title: Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.
abstract: BACKGROUND
  Jatropha curcas L., also called the Physic nut, is an oil-rich shrub with multiple uses, including biodiesel production, and is currently exploited as a renewable energy resource in many countries. Nevertheless, because of its origin from the tropical MidAmerican zone, J. curcas confers an inherent but undesirable characteristic (low cold resistance) that may seriously restrict its large-scale popularization. This adaptive flaw can be genetically improved by elucidating the mechanisms underlying plant tolerance to cold temperatures. The newly developed Illumina Hiseq™ 2000 RNA-seq and Digital Gene Expression (DGE) are deep high-throughput approaches for gene expression analysis at the transcriptome level, using which we carefully investigated the gene expression profiles in response to cold stress to gain insight into the molecular mechanisms of cold response in J. curcas.
  
  
  RESULTS
  In total, 45,251 unigenes were obtained by assembly of clean data generated by RNA-seq analysis of the J. curcas transcriptome. A total of 33,363 and 912 complete or partial coding sequences (CDSs) were determined by protein database alignments and ESTScan prediction, respectively. Among these unigenes, more than 41.52% were involved in approximately 128 known metabolic or signaling pathways, and 4,185 were possibly associated with cold resistance. DGE analysis was used to assess the changes in gene expression when exposed to cold condition (12°C) for 12, 24, and 48 h. The results showed that 3,178 genes were significantly upregulated and 1,244 were downregulated under cold stress. These genes were then functionally annotated based on the transcriptome data from RNA-seq analysis.
  
  
  CONCLUSIONS
  This study provides a global view of transcriptome response and gene expression profiling of J. curcas in response to cold stress. The results can help improve our current understanding of the mechanisms underlying plant cold resistance and favor the screening of crucial genes for genetically enhancing cold resistance in J. curcas.
authors.affiliation: School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming, Yunnan, P. R. China ; College of Biological Resources and Environmental Science, Qujing Normal University, Qujing, Yunnan, P. R. China.
authors.forename: Haibo
authors.initials: H
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming, Yunnan, P. R. China.
authors.forename: Zhurong
authors.initials: Z
authors.lastname: Zou
authors.affiliation: School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming, Yunnan, P. R. China.
authors.forename: Shasha
authors.initials: S
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming, Yunnan, P. R. China.
authors.forename: Ming
authors.initials: M
authors.lastname: Gong
mesh_terms: D050260:Carbohydrate Metabolism / Q000235:genetics; D016000:Cluster Analysis; D003080:Cold Temperature; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D031286:Jatropha / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D015398:Signal Transduction; D013213:Starch / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome
chemical_list: D013213:Starch