Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds

Abstract

BackgroundJatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs).ResultsA normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 106 clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes.ConclusionsThe high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

“…4l). Contrary to earlier reports in J. curcas (Costa et al 2010;King et al 2011;Natarajan et al 2010;Jiang et al 2012;Xu et al 2011;Chen et al 2011) which focussed primarily on accumulation of oil, our results suggest a complex regulation of oil metabolism, possibly involving a delicate balance between diversion of carbon to lipid biosynthesis and catabolism of storage reserves to meet energy demands during seed maturation in J. curcas. For example, up regulation of transcripts for glyoxylate cycle specific enzymes like malate synthase and gluconeogenesis related enzymes like fructose 1, 6 bisphosphatase and phosphoenolpyruvate carboxykinase in JC3 suggests a possible breakdown of lipids for energy.…”

“…In J. curcas, volumes of genomic data that include the whole genome (Sato et al 2011) and seed transcriptome information have been generated in the last few years (King et al 2011). A total of 12,084 expressed sequence tags (ESTs), from developing J. curcas seeds were sequenced and they represented genes coding for diverse biological functions (Natarajan et al 2010). Costa et al (2010) reported EST sequencing based identification of genes related to oil accumulation and degradation using developing and germinating seeds of J. curcas.…”

Upgraded genomic information of <i>Jatropha curcas</i> L.

“…Natarajan et al have reported 12,084 ESTs using a normalized cDNA library from developing seeds (Natarajan et al 2010), and Costa et al have reported 13,249 ESTs using non-normalized cDNA libraries from developing and germinating endosperm (Costa et al 2010). In addition to these approaches using the conventional Sanger sequencing method, e orts have been made to accumulate transcriptome data for Jatropha by using a next-generation sequencer.…”

Differential Gene Regulation of Lipid Synthesis in the Developing Seeds of Two Biodiesel Tree Species, Jatropha and Vernicia

“…The transcriptome, proteome and genome of Jatropha seeds have been analyzed to facilitate the understanding of the mechanisms of oil production (Yang et al, 2009;Natarajan et al, 2010;Jiang et al, 2012).…”