Flood tolerant Cardamineae
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB73992 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Rsyl_trans.fasta.gz | Fasta.gz | |||
| Rpal_trans.fasta.gz | Fasta.gz | |||
| Cpra_trans.fasta.gz | Fasta.gz | |||
| Chir_trans.fasta.gz | Fasta.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:RNAseq of submergence response of the flood tolerant Cardamineae tribe
| PRJEB73986 | ENA
Project description:While the molecular mechanisms mediating submergence tolerance have been extensively studied, those underpinning age-dependent resilience remain poorly characterized. In Arabidopsis thaliana, submergence elicits a leaf-age dependent phenotype in which senescence and death progress across an age gradient starting with older leaves. Here we sought to investigate the mechanisms mediating this observed differential flood resilience by interrogating leaf age-specific transcriptome and proteome changes during submergence and recovery. Following submergence, most age-dependent differences were in the magnitude or speed of transcript abundance changes, whereas qualitative leaf-age dependent responses were most apparent during recovery. This included a strong desiccation response in old leaves despite a stronger ABA-signaling response. Physiological measurements suggested that faster dehydration was mediated by a combination of submergence-mediated reduction of ABA sensitivity and higher conductance in old leaves. We also observed a stronger induction in young shoot tissue of genes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Mutants disabled in the two UPR signaling branches were affected in new leaf formation and the ability to restore the proteome, but not in senescence, suggesting that young tissues activate ER stress recovery to permit continuation of growth. Of the mitochondrial membrane proteins differentially regulated in young leaves, loss of mitochondrial voltage-dependent anion channel function impacted submergence-recovery tolerance. Our data reveal multiple mechanisms underlying leaf age-dependent differential submergence recovery and demonstrate how tolerance is determined by an interplay between age related developmental traits and stress signaling pathways.
2026-08-14 | PXD067068 | Pride
Project description:Pot grown plants of Arabidopsis thaliana, Cardamine hirsuta, Cardamine pratensis, Rorippa palustris and Rorippa sylvestris where completely submerged under ambient light conditions. After 24 and 48 hours the shoots were harvested for expression analysis. Differential expression analysis, taking into account unsubmerged control plants revealed that the Rorippa genus had a pronounced down regulation of the cell cycle whereas the Cardamine had an attenuated response to submergence.
2024-04-01 | E-MTAB-13910 | biostudies-arrayexpress
Project description:RNA sequencing (RNA-seq) was performed to investigate potential roles of the unfolded protein response in submergence and recovery responses of Arabidopsis thaliana. Plants were grown to the 10-leaf stage and then subjected to 4 days of complete submergence. Samples were collected at four time points: prior to submergence (T0), after 1 day of submergence (1d), after 4 days of submergence (4d - end of submergence period), and 3 hours after de-submergence (recovery). For each time point, rosettes were collected and divided into two developmental zones: (i) old leaves (leaves 1 to 5) and (ii) young leaves (leaves 6 to 10 including the shoot apical meristem (SAM)). There were three biological replicates per tissue type of each genotype at each time point. Each biological replicate consisted of tissue pooled from two plants. Two genotypes were examined: Col-0 (wild type) and the bzip60/bzip28 double mutant, which is impaired in unfolded protein response signaling. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina platform to generate paired-end reads.
2025-11-15 | E-MTAB-15812 | biostudies-arrayexpress
Project description:Waterlogging and submergence are major abiotic stresses impairing rapeseed development and hence evaluation of waterlogging tolerance ability is crucial for the development of tolerant lines through breeding approaches. This study investigated submergence impact on the survival rate, physiological responses, and transcriptomic variation of the young seedlings of 706 Brassica napus germplasm. We identified 57 highly tolerant and 109 highly susceptible accessions underwent six days submergence. Most accessions originated from the downstream of Yangtze River region had higher tolerance level. SOD enzymic activity increased both in the five representative tolerant and susceptible genotypes under submergence stress. POD activity also increased in the tolerant genotypes whereas CAT activity decreased, showing a opposite trend compared to the susceptible genotypes. The tolerant genotypes showed less chlorosis and produced less malondialdehyde than that in the susceptible group, while soluble protein content increased more than that in the susceptible genotypes. Transcriptome analysis detected 5,072 and 5,063 up-regulated genes, as well as 3,512 and 3,889 down-regulated genes in the tolerant / susceptible group in comparison to their respective control. Many genes encoding the transcription factors in AP2/ERF, bHLH, MYB, WRKY, and NAC families were also significantly regulated. The differentially expressed genes shared by the two pairs comparison were mainly enriched in such KEGG pathways as circadian rhythm, tryptophan metabolism, and porphyrin and chlorophyll metabolism. The specific pathways in the tolerant group were enriched in carbon metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acid etc. while the specific pathways in the susceptible group were more distributed in hormone signal transduction, sucrose and starch metabolism, and vitamin B6 metabolism etc. The results uncovered distinct physiological and transcriptomic differences between tolerant and susceptible genotypes.
2025-12-26 | GSE314699 | GEO
Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response
2010-03-09 | GSE17704 | GEO
Project description:Leaf age determines flood resilience through distinct submergence and recovery effects
| PRJEB101178 | ENA
Project description: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.
2020-10-28 | GSE140828 | GEO
Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response Three-condition experiment, M202(Sub1) vs wild type control (M202) at three durations of submergence (0d, 1d and 6d). Biological replicates: 2, independently grown and harvested. Technical replicates replicates: 1-2 control.
2010-03-08 | E-GEOD-17704 | biostudies-arrayexpress
Project description:An ERF transcription factor, Submergence-1A (Sub1A), dramatically enhances the tolerance to prolonged submergence in rice. For instance, rice accessions which lack Sub1A (e.g. M202) die within 7-10 d of complete submergence. By contrast, genotypes which posses Sub1A (e.g. M202(Sub1)) can endure submergence stress for 14 d. In this study, the two near isogenic lines with and without Sub1A were subjected to microarray analysis using Affymetrix Gene Chip technology. This analysis provided beneficial information to elucidate general response to submergence stress and to estimate Sub1A-dependent defense response to the stress at mRNA accumulation level.
2010-02-04 | GSE18930 | GEO