title: Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea.
abstract: BACKGROUND
  Brassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore 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 stresses.
  
  
  RESULTS
  We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo 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. Many of these were responsive to high temperature, drought or both stresses. 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 resource 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.
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. ankurbio.du@gmail.com.
authors.forename: Ankur R
authors.initials: AR
authors.lastname: Bhardwaj
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. gopal_joshii@yahoo.com.
authors.forename: Gopal
authors.initials: G
authors.lastname: Joshi
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. together4gud@gmail.com.
authors.forename: Bharti
authors.initials: B
authors.lastname: Kukreja
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. vidhi0205@gmail.com.
authors.forename: Vidhi
authors.initials: V
authors.lastname: Malik
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. hindu.priyanka@gmail.com.
authors.forename: Priyanka
authors.initials: P
authors.lastname: Arora
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Delhi, 110021, India. ritupandey84@gmail.com.
authors.forename: Ritu
authors.initials: R
authors.lastname: Pandey
authors.affiliation: Bionivid Technology [P] Ltd, Bangalore, 560043, India. rohit@bionivid.com.
authors.forename: Rohit N
authors.initials: RN
authors.lastname: Shukla
authors.affiliation: Bionivid Technology [P] Ltd, Bangalore, 560043, India. kiran@bionivid.com.
authors.forename: Kiran G
authors.initials: KG
authors.lastname: Bankar
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Delhi, 110021, India. katiyars@south.du.ac.in.
authors.forename: Surekha
authors.initials: S
authors.lastname: Katiyar-Agarwal
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. shailendragoel@gmail.com.
authors.forename: Shailendra
authors.initials: S
authors.lastname: Goel
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. jagannatharun@yahoo.co.in.
authors.forename: Arun
authors.initials: A
authors.lastname: Jagannath
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. akumar23j@googlemail.com.
authors.forename: Amar
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Botany, University of Delhi Main Campus, Delhi, 110007, India. agarwalm71@gmail.com.
authors.forename: Manu
authors.initials: M
authors.lastname: Agarwal
mesh_terms: D018556:Crops, Agricultural / Q000191:economics* / Q000235:genetics*; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D058977:Molecular Sequence Annotation; D009149:Mustard Plant / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics*; D013696:Temperature; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger