference annotation based transcript assembly allowed the identification both of new expressed loci and splicing variants, improving the current maize transcriptome annotation. Many antisense transcripts matching on the opposite strand of annotated loci were also identified, while more than the 20% of transcripts represent non coding RNA belonging to four classes: siRNAs, shRNAs, lncRNAs and transposable elements (or their relics). Several lncRNAs are modulated by stress application while TE-related sequences are mainly expressed in rmr6 and up-regulated by the stress.

Results: We identified commonly up-regulated genes (317) and exclusively up-regulated in Bd2-3 (466) or Bd21 (706). Regarding down-regulation, 330 transcripts were common, an exclusively 851 and 1026 for Bd2-3 and Bd21, respectively. GO analysis indicated that oxidative stress, pathogen responses and nitric oxide homeostasis were the most differential characteristics of tolerant ecotype Bd2-3.Conclusions: The use of triplicate RNAseq data of transcriptomes expressed in ecotypes with contrasting tolerance to submergence under long-day light regime, allowed us to identify common responsive routes such as SUSY, glycolysis, anaerobic routes (alanine, ethanol, lactate, GABA) and glyoxylate cycle. It also enabled us to discover integrated oxidative stress and NO homeostasis pathways that are differentially expressed in the tolerant ecotype. We expect that this information can be translated to agricultural relevant plants to increase our knowledge and biotechnological possibilities on plant submergence stress.

Transcriptome measurements of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery - samples collected every 15 minutes for up to 4h - 480 samples (240 conditions, 2 biological replicates)

Jatropha curcas, a multipurpose plant attracting much attention due to its high oil content and quality for biofuel, is recognized as a drought tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, with the use of a combined approach of transcriptional profiling and morphophysiological characterization along a period of water withholding (49 days) followed by rewatering (7 days). Morphophysiological measurements evidenced that J. curcas plants presented different adaptations to withstand moderate and severe drought. Thus, RNA-Seq was performed for samples collected at moderate and severe stress followed by rewatering, for both roots and leaves. Transcriptomic analysis revealed organ-specific adaptations across all investigated conditions, except under severe stress, in which the drought response of J. curcas surpassed organ-specificity by dramatic transcriptomic reorganization. These changes in gene expression were clearly evidenced by the down-regulation of genes involved in growth and water uptake, and up-regulation of osmotic adjustments and cellular homeostasis related genes. However, organ-specific variations were also detected, such as strong up-regulation of chlorophyll and trehalose metabolism in leaves. Functional validation further corroborated the differentially expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway.

Results:We have analyzed different aspects of miRNA modifications in plants. To achieve this end, we developed a PERL script to find the modifications in the sequences using small RNA deep sequencing data. The modification occurs in both mature and passenger (star) strands, as well as at both the 5' and 3' ends of miRNAs. Interestingly, we found a position-specific nucleotide biased modification, as evident by increased number of modification at the 5' end with the presence of Cytosine (nucleotide 'C') at the 3’end of the miRNA sequence. The level of modifications is not strictly dependent on the abundance of miRNA. Our study showed that the modification events are independent of plant species, tissue and physiological conditions. Our analysis also indicates that the RNAi enzyme, namely, the RNA dependent RNA polymerase 6 (RDR6) may not have any role in Arabidopsis miRNA modifications. Some of these modified miRNAs are bound to AGO1, suggesting their possible roles in biological processes.Conclusions:This is a first report that reveals that 5' nucleotide additions are preferred for mature miRNA sequences with 3’ terminal ‘C’ nucleotide. Our analysis also indicates that the miRNAs modifications involving addition of nucleotides to the 5’ or 3’ end are independent of RDR6 activity and are not restricted by plant species, physiological conditions and tissue types. The results also indicate that such modifications might be important for biological processes.

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of abiotic stress molecular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of contrasting slow wilting lines to quantify transcript abumdance under drought stress condition。Methods: The three biological replicates of DS line, Pana (control and drought samples) and DT line, PI 567690 (control and drought samples) leaf sample RNA were multiplexed and sequenced on an Illumina Hi-Seq 2000 platform. The RNA concentration of each sample was approximately 200ng/µl with a quantity of 50 µl.isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species.

Results: A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume specific miRNAs, miR5213, miR5232, miR2111 and miR2118 were found in all the libraries. The Poly (A) tailing assay based qRT-PCR was used to validate eleven conserved and five novel miRNAs. miR530 was highly up regulated in response to fungal infection and targets zinc knuckle and microtubule-associated proteins. Many miRNAs responded in a similar fashion under both biotic and abiotic stresses indicating a cross talk between the pathways involved in regulating these stresses. The potential target genes for the conserved and novel miRNAs were predicted based on sequence homology. miR166 targets a HD-ZIPIII transcription factor and was validated by 5’ RLM-RACE.Conclusions: The present study has led to identification of several conserved and novel miRNAs in chickpea associated with gene regulation in reference to wilt and salt stress conditions. This study will help in better understanding of how chickpea functions in response to stresses.

Coordinated functioning of the cob and florets of the maize ear confers grain yield. However, comprehensive molecular differentiation of the cob and florets and their responses to low nitrogen (LN) stress remain elusive. We compared transcriptional profiles of the cob and peripheral florets of a maize hybrid at the silking stage at two N levels in the field and found 1,864 differentially expressed genes between the cob and florets, with 1314 genes up-regulated in the cob and 550 genes up-regulated in florets. The cob was featured by preferential expression of 161 genes, with striking enrichment of genes that are involved in transport facilitation and energy metabolism, consistent with the physiological role of the cob in C/N storage and transfer during ear development. The florets were characteristic of preferential expression of 108 genes, with enrichment of genes that are involved in the cellular process and lipid biosynthetic process. LN caused differential expression of 588 genes in the cob and only 195 genes in florets, indicating that the cob dominated the response of the ear to LN at the transcriptional level. Differentially expressed genes under LN were involved in C/N metabolism, transcriptional regulation, development, cell rescue and defense, and signal transduction in the cob and/or florets. The expression level of 106 genes was regulated by LN in both tissues, suggesting a common regulatory network in these two functionally distinct tissues under LN. Compared with P or K deficiency, LN specifically caused differential expression of 14 genes, revealing unique biological consequences in the ear caused by N limitation at a critical reproductive stage. Collectively, our studies identified unique transcriptomic signatures of the cob and florets, revealed the dominance of the cob in response to LN at the silking stage, and provided molecular markers for N nutritional diagnosis and N efficient maize breeding.

By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.

We estimate Allele-specific expression in F1 hybrids between Col-0 and Cvi-0 accessions grown under well watered and drought stress conditions. We found that ~90% of the genes showed similar ASE under both stresses. Trans-effects were less robust across environments, however its effect was milder compared to cis-variation.

Results: This study investigated the influence of elevated CO2 (800 μL L−1) on physiological and transcriptomic profiles in Arabidopsis cultured in hydroponic media treated with 1 μM (low), 1000 μM (normal) and 10000 μM (high) Mg2+. Following 7-d treatment, elevated CO2 increased the shoot growth and chlorophyll content under both low and normal Mg supply, whereas root growth was improved exclusively under normal Mg nutrition. Notably, the effect of elevated CO2 on mineral homeostasis in both shoots and roots was less than that of Mg supply. Irrespective of CO2 treatment, high Mg increased leaf number but decreased root growth and absorption of P, K, Ca, Fe and Mn whereas low Mg increased the concentration of P, K, Ca and Fe in leaves. Elevated CO2 decreased the expression of genes related to cadmium response, cell redox homeostasis and lipid localization, but enhanced photosynthesis, signal transduction, protein phosphorylation, NBS-LRR disease resistance proteins and subsequently programmed cell death in low-Mg shoots. By comparison, elevated CO2 enhanced the response of lipid localization (mainly LTP transfer protein/protease inhibitor), endomembrane system, heme binding and cell wall modification in high-Mg roots. Some of these transcriptomic results are substantially in accordance with our physiological and/or biochemical analysis.Conclusions: Contrasting changes were found between roots and shoots with the shoot transcriptome being more severely affected by low Mg while the root transcriptome more affected by high Mg. Elevated CO2 had a greater effect on transcript response in low Mg-fed shoots as well as in high Mg-fed roots. The present findings broaden our current understanding on the interactive effect of elevated CO2 and Mg levels in the Arabidopsis, which may help to design the novel metabolic engineering strategies to cope with Mg deficiency/excess in crops under elevated CO2.

Root samples of ‘Sanhu’ red tangerine trees infected with and without Candidatus Liberibacter asiaticus (CLas) were collected at 50 days post inoculation and subjected to RNA-sequencingto profile the differentially expressed genes (DEGs) . Results showed that a total of 3956 genes were differentially regulated by HLB-infection. Comparison between our results and those of the previously reported showed that known HLB-modulated biological pathways including cell-wall modification, protease-involved protein degradation, carbohydrate metabolism, hormone synthesis and signaling, transcription activities, and stress responses were similarly regulated by HLB infection but different or root-specific changes did exist. The root unique changes included the down-regulation in genes of ubiquitin-dependent protein degradation pathway, secondary metabolisms, cytochrome P450, UDP-glucosyl transferase and pentatricopeptide repeat containing protein genes. Notably, nutrient absorption was impaired by HLB-infection as the expression of the genes involved in Fe, Zn, N and P adsorption and transportation were significantly changed. HLB-infection induced some cellular defense responses but simultaneously reduced the biosynthesis of the three major classes of secondary metabolites, many of which are known to have anti-pathogen activities. Genes involved in callose deposition were up-regulated whereas those involved in callose degradation were also up-regulated, indicating that the sieve tube elements in roots were hanging on the balance of life and death at this stage. In addition, signs of carbohydrate starvation were already eminent in roots at this stage. Other interesting genes and pathways that were changed by HLB-infection were also discussed based on our findings.

Results: Hormone profiling of susceptible and moderately resistant clonal E. grandis genotypes indicated a reduction in salicylic acid and gibberellic acid levels at 3 days post inoculation. We hypothesized that these signaling pathways may facilitate resistance. To further investigate other defence mechanisms at this time point, transcriptome profiling was performed. This revealed that cell wall modifications and response to oxidative stress form part of the defence responses common to both genotypes, whilst changes in the hormone signaling pathways may contribute to resistance. Additionally the expression of selected candidate defence response genes was induced earlier in moderately resistant trees than in susceptible trees, supporting the hypothesis that a delayed defence response may occur in the susceptible interaction.Conclusion: The ability of a host to fine-tune its defence responses is crucial and the responses identified in this study extends our understanding of plant defence, gained from model systems, to woody perennials.

A better understanding of the mechanisms for plant in response to abiotic stresses is key for the improvement of plant to resistant to the stresses. Much has been known for the regulation of gene expression in response to salt stress at transcriptional level, however, little is known at posttranscriptional level for this response. Recently, we identified that SKIP is a component of spliceosome and is necessary for the regulation of alternative splicing and mRNA maturation of clock genes. In this study, we observed that skip-1 is hypersensitive to salt stress. SKIP is necessary for the alternative splicing and mRNA maturation of several salt tolerance genes, e.g. NHX1, CBL1, P5CS1, RCI2A, and PAT10. Genome-wide analysis reveals that SKIP mediates the alternative splicing of many genes under salt stress condition, most of the new alternative splicing events in skip-1 is intron retention, which leads to the premature termination codon in their mRNA. SKIP also controls the alternative splicing by modulating the recognition or cleavage of 5' and 3' splice donor and acceptor sites under salt stress condition. Therefore, this study addresses a fundamental question on how the mRNA splicing machinery contributes to salt response at a posttranscriptional level.

In the vineyard, symptoms of the grapevine trunk disease Botryosphaeria dieback do not appear until 1 or 2 years after the causal fungus Neofusicoccum parvum establishes a necrotic canker in the permanent woody structure of the vine. There are preventative management practices, but growers tend to wait until symptoms are widespread, at which point prevention has limited efficacy.Toward development of an early detection tool, we examined the leaves of inoculated vs. non-inoculated plants for differential gene expression via RNASeq. Stems were examined to monitor spread of the infection, and its spatial and temporal relationship to anatomical changes via light microscopy and high resolution computed tomography (HRCT).The early stage of infection occurred prior to 2 months post-inoculation (MPI), at which point spread of the pathogen beyond the inoculation site was greatest. This incubation period was also characterized by the largest stem lesions, the highest levels of fungal colonization and xylem vessels fully-occluded by gels, and the lowest starch content of xylem fibers and rays.Prior to 2 MPI, RNASeq and validative qPCR analysis identified eight candidate markers, which are transcriptionally activated by infection, but not by wounding alone. Our best marker genes, a dehydrin, a BURP domain containing protein and an abscissic acid-induced wheat plasma membrane polypeptide 19 (AWPM-19), identified the pathogen’s presence with high specificity. Screening of genome-wide expression data revealed that this signature is not affected by many abiotic and biotic stresses.

As sessile organism, plants evolved a highly complicated signaling system to cope with unfavorable and fluctuating environmental conditions. Rapid and transient Reactive Oxygen Species (ROS) burst is a common response to both biotic and abiotic stresses. Plants exposed with O3 could trigger extracellular similar ROS production through cell wall peroxidases and NPADPH oxidases, resulting in changes in the gene expression and cell death. Whereas ROS induced cell death is not simply due to its toxicity, rather due to interplay with several other signaling pathways, such as salicylic acid (SA), jasmonic acid (JA) and ethylene signaling pathways. Furthermore, the three hormones have both synergistic and antagonistic interactions, where the suppression of JA signaling by SA is the mostly studied. In addition, ethylene promotes cell death while JA has a protective role upon O3 exposure. The role of SA is more complicated; depending on the genetic background it can have either cell death promoting or protecting roles. Hence, a clean system to deliver apoplastic ROS is required to study the role of ROS apart from con-current activation of other signaling pathways. Arabidopsis thaliana offer a convenient system to study apoplastic ROS signaling due to the availability of hormone signaling or biosynthesis mutants including the JA receptor mutant coi1-16 (CORONATINE INSENSITIVE1), the essential ethylene signaling mutant ein2 (ETHYLENE INSENSITIVE2), the SA biosynthesis mutant sid2 (SALICYLIC ACID INDUCTION DEFICIENT2 also known as ISOCHORISMATE SYNTHASE1), and essential regulators in SA/JA/ethylene-induced defense response triple mutant tga2 tga5 tga6 (Clade II TGA transcription factors). Here we used a combination of transcriptome analysis, cell death assays and mutant analysis to systematically quantified the contribution of hormone signaling in relation to apoplastic ROS signaling, identified transcription factors (TFs) involved in ROS regulation and dissected the components involved in defense hormones associated cell death.

ABSTRACT: Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional 70 and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited.Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group 75 of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3′UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutr- siRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium,sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements 80 through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes.

The members of bHLH transcription factor superfamily are known to play key role in plant development and abiotic stress response. Loss-of-function of OsbHLH148 gene resulted in increased sensitivity of rice plants to drought stress. To identify the targets of OsbHLH148 and dissect the drought stress response pathway regulated by it, we performed transcriptome profiling of Osbhlh148 mutant plants under drought stress as well as well-watered conditions by RNA-sequencing.

Research conducted, including the rationale: Alligatorweed is an invasive perennial primarily aquatic weed that can also grow terrestrially and thus has potential to become problematic in agricultural settings. It is invasive on at least three continents. Despite its invasiveness, less than 100 genes have been sequenced from this species. Alligatorweed has recently increased its range northwards in China, and it is unknown if the range expansion has a genetic or epigenetic basis. We have used a next generation RNA sequencing approach to examine gene expression in a three individuals from the northern edge of its range and from the central portion of its range in China to look for different responses to cold temperatures using a common garden approach. We identified numerous differences in gene expression associated with the cold response between these two populations. Gene set and sub-network enrichment analysis indicated differences in the response of photosynthetic processes and oxidative stress responses were different between the two populations. However, alterations in genes controlling the C-REPEAT/DRE BINDING FACTOR (CBF) regulon were not indicated. Additionally, we assembled over 75,000 genes of which over 65,000 had long open reading frames with similarity to sequences from arabidopsis. Single nucleotide polymorphisms unique to the northern and southern individuals were identified, and several of these were in genes such as RESPONSIVE TO DEHYDRATION 21 that could impact the cold response of the plants.

UV radiation is a ubiquitous component of solar radiation that affects plant growth and development. Analysis of natural variation in response to UV radiation revealed significant differences among natural accessions of Arabidopsis thaliana. However, the genetic basis of this is to a large extent unknown. Here, we analyzed the response of Arabidopsis accessions to UV radiation stress by performing RNA-sequencing of three UV sensitive and three UV resistant accessions. The genome-wide transcriptional analysis revealed a large number of genes significantly up- or down-regulated only in sensitive or only in resistant accessions, respectively. Mutant analysis of few selected candidate genes suggested by the RNA-sequencing results indicate a connection between UV radiation stress and plant-pathogen-like defense responses.

To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing.Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing.The drought stress treatment was started by withholding water at the tillering stage. The days were counted after the AWC in the soil reached 20% to allow drought measurements at precisely determined intervals, and the soil water content reached 15%, 10% and 7.5% after 1d, 3d and 4d drought treatment, respectively.Three top leaves for each sample were harvested for each genotype under 1d and 3d drought stress and control conditions. All samples were immediately frozen in liquid nitrogen and stored at -80°C and then for transcriptome sequencing.

In the current study we have profiled changes in the transcriptome of somatic and reproductive tissues of B.rapa plants following heat shock stress exposure. For this we used Illumina GAIIx platform. We have demonstrated that the highest tissue-specific alterations in the transcriptome profile are detected in tissues that were not directly exposed to stress, namely, in the endosperm and pollen. The progeny of exposed plants also exhibited significant alterations in the gene expression as compared to progeny of control plants.

RNA-Seq based transcriptome profiling were performed on these samples with a minimum of 20 million reads per sample; read mapping, transcript discovery and differentially expressed gene (DEG) identification were carried out using CLC Genomics Workbench software suit, followed by Gene Ontology and pathway analyses. The highest defense response occurred at 48 hpi based on the number of the identified DEGs along the infection process. Transcriptomic changes related to oxido-reduction balance, trans-membrane trafficking and metabolic activities indicated the re-direction of cellular activities to combat P. ultimum infection. DEGs functioning in hormone signaling including ethylene, jasmonate, gibberellin, cytokinin and auxin, and those encoding NAC, WRKY, MYB and ERF transcription factors were identified from 24-48 hpi; DEGs encoding enzymes in several biosynthesis pathways of secondary metabolisms and cell wall modification proteins are among the consistently up-regulated in the later stages. DEGs encoding defense and stress related protein such as wall-associated receptor kinase (WAK), endochitinase (PR4), thaumatin (PR5)-like protein, laccase, mandelonitrile lyase and cyanogenic beta-glucosidase were also highly induced.

Background：The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement.Results：In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses.Conclusions：We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.

The formation of Reactive oxygen species (ROS) has been detected in all cellular departments and even in apoplastic space of plants. As multifaceted molecule, ROS are known to accumulate in response to various stresses, and ROS burst accompanied with transcriptomic reprogramming leading to defense response or programmed cell death. Acute ozone exposure has been used as a noninvasive tool to study ROS burst induced defense response and cell death for a long time. Moreover the variation of ozone sensitivity in different Arabidopsis accessions highlights the flexibility of complex genetic architecture to adapt to specific stresses. In this study, we combine classic Quantitative Trait Loci (QTL) mapping and RNA-seq to identify the cause QTLs and potential gene candidates in response to ozone. RNA sequencing was performed on both control and ozone treated 3 weeks old accessions C24 (ozone tolerant), Te (ozone sensitive) and on a RIL line CT101 (a hypersensitive line of RIL population from reciprocal cross between C24 and Te), in triplicate. We identified 69 potential genes candidates inside the QTL regions and about 200 potential genes outside QTL region in response to ozone by comparing control to treatment within same genotype or comparing control between genotypes.

We sequenced the total RNA from a tissues mixed sample (inflorescences, rosette leaves, cauline leaves and stems) of Arabidopsis thaliana. After total RNA extraction, the same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times. We also sequenced 9 poly(A)- RNAs from seedlings treated with different stress conditions at different times. The poly(A)- RNAs were collected by removing poly(A)+ RNAs four times . Then rRNAs were removed from poly(A)- RNAs three times.

Melatonin is a well-known agent that plays multiple roles in animals. Its possible function in plants is less clear. In the present study, we tested the effect of melatonin (N-acetyl-5-methoxytryptamine) on soybean growth and development. Both spraying of leaves and seed-coating with melatonin significantly promoted soybean growth as judged from leaf size and plant height. This enhancement was also observed in soybean production and their fatty acid content. Melatonin increased pod number, seed number and seed weight. However, the 100-seed weight was not influenced by melatonin application. Melatonin also improved soybean tolerance to salt and drought stresses. Transcriptome analysis revealed that melatonin up-regulated the expression of many genes and alleviated the inhibitory effects of salt stress on gene expressions. Further detailed analysis of the affected pathways documents that melatonin likely achieved its promotional roles in soybean through enhancement of genes involved in cell division, photosynthesis, carbohydrate metabolism, fatty acid biosynthesis and ascorbate metabolism. Our results demonstrate that melatonin has significant potential for improving of soybean growth and seed production. Further study should uncover more about the molecular mechanisms of melatonin’s function in soybeans and other crops.

Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum)Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed.Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity.

Purpose: To identify high temperature, sailinity and drought-responsive miRNAs at genome wide level in B. juncea var varuna.Results: In this study four small RNA libraries viz. B. juncea control (BJC), B. juncea high temperature stressed (BJH), B. juncea salinity stressed (BJS) and B. juncea drought stressed (BJD) were prepared and sequenced. With the help of UEA sRNA workbench software package 51 conserved miRNAs belonging to 30 miRNA families were identified. As there was limited genomic information available for B. juncea, we generated and assembled its genome sequence at a very low coverage. Using the generated sequence and other publically available Brassica genomic/transcriptomic resources as mapping reference, 126 novel (not reported so far in any plant species) were discovered for the first time in B. juncea. Further analysis also revealed existence of 32 and 37 star sequences for conserved and novel miRNAs, respectively. The expression of a few selected conserved and novel miRNAs under conditions of different abiotic stresses was revalidated through universal TaqMan based real time PCR. Putative targets of identified conserved and novel miRNAs were predicted in B. rapa to gain insights into functional roles manifested by B. juncea miRNAs. Furthermore, SPL2-like, ARF17-like and a NAC domain containing protein were experimentally validated as targets of miR156, miR160 and miR164 respectively. Investigation of gene ontologies linked with targets of known and novel miRNAs forecasted their involvement in various biological functions.Conclusions: We have generated in this study, the first comprehensive abiotic stress influenced small RNA dataset in B. juncea. The combinatorial approach of NGS and computational methods led to the discovery of 51 conserved and 126 novel miRNAs. The present study provides a holistic view of B. juncea miRNAome under conditions of high temperature, salinity and drought. The catalogue of miRNA sequences, their expression and putative targets, generated in this study can be utilized to design crop improvement strategies in B. juncea and related species.

Stress acclimation is an effective mechanism that plants acquired for adaption to dynamic environmental conditions. After undergoing cold acclimation, plants become more tolerant to cold stress. In order to understand the mechanism of cold acclimation, we performed a systematic, comprehensive study of cold response and acclimation in Cassava (Manihot esculenta), a staple crop and major food source in the tropical regions of the world. We profiled mRNA genes and small-RNA species, using next generation sequencing, and performed an integrative analysis of the transcriptome and microRNAome of Cassava across the normal condition, a moderate cold stress at 14°C, a harsh stress at 4°C after cold acclimation at 14°C, and a cold shock from 24°C to 4°C. Two results from the analysis were striking. First, the moderate stress and cold shock, despite a difference of 10°C between the two, triggered comparable degrees of perturbation to the transcriptome; in contrary, further harsh stress after cold acclimation resulted in a much smaller degree of transcriptome variation. Second and more importantly, about two thirds of the up- or down-regulated genes after moderate stress reversed their expression to down- or up-regulation, respectively, under harsh stress after cold acclimation, resulting in a genome-wide rewiring of regulatory networks. MicroRNAs, which are key post-transcriptional gene regulators, were major players in this massive rewiring of genetic circuitry. Further, a function enrichment analysis of the perturbed genes revealed that cold acclimation helped the plant to develop immunity to further harsh stress by exclusively inducing genes with functions of nutrient reservoir; in contrast, many genes with functions of viral reproduction were induced by cold shock. Our study revealed, for the first time, the molecular basis of stress acclimation in plants, and shed lights on the role of microRNA gene regulation in cold response and acclimation in Euphorbia.

To incorporate the far-red light (FR) signal into a strategy for optimizing plant growth, FAR-RED ELONGATED HYPOCOTYL1 (FHY1) mediates the nuclear translocation of the FR photoreceptor phytochrome A (phyA) and facilitates the association of phyA with the promoters of numerous associated genes crucial for the response to environmental stimuli. However, whether FHY1 plays additional roles following FR irradiation remains elusive. Here, by the global identification of FHY1 chromatin association sites through ChIP-seq analysis and by the comparison of FHY1-associated sites with phyA- associated sites, we demonstrated that nuclear FHY1 can either act independently of phyA or act in association with phyA to activate the expression of distinct target genes. We also determined that phyA can act independently of FHY1 in regulating phyA-specific target genes. Furthermore, we determined that the independent FHY1 nuclear pathway is involved in crucial developmental aspects, as in the case of inhibited seed germination under FR during salt-stress. Notably, the differential presence of cis-elements and transcription factors in common and unique FHY1 and/or phyA associated genes are indicative of the complexity of the independent and coordinated FHY1 and phyA pathways. Our study uncovers new aspects of FHY1 function beyond its currently recognized role in phyA-dependent photomorphogenesis

Heat shock proteins (Hsps) are molecular chaperones primarily involved in maintenance of protein homeostasis. Their function has been best characterized in heat stress (HS) response during which Hsps are transcriptionally controlled by heat stress transcription factors (Hsfs). The role of Hsfs and Hsps in HS-response in tomato was initially examined by transcriptome analysis using the Massive Analysis of cDNA Ends (MACE) method. Approximately 9.6% of all genes expressed in leaves are enhanced in response to HS, including a subset of Hsfs and Hsps. The underlying Hsp-Hsf networks with potential functions in stress responses or developmental processes were further explored by meta-analysis of existing microarray datasets. We identified clusters with differential transcript profiles with respect to abiotic stresses, plant organs and developmental stages. The composition of two clusters points toward two major chaperone networks. One cluster consisted of constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis. The second cluster represents genes strongly induced by heat, drought and salinity stress, including HsfA2 and many stress-inducible chaperones, but also potential targets of HsfA2 not related to protein homeostasis. This observation attributes a central regulatory role to HsfA2 in controlling different aspects of abiotic stress response and tolerance in tomato.

Arabidopsis thaliana plants that have experienced an initial exposure to dehydration stress (“trained plants”) have an increased ability to maintain leaf relative water content (RWC) during subsequent stresses than plants experiencing the stress for the first time and transcription of selected dehydration response genes is altered during successive exposures to dehydration stress. This physiological and transcriptional behavior of trained plants is consistent with a “memory “of an earlier stress. It is unknown whether such memory is present in other Angiosperm lineages and whether it is an evolutionarily conserved response to stress. Here, we analyzed the behavior and transcriptomes of maize (Zea mays) plants experiencing multiple dehydration stresses and compare them with responses of the evolutionarily distant A. thaliana. We found structurally related genes in maize that displayed the same memory-type responses as in A. thaliana, providing evidence of the conservation of function and transcriptional memory in the evolution of plants’ dehydration stress response systems. Similar to A. thaliana, trained Z. mays plants retained higher RWC during dehydration stress than untrained plants, due in part to maintaining reduced stomatal conductance, despite full recovery of RWC, after the first stress. Divergent transcriptional memory responses were also expressed, suggesting diversification of function among stress memory genes. Some dehydration stress memory genes were also shared with other stress and hormone responding pathways, indicating complex and dynamic interactions between different plant signaling networks. The results provide new insight into how plants respond to multiple dehydration stresses and provide a platform for studies of the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants .

Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAs’ roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava.

In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light:dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.

Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform.Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously , Seeds were planted in soil and kep in the greenhouse at temperature of 25-30℃ and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction. For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 µmol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel. After treatments, Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA).Results: we generated 4.96×107 raw sequence reads and assembled the high quality reads into 92,390 unique genes. Compared with the control, we found that 621 genes (≥1.5 fold change) responded rapidly to water deficit and 2665 genes (≥1.5 fold change) responded rapidly to ABA. We found 279 genes that overlapped between water deficit and ABA responses, 264 genes that showed the same trend in expression while 15 genes expression that showed opposite trend. Among the identified genes, 257 showed high induction by ABA (>5 fold), and 19 showed high induction by drought (>5 fold). In addition, we identified 100 transcription factor genes among the ABA-inducible genes but only 22 transcription factor genes among the water deficit-inducible genes.Conclusions: we identified genes differentially expressed in the early response to water deficit or ABA. These genes were annotated with GO functional categories for water deficit (33 categories) or ABA (31 categories). We found that only 19 genes were highly induced by water deficit, but 257 genes were highly induced by ABA. Our previous work has examined many of these genes and our future work will reveal their functions and relationships. These data will facilitate functional genomic studies and have established a biotechnological platform for examination of the early drought- and ABA-responsive transcriptome regulatory network in peanut.

We report the identification of a heat-stress mediated mRNA decay in arabidopsis that is mediated by the XRN4 exonuclease and LARP1 RNA-binding protein.

We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta.

Arabidopsis plants that have experienced stress from water withdrawal show an improved ability to tolerate subsequent exposures as a ‘memory’ from the previous stress. This physiological stress memory is associated with ‘transcriptional memory’ illustrated by a subset of dehydrations stress responding genes that produce significantly different transcript amounts during repeated dehydration stresses relative to their response in the first. Here we report the genome-wide representation of dehydration stress transcriptional memory genes in A. thaliana. We identify four novel transcription patterns in response to repeated dehydration stress treatments. The nature of the proteins encoded by genes from each type of memory-response pattern is analyzed and the consequences of the genes’ memory behavior are considered in the context of possible biological relevance. The memory behavior of genes co-regulated by the dehydration/ABA and other abiotic stress and hormone responding pathways suggested that the crosstalk at the transcriptional level between them was affected as well. The intensity and the nature of specific biochemical, membrane, chloroplast, and stress response-related interactions during multiple exposures to dehydration stress are different from the responses to a single dehydration stress. The results reveal additional, hitherto unknown, levels of complexity of the plants’ transcriptional behavior when adjusting and adapting to recurring water deficits.

MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis thaliana, 27 small RNA libraries were constructed and sequenced from various tissues, stresses and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences. The use of rdr2 to enrich the miRNA population greatly enhanced this analysis and led to the discovery of 44 new miRNAs arising from both known and new precursors. Parallel Analysis of RNA Ends (PARE) data provide evidence that the majority guide target cleavage. The inclusion of novel stress/tissue conditions, such as submergence-stressed flowers, enabled identification of new stress regulation of both miRNAs and their targets, all of which were validated in wild type plants. By combining small RNA expression analysis with ARGONAUTE (AGO) immunoprecipitation data and global target cleavage data from PARE, a much more complete picture of Arabidopsis miRNAs was obtained. This combinatorial approach led to the discovery of AGO loading and target cleavage biases, which gave important insights into tissue-specific expression patterns, pathogen responses and the role of sequence variation among closely related miRNA family members.

In this study, we aim to present the complete transcriptome of Asian wild rice, Porteresia. We generated about 375 million high-quality reads for five different conditions (ranging from 65 to 90 million reads for each condition) using Illumina high-throughput sequencing GAII platform. We mapped the reads to Porteresia transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during conditions.

The transition metal copper (Cu) is an essential element for all living organisms. In plants, Cu plays key roles in electron transport chains of chloroplasts and mitochondria, as well as in cell wall metabolism, ethylene perception, molybdenum cofactor synthesis and oxidative stress protection. Because of its physiological importance, suboptimal concentrations of Cu trigger a re-organization of metabolism to economize on Cu, and pronounced Cu deficiency causes severe growth reduction and defects in male fertility. However, when present in excess, Cu can be highly toxic. Therefore, Cu uptake, utilization and cellular concentrations are strictly regulated. A number of components of the Cu-homeostatic network of Arabidopsis have already been identified. However, the mechanisms that control responses of plant gene expression to Cu-deficiency are only partly understood. In Chlamydomonas reinhardtii, the transcription factor Crr1 is required for activating and/or repressing the expression of a number of genes in response to Cu deficiency. This protein contains a plant-specific DNA-binding domain (SBP domain), ankyrin repeats and a C-terminal cysteine-rich region with similarity to a Drosophila metallothionein (MT). In Arabidopsis, there is a family of 16 proteins with SBP domains named SPL family (SBP-like) of which a subset of proteins have been implicated in flowering time control and floral development. Among all of them, AtSPL7 is the most similar to Crr1 (27 % identity), and AtSPL1 (25 % identity), AtSPL12 (24 % identity) and AtSPL14 (23 % identity) share a common protein architecture. The goal of this work was to obtain a complete account of the response of the Arabidopsis thaliana transcriptome to Cu deficiency, as well as to determine the role of AtSPL7 in the transcriptional response to Cu deficiency. For this purpose, three independent experiments were carried out including Col-0 wild-type and spl7-2 mutant plants grown in Cu-sufficient and Cu-deficient hydroponic media, respectively. Root and shoot transcriptomes were established by RNA-Seq for quantitative comparisons.

PARE (parallel analysis of RNA ends) was performed to study the change of uncapped mRNAs before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of uncapped transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.

Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.

Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. We constructed four small RNAs libraries prepared from plants grown on hydroponic culture submitted to 170 mM NaCl and harvested after 1 h, 6 hs and 24 hs. Each library was sequenced individually and together generated more than 50 million short reads. Ninety-eight conserved miRNAs and 33 miRNAs* were identified by bioinformatics. Several of the microRNA showed considerable differences of expression in the four libraries. To confirm the results of the bioinformatics-based analysis, we studied the expression of the 10 most abundant miRNAs and 1 miRNA* in plants treated with 170 mM NaCl and in plants with a severe treatment of 340 mM NaCl. The results showed that 11 selected miRNAs had higher expression in samples treated with severe salt treatment compared to the mild one. We also investigated the regulation of the same miRNAs in shoots of four cultivars grown on soil treated with 170 mM NaCl. Cultivars could be grouped according to miRNAs expression in response to salt stress. Furthermore, the majority of the predicted target genes had an inverse regulation with their correspondent microRNAs. The targets encode a wide range of proteins, including transcription factors, metabolic enzymes and genes involved in hormone signaling, probably assisting the plants to develop tolerance to salinity. Our work provides insights into the regulatory functions of miRNAs, thereby expanding our knowledge on potential salt-stressed regulated genes.

In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress.

To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions.