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.ResultsIn 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.ConclusionsThis 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.

MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

“…Among these genes, bhlhe41 , bhlhe40 , nr1d4b , nr1d4a , nr1d1 , nr1d2a have been reported to be enriched in cold-induced carp larvae [11], suggesting transcription of certain genes should be induced by the cold in the fish larvae stage. The protein phosphorylation landscape is changed during cold treatment in aquatic creatures [46]. In the same token, we also observed the up-regulation of many kinase proteins such as MAP kinase interacting serine/threonine kinase 1 cascades, calcium/calmodulin-dependent protein kinase, protein kinase C and casein kinase 1.…”

Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

“…With the advent of low-cost next generation sequencing (NGS) technologies, transcriptome analysis through NGS has become a fast and powerful approach for genome-wide gene discovery and molecular marker development [19–21]. Transcriptomics has been used in jatropha to study gene expression profiles related to cold stress [22]; gene expression in seeds [23]; oil metabolism in maturing seeds [24]; impact of cytokinin on inflorescence buds [25]; metabolic pathways in drought tolerance [26]; and apical meristem [27]. Availability of these resources helps in jatropha gene discovery and crop improvement using molecular tools.…”

Molecular Cloning and Expression Analysis of the Gene Encoding Proline Dehydrogenase from Jatropha curcas L

“…A complete understanding of the molecular mechanism of proline metabolism regulation could lead to an improvement in the tolerance of plants to environmental stress conditions. Based on our previous data of the transcriptome and digital gene expression (DGE) of cold-hardened J. curcas [56,29], as well as the RT-PCR results presented herein (Figs. 6 and 7), JcProDH was found with tissue-differential expression and abiotic stress-induced expression and then gradually depressed expression.…”

“…After being treated with DNaseI (Takara, Dalian, China) to remove traces of contaminant genomic DNA, the firststrand cDNA was synthesized using 5 μg of total RNA with oligo(dT) 18 (TransScript FirstStrand cDNA Synthesis SuperMix). Based on our early transcriptome data and the sequence in GenBank (Accession number GAHK01001669) [29], two primers were designed with Primer Premier (Version 5.0) (Premier Biosoft International, USA) and synthesized for amplifying the full-length cDNA. Their sequences are as follows: JcProDH_F 5′-GTCTTAGGTACCCAAA TCCCTTTCTCCAAAAC-3′ and JcProDH_R 5′-GCTACTATCAGTACTCATAGCCACAA ACTTCA-3′.…”