De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

Abstract

BackgroundJatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas.ResultsFrom 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs) and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis.ConclusionThe large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil biosynthesis could be used for metabolic engineering of jatropha to increase oil content, and to modify oil composition.

Proteomic analysis of oil bodies in mature Jatropha curcas seeds with different lipid content

“…Compared with other oil seed plant, the lipid content in J. curcas seeds is as high as 36% [25]; moreover, lipids from J. curcas are more suitable for biodiesel due to its fuel rate [26]. With the development of high throughout sequence technology, J. curcas has been studied at the genomic and transcriptomic level to unveil the genes with important roles involved in multi-metabolic networks [27][28][29][30]. These databases are valuable for further identification of OB associated protein species from J. curcas seeds.…”

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

“…Sato et al [15] sequenced whole genome as well as cDNAs from callus and leaf tissues and generated a total of 21,225 unigenes. Natarajan and Parani [17] reported 14,327 new assembled transcripts with 2,589 full-length cDNA and 27 transcripts directly involved in oil biosynthesis. Subsequently, Eswaran et al [18] reported 1,240 ESTs generated from root cDNA libraries of jatropha grown at different drought conditions.…”

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

“…Since the generated reads can assemble without a reference genome, it is also an ideal tool for transcriptome sequencing for those species without a sequenced genome [17]. Recently, RNA-Seq has been used to analyze the transcriptomic profiles of oil accumulation in oil plants such as Jatropha ( Jatropha curcas ) [18], oil tea ( Camellia oleifera ) [19], oil palm ( Elaeis guineensis ) [20], peanut ( Arachis hypogaea ) [21], rapeseed ( Brassica napus ) [22], and sesame ( Sesamum indicum ) [23]. However, the functional genes involved in the oil biosynthesis and metabolism of S. paniculata are not yet to be investigated.…”