Ontology highlight
ABSTRACT:
PROVIDER: PRJNA970846 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24487900_1.fastq.gz | Fastqsanger.gz | |||
| SRR24487900_2.fastq.gz | Fastqsanger.gz | |||
| SRR24487901_1.fastq.gz | Fastqsanger.gz | |||
| SRR24487901_2.fastq.gz | Fastqsanger.gz | |||
| SRR24487902_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Brassica. juncea is vulnerable to abiotic stresses at specific stages in its life cycle. However, till date no attempts have been made to elucidate the genome-wide changes in the transcriptome of B. juncea subjected to either high temperature or drought stress. Hence, to gain global insights into genes, transcription factors and kinases regulated by these stresses and to provide basic information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de novo assembly to discover B. juncea transcriptome associated with high temperature and drought. Results: We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS) from control, high temperature treated and drought treated seedlings of Brassica juncea. More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPde-novo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Investigation of identified transcription factors revealed that 92 responded to high temperature, 72 exhibited alterations in expression during drought stress, and 60 were commonly associated with both the stresses. Similarly, 217, 259 and 193 kinases were responsive to high temperature, drought or both stresses, respectively. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes. Conclusions: Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resources generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity.
2015-08-28 | GSE64242 | GEO
Project description:Purpose: Brassica. juncea is vulnerable to abiotic stresses at specific stages in its life cycle. However, till date no attempts have been made to elucidate the genome-wide changes in the transcriptome of B. juncea subjected to either high temperature or drought stress. Hence, to gain global insights into genes, transcription factors and kinases regulated by these stresses and to provide basic information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de novo assembly to discover B. juncea transcriptome associated with high temperature and drought. Results: We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS) from control, high temperature treated and drought treated seedlings of Brassica juncea. More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPde-novo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Investigation of identified transcription factors revealed that 92 responded to high temperature, 72 exhibited alterations in expression during drought stress, and 60 were commonly associated with both the stresses. Similarly, 217, 259 and 193 kinases were responsive to high temperature, drought or both stresses, respectively. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes. Conclusions: Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resources generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity. Total three RNA-Seq libraries were prepared and sequenced independently [B. juncea control (BC), B. juncea high temperature stressed (BHS) and B. juncea drought stressed (BDS) on Illumina GAIIx sequencer].
2015-08-28 | E-GEOD-64242 | biostudies-arrayexpress
Project description:DREB2A is a transcription factor responsive to drought, high salt and high temperature stress.In this experiment, gene expression profiles of DREB2A KO mutants were compared with wild type under stress condition.
2007-02-21 | E-MEXP-603 | biostudies-arrayexpress
Project description:Potato plants are sensitive to multiple abiotic stresses such as drought, low temperature and high light. We analyzed the transcriptome of WT potato plants as well as that of transgenic potato plants expressing the Arabidopsis stress related transcription factor CBF1 that confers tolerance to multiple stresses. Wild type and AtCBF1OX transgenic potato plants were exposed to low temperature, high light, drought or kept under control conditions as described below in detail, and transcriptional changes induced by the different stresses were analyzed.
2015-03-01 | E-GEOD-61004 | biostudies-arrayexpress
Project description: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.
2018-03-21 | GSE106150 | GEO
Project description:Plants continuously respond to changing environmental conditions to prevent damage and maintain optimal performance. To regulate gas exchange with the environment and to control abiotic stress relief, plants have pores in their leaf epidermis, called stomata. Multiple environmental signals affect the opening and closing of these stomata. High temperatures promote stomatal opening (to cool down), and drought induces stomatal closing (to prevent water loss). Coinciding stress conditions may evoke conflicting stomatal responses, but the cellular mechanisms to resolve these conflicts are unknown. Here we demonstrate that the high-temperature-associated kinase TARGET OF TEMPERATURE 3 directly controls the activity of plasma membrane H+-ATPases to induce stomatal opening. OPEN STOMATA 1, which regulates stomatal closure to prevent water loss during drought stress, directly inactivates TARGET OF TEMPERATURE 3 through phosphorylation. Taken together, this signalling axis harmonizes stomatal opening and closing under high temperatures and drought. In the context of global climate change, understanding how different stress signals converge on stomatal regulation allows the development of climate-change-ready crops.
2024-11-12 | PXD044300 | Pride
Project description:To undersand the machanism underlying the drought and cold srress tolerance of Ammopiptanthus mongolicus,we investigate the gene expression profile of Ammopiptanthus mongolicus leaves under drought stress(1hours,24hours,72hours) and low temperature (1hours,72hours ).
2016-01-21 | GSE54251 | GEO
Project description:Potato plants are sensitive to multiple abiotic stresses such as drought, low temperature and high light. We analyzed the transcriptome of WT potato plants as well as that of transgenic potato plants expressing the Arabidopsis stress related transcription factor CBF1 that confers tolerance to multiple stresses.
2015-03-01 | GSE61004 | GEO
Project description:Drought is an inevitable stress almost all terrestrial plants face in their life cycles. Desert dwelling plants show extreme adaptations to drought but their genomes are largely unexplored compared to drought sensitive model plants generally studied to understand plant drought tolerance. Haloxylon ammodendron is a pioneer species extremely tolerant to drought and capable of colonizing desert sand dunes. Seedling establishment is the most critical development stage in the survival of H. ammodendron. H. ammodendron seedlings are able to withstand high light, and low temperature stresses characteristic of temperate desert environments in addition to drought. We have investigated the genome-wide transcript responses under induced drought stress during early seedling establishment to identify prevailing basal and induced gene clusters that likely contribute to survival and stress adapted growth in H. ammodendron. We find staggering support for drought response transcript accumulation together with other transcripts that may transform the cellular expression space into a preadapted state for salt, light, osmotic, and temperature stress tolerance. While transcript accumulation is excessive for genes associated with abiotic stress tolerance under an induced drought treatment, H. ammodendron seems to enhance biotic stress tolerance simultaneously by down-regulation of several genes that would be found at an up-regulated state during pathogen entry in susceptible plants. We detected enriched basal level transcript allocation that suggests preadaptation to abiotic stresses as well as pathogen defense in H. ammodendron when compared to other Amaranthaceae family transcriptomes under stress neutral conditions. Amaranthaceae is one of the most enriched plant families for extremophytes. We found transcripts that are generally maintained at low levels and some induced only under abiotic stress in Arabidopsis thaliana to be highly expressed under basal conditions in the Amaranthaceae transcriptomes including H. ammodendron. These could be novel candidates to expand or initiate discovery of new stress adaptive gene networks and mechanisms naturally selected in extremophytes that allow survival under environmental stresses.
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