The genus Jatropha of Euphorbiaceae family contains about 175 known species  of which Jatropha curcas L. is the most promising and suitable species for biodiesel production worldwide. Biodiesel is produced by transesterification of the oil to fatty acid methyl esters. Being non-edible crop, use of jatropha oil for biodiesel production does not threaten food security. Its cultivation in degraded soil can control erosion, and help in land reclamation. It is used for manufacturing soap, purgative agents, candles, coloring dyes and astringents . Medicinal properties of jatropha include anti-tumor, anti-microbial, anti-parasitic, and anti-diarrheal activities [3–6].
The oil content of Jatropha which is around 30% could be increased to about 50% in order to make it commercially viable. In terms of oil composition, decreasing the content of unsaturated fatty acids (to increase oxidative stability), free fatty acids (to prevent soap formation and to increase the yield of biodiesel), and 18-carbon fatty acids (to lower the viscosity for better atomization of the biodiesel) would help to improve the quality of jatropha biodiesel. Jatropha oil cake - the by product of oil extraction, is not used as animal feed due to the presence of toxic curcin and phorbol esters. Since it is not economical to remove these compounds, it would be desirable to block their accumulation itself by seed-specific silencing of the relevant genes. This will add economic value to the crop. Large scale cultivation of jatropha also requires the development of varieties that are tolerant to drought, and resistant to pests and diseases.
Genetic engineering methods could play a major role in jatropha crop improvement, because the scope for classical breeding is limited due to longer breeding cycle. Genetic manipulations in jatropha require genomic information and cloning of all the important genes. The genome size of J. curcas is estimated to be 410Mb . The jatropha genome has been fully sequenced by Synthetic Genomics Inc, California, USA but it is not available for public use . Partial genomic sequence of 285.8Mb is available in public databases but it is not assembled and annotated . Natarajan et al., 2010  have reported 12,084 ESTs using a normalized cDNA library from developing seeds, and Costa et al., 2010  have reported 13,249 ESTs using non-normalized cDNA libraries from developing and germinating endosperm. Contig assembly of these ESTs showed the presence of 10,983 unigenes (6,361 from Natarajan et al., 2010  and 4,622 from Costa et al., 2010 ). Recently, Sato et al., 2011  have reported 991,050 pyrosequencing reads from leaf and callus transcriptome which were assembled in to 4,751 contigs. Hybrid assembly of the unigenes and the assembled transcripts revealed the presence of 14,467 unique sequences (10,983 unigenes and 3,484 unique assembled transcripts). This is far below the number of sequences required to represent the whole transcriptome of jatropha. Annotation of the currently available unique sequences showed that several important genes are yet to be cloned.
High throughput 454 pyrosequencing of uncloned cDNAs is a powerful method for whole genome transcriptome analysis and gene discovery. 454 pyrosequencing using GS FLX platform was done in many plants including arabidopsis , artemisia , cucumber , medicago , maize  and barley , and an average read length of 100-200 bases was obtained. Shorter read length was a major problem in assembly, especially in case of de novo assembly of the data from novel organisms, which do not have previously assembled and annotated reference sequences [18, 19]. This limitation has been quickly overcome by using the newly launched titanium platform of GS FLX which increased the average read length to as high as 422 bases . Concurrent improvements in de novo assembly software made it possible to assemble large number of full-length transcripts from novel organisms using 454 pyrosequencing data. Here, we report 454 pyrosequencing of normalized cDNAs from roots, mature leaves, flowers, developing seeds, and mature embryo of J. curcas using GS FLX titanium platform, and report de novo assembly of 17,457 transcripts.