RNA-Sequencing of PEG-stressed Sesame roots in drought sensitive and tolerant genotypes
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ABSTRACT:
PROVIDER: PRJNA623932 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11511141_1.fastq.gz | Fastqsanger.gz | |||
| SRR11511141_2.fastq.gz | Fastqsanger.gz | |||
| SRR11511142_1.fastq.gz | Fastqsanger.gz | |||
| SRR11511142_2.fastq.gz | Fastqsanger.gz | |||
| SRR11511143_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goals of this study are to understand transcriptional changes in the roots of drought-tolerant and sensitive sesame genotypes using PEG (Polyethylene glycol) induced osmotic stress.
2020-07-02 | GSE148340 | GEO
Project description:We study differences in gene expression between 5% PEG treated and control plants’ roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by water limitation mimicked by PEG treatment.treated
2018-07-12 | GSE116922 | GEO
Project description:BackgroundSesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes.ResultsTranscriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame.ConclusionThe results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.
| S-EPMC6585049 | biostudies-literature
Project description:To detect salt-tolerance-related miRNAs, comparative analysis of miRNA expression profiles was performed between the salt-tolerant and -sensitive cotton cultivars in control and salt-stressed conditions (treated with 300 mM NaCl for 24 h) using microRNA microarray Total RNA was extracted from (1) the seedling of salt-tolerant cotton cultivar in normal growth conditions, (2) the seedling of salt-tolerant cotton cultivar in salt-stressed growth conditions, (3) the seedling of salt-sensitive cotton cultivar in normal growth conditions, and (4) the seedling of salt-sensitive cotton cultivar in salt-stressed growth conditions. Then, the low-molecular-weight RNA (LMW-RNA) was isolated using the PEG solution precipitation method and used to hybridization.
2011-05-03 | E-GEOD-19009 | biostudies-arrayexpress
Project description:In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT seedling roots exposure to PEG, and from roots under 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM for 0, 1, 2, 3 h.
2021-05-26 | GSE152457 | GEO
Project description:In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT seedling roots exposure to PEG, and from roots under 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM for 0, 1, 2, 3 h.
2021-05-26 | GSE152456 | GEO
Project description:Expression data from PEG treated roots
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Project description:Sesame seeds is an important traditional crop with high oil content and other abundant nutrients which are very beneficial for diet and health of human being. However, the molecular mechanism for metabolite accumulation, especially for oil and phenylpropanoid biosynthesis, is still not very clear in sesame. In this study, the transcriptome profiles of black and white sesame seeds were compared by RNA-sequencing. Transcriptome analysis showed that the expression patterns of genes encoding phenylpropanoid pathway enzymes were different between the two sesame cultivars. Compared with white sesame, most of genes involved in oil biosynthesis were significantly down-regulated in black sesame.
2024-06-30 | GSE223079 | GEO
Project description:Waterlogging is a common adverse environmental condition that limits plant growth. Sesame (Sesamum indicum) is considered a drought-tolerant oil crop but is typically susceptible to harmful effects from waterlogging. The present study used comparative analysis to explore the waterlogging stress response associated with two sesame genotypes. The RNA-seq dataset generated during a time course of 0, 3, 9 and 15 h of waterlogging as well as 20 h post-drainage indicated that stress gradually suppressed the expression of sesame genes, with 9 h as the critical time point for the response of sesame to waterlogging stress. Of the 19,316 genes expressed during waterlogging, 72.1% were affected significantly. Sesame of both tolerant and susceptible genotypes showed decreased numbers of upregulated differentially expressed genes (DEGs) but increased numbers of downregulated DEGs at the onset of waterlogging. However, the tolerant-genotype sesame exhibited 25.5% more upregulated DEGs and 29.7% fewer downregulated DEGs than those of the susceptible-genotype strain between 3 and 15 h. The results indicated that the tolerant sesame displayed a more positive gene response to waterlogging. A total of 1,379 genes were significantly induced and commonly expressed in sesame under waterlogging conditions from 3 to 15 h regardless of tolerance level; of these genes, 98 are known homologous stress responsive genes, while the remaining 1,281 are newly reported here. This gene set may represent the core genes that function in response to waterlogging, including those related mainly to energy metabolism and phenylpropanoid biosynthesis. Furthermore, a set of 3,016 genes functioning in energy supply and cell repair or formation was activated in sesame recovery from waterlogging stress. A comparative analysis between sesame of the tolerant and susceptible genotypes revealed 66 genes that may be candidates for improving sesame tolerance to waterlogging. This study provided a comprehensive picture of the sesame gene expression pattern in response to waterlogging stress. These results will help dissect the mechanism of the sesame response to waterlogging and identify candidate genes to improve its tolerance.
| S-EPMC4774966 | biostudies-literature