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| Status |
Public on Aug 28, 2015 |
| Title |
Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea |
| Organism |
Brassica juncea |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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].
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| Contributor(s) |
Bhardwaj AR, Joshi G, Kukreja B, Malik V, Arora P, Pandey R, Shukla RN, Bankar KG, Katiyar-Agarwal S, Goel S, Jagannath A, Kumar A, Agarwal M |
| Citation(s) |
25604693 |
| Submission date |
Dec 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gopal Joshi |
| E-mail(s) |
gopal_joshii@yahoo.com
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| Phone |
+91-11-27662609
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| Organization name |
Delhi University
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| Department |
Department of Botany
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| Lab |
Plant Genomics & Stress Biology
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| Street address |
First Floor
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| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110007 |
| Country |
India |
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| Platforms (1) |
| GPL16439 |
Illumina Genome Analyzer IIx (Brassica juncea) |
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| Samples (6)
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| GSM1566887 |
B. juncea control (BC) (PAIRED-END) |
| GSM1566888 |
B. juncea control (BC) (UNPAIRED) |
| GSM1566889 |
B. juncea high temperature stressed (BHS) (PAIRED-END) |
| GSM1566890 |
B. juncea high temperature stressed (BHS) (UNPAIRED) |
| GSM1566891 |
B. juncea drought stressed (BDS) (PAIRED-END) |
| GSM1566892 |
B. juncea drought stressed (BDS) (UNPAIRED) |
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| Relations |
| BioProject |
PRJNA270523 |
| SRA |
SRP051212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE64242_AnnotationTable.txt.gz |
4.8 Mb |
(ftp)(http) |
TXT |
| GSE64242_Brassica_Juncea_Ref.fa.gz |
21.7 Mb |
(ftp)(http) |
FA |
| GSE64242_accepted_hits_BC.bed.gz |
444.4 Mb |
(ftp)(http) |
BED |
| GSE64242_accepted_hits_BDS.bed.gz |
269.4 Mb |
(ftp)(http) |
BED |
| GSE64242_accepted_hits_BHTS.bed.gz |
283.4 Mb |
(ftp)(http) |
BED |
| GSE64242_cufdiff_isoform_exp.diff.gz |
9.3 Mb |
(ftp)(http) |
DIFF |
| GSE64242_matrix_isoforms.fpkm_tracking.gz |
4.3 Mb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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