Ontology highlight
ABSTRACT:
PROVIDER: PRJNA727101 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14432600_1.fastq.gz | Fastqsanger.gz | |||
| SRR14432600_2.fastq.gz | Fastqsanger.gz | |||
| SRR14432601_1.fastq.gz | Fastqsanger.gz | |||
| SRR14432601_2.fastq.gz | Fastqsanger.gz | |||
| SRR14432602_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
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Project description:comparative transcriptomics of two temperate C3 bioenergy and forage grasses under water stress
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Project description: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.
2021-08-03 | GSE168920 | GEO
Project description: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.
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Project description: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.
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Project description: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.
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Project description:Alfalfa is the most produced perennial forage crop in Canada. Drought stress is a major form of abiotic stress, affecting its productivity and annual yield. A small RNA, miR156, plays a major role in drought tolerance by downregulating downstream SPL genes, but its effects at the proteome level are unknown. In this study, the protein level perturbations of miR156 overexpression (A8) and empty vector (EV) control genotypes were compared under drought stress. Using label-free quantification, 3,000 protein groups were identified, of which 68 were upregulated in A8 and 84 were downregulated relative to EV under control conditions. Conversely, under drought stress, 610 proteins were upregulated and only 52 proteins were downregulated in A8 relative to EV. Functional analysis using PlantRegMap showed that the enriched proteins are likely involved in biological and molecular processes including antioxidant response, response to stress, signal transduction and biosynthesis of secondary metabolites. These proteins/pathways might be involved in the enhancement of drought stress tolerance mediated by miR156. Protein groups related to signaling, such as MAP kinase, calcium-dependent protein kinase, protein phosphatase 2C, and transcriptional regulators including bZIP and zinc finger proteins were found to be differentially expressed when a search was conducted against a drought stress gene database. The proteomic dataset was validated by immunoblotting of selected proteins. The results of this study provide a better understanding and insight into the role of miR156 in drought stress tolerance in alfalfa at the proteomic level.
2023-10-19 | PXD028329 | Pride
Project description:Drought stress is a major abiotic stress affecting plant growth and development. Brachypodiumdistachyon L. is a special model plant for wheat, barley, and several potential biofuel grasses. In this study, we make comparative phosphoproteome analysis of seeding leaves at the three leaf stage in Brachypodiumdistachyon L. for the different treatment conditions (6h, 24h). A total of 480 unique phosphopeptides, representing 439 phosphoproteins, were identified under drought stress. Motif-X analysis identified six motifs, such as [SP], [RxxS], [LxRxxS], [SxD], [SF] and [TP]. Molecular function and PPI analysis suggested that many proteins may take participation in signal transduction, gene expression, drought response and defense with energy metabolism and material transmembrane transport under moisture deficiency condition. Further analyses revealed that these SCPL phosphoproteins may play important roles in regulating signal transduction and material transmembrane transport to cope with the adverse environmental conditions. This study first focus on the effects of phosphorylation modification mechanisms on the growth and development of seeding leaves at different drought stresses.
2018-10-26 | PXD003522 | Pride
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