Comprehensive Functional Analyses of Expressed Sequence Tags (ESTs) in Jatropha curcas L.

Jatropha (Jatrohpa curcas L.) is an economically important plant with great potential for biodiesel and jet fuel production because its seeds contain high quality oil. However, jatropha remains a wild plant since it has not yet undergone a systematic selection and breeding program. The availability of genetic and genomic information of jatropha is very limited. Genomic resources are important foundations for gene discovery and marker development, which can assist and accelerate jatropha breeding programs through genetic diversity analysis, marker-assistant selection, and other approaches. Expressed sequence tags (ESTs), providing informative transcript sequences, is a fast way for gene discovery and gene expression pattern analysis. To date, only a small portion of about 40,000 predicted genes have been identified. The objectives of this study were: 1) to study the jatropha transcriptome and the transcript sequence feature in depth by enriching the jatropha EST database utilizing next generation sequencing technology; 2) to identify the abundant transcripts of mature jatropha leaves; and 3) to discover the transcript sequence variance. The mRNA sample of mature jatropha leaves was sequenced using 454 Roche GS FLX platform. A total of 1,714,433 raw reads were generated. After trimming the adaptors and primers, the sequences were assembled into 38,716 contigs and 58,317 singletons using a combination of Newbler 2.8 and CAP3. The average length of contigs and singletons are 1,147 and 399 bases, respectively. A total of 96,677 unigenes were obtained after removing short sequences (< 20bp). About 73.5% of unigenes were annotated using blast tools (e-value ≤ E-06). This unigene set will be compared to the nucleotide and amino acid sequences of Arabidopsis thaliana, cassava (Manihot esculenta) and castor oil plant (Ricinus communis) for similarity comparison. Some sequence features and allele variance will be identified. This unigene set will significantly enrich the current jatropha EST database by adding a large amount of new ESTs to Genbank. Together, this study will not only allow the identification of new unigenes in jatropha, but also provide additional marker resources to be used in breeding programs.