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.
Highlights
To alleviate the energy crisis caused by increasing consumption of fossil fuels with limited reserves, more attention has shifted to the use of alternate renewable energy forms, such as biofuels, that are generally obtained from either carbohydrate- or oil-based feedstock or biomass
Additional BlastX and ESTScan analyses revealed that 34,274 unigenes had reliable coding sequences (CDSs) (33,362 derived from the database alignment by BlastX and 912 from the ESTScan prediction)
A total of 4.95, 4.68, 4.87, and 4.95 million raw tags of the mRNAs extracted from the leaves after 12 h of cold (12°C) cold treatments for 0, 12, 24, and 48 h were obtained, and approximately 4.81, 4.49, 4.70, and 4.79 million high-quality, non-redundant clean tags were identified after filtering the dirty tags, respectively
Summary
To alleviate the energy crisis caused by increasing consumption of fossil fuels with limited reserves, more attention has shifted to the use of alternate renewable energy forms, such as biofuels, that are generally obtained from either carbohydrate- or oil-based feedstock or biomass. J. curcas, a woody shrub belonging to the Euphorbiaceae family, has been widely regarded as an excellent source of renewable biofuels, owing to its distinct features, including high seed oil content (30–50%) [2], fossil fuel-like oil composition (more than 75% unsaturated fatty acids) [3,4], and growth on degraded lands or wastelands in arid and semi-arid regions [1,5] This plant species, primarily originating from Central America, has been recently introduced into many tropical and subtropical countries in Asia and Africa [3,6]. 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
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