Setaria drought RNAseq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21225 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2003560_1.fastq.gz | Fastqsanger.gz | |||
| ERR2003560_2.fastq.gz | Fastqsanger.gz | |||
| ERR2003561_1.fastq.gz | Fastqsanger.gz | |||
| ERR2003561_2.fastq.gz | Fastqsanger.gz | |||
| ERR2003562_1.fastq.gz | Fastqsanger.gz |
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Project description:We report here the RNAseq data generated from a drought experiment using tomato leaves (Solanum lycopersicum), in which three timepoints and two treatments were collected. More specifically, RNAseq was generated from tomato plants prior to drought (T0), during a period of drought (T1) and after a period of recovery from drought (T2). At timepoints 1 and 2 (T1 & T2), a control set of plants that were continuously watered are also included. Furthermore, at each timepoint, each leaf was dissected into two parts, including the vein and intervein. The samples are therefore named as Tissue/Timepoint/Treatment, and include VT0W (vein, T0, watered), VT1W (vein, T1, watered), VT1D (vein, T1, drought), VT2D, VT2W and IVT0W (intervein, T0, Watered), IVT1D, IVT1W, IVT2D, IVT2W. Note that VT2D and IVT2D, while named "drought", were actually recovered from drought.
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Project description:Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare in gene expression in the S. viridis crown between drought vs watered treatments.
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Project description:Vein and Intervein Drought RNAseq
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Project description: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.
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Project description:Our recently published results demonstrated a crucial role for plastid terminal oxidase (PTOX) as an alternative electron pathway in the halophyte Spartina alterniflora (S. alterniflora) under salt stress but not for the glycophyte Setaria viridis (S. viridis). Herein, the effect of salt on the photosynthetic electron transport and RNA-seq analysis was probed in Setaria and its salt-tolerant close relative S. alterniflora. Initially, plants were grown at soil then were salt-treated under hydroponic conditions for two weeks. Setaria shows high vulnerability to salt compared to Spartina; while, Setaria was unable to survive exposure to greater than 100 mM, Spartina could tolerate salt concentrations as high as 550 mM with merely negligible effect on gas exchange and conductance of electrons transport chain (gETC). After exposure to salt, the prompt fluorescence (OJIP-curves) reveals an increase in the O- and J-steps in Setaria and very less or no change for SA. This suggests a higher QA over-reduction in Setaria than in Spartina. Following salt treatment, a dramatic decline in PSII primary photochemistry for Setaria was observed, as displayed by the drastic drop in Fv/Fm, Fv/Fo and ΦPSII. However, no substantial change was recorded regarding these parameters for Spartina under NaCl treatment. Interestingly, we report an improvement in primary PSII photochemistry (ΦPSII) for Spartina with increasing either salt concentration or duration. Besides, the magnitude of NPQ dynamics was strongly enhanced for Setaria even at low NaCl level (50 mM); however, it remains unchangeable or slightly increased for Spartina at high NaCl concentrations (above 400 mM). For plants endured salt, we notice an increase in both the proportion of oxidized P700 and the amount of active P700 in Setaria and almost no change for Spartina. The slowdown of electrons flow through PSII was accompanied by a dramatic decline in gETC. Under salt, CO2 assimilation (A) and stomatal conductance (gs) evaluations demonstrate that A decreases earlier, even after one week exposure to only 50 mM NaCl for Setaria; however, the effect of salt was negligible in Spartina regarding these two parameters even after exposure for two weeks to high salt levels (400 and 550 mM). For Setaria exposed for 12 d to salt, the use of 2,000 μmol m-2 s-1 external CO2 was not sufficient to fully restore A to the control level as assessed by A-Ci curves, even for 50 mM salt. The A at all NaCl levels, except 550 mM, was able to completely recover to initial level before stress in Spartina. RNAseq analysis shows a stimulation of oxido-reduction reactions in Setaria. Gene onthology (GO) enrichment emphasizes differentially expressed genes (DEGs) and some transcription factors (TFs) under salt. The up-regulated genes in Setaria are related to three metabolic processes; C4, photorespiration and the oxidation/reduction pathways. Some other specifically highly up-regulated genes in Setaria are mostly related to TFs including DNA-binding transcription factor activity, stress marker genes such as peroxidase and senescence-related genes such as flavonol synthase.
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Project description:Transcriptional and translational status of genes responding to drought stress - Drought-stressed plants were compared to non-stressed plants, using total, polysomal or non-polysomal RNAs. Keywords: treated vs untreated comparison
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Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.
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