Natarajan et al. BMC Genomics 2010, 11:606 http://www.biomedcentral.com/1471-2164/11/606 Page 4 of 14 Figure 2 Distributions of ESTs in Contigs. Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig. Annotation of Unigenes In total, 3982 unigenes (56.8%) showing significant simi- larity with genes available in the non-redundant data- base were identified. Most of these unigenes showed highest similarity with genes from castor (Ricinus com- munis). This is expected because jatropha itself is called ‘wild’ castor and both species belong to the family Euphorbiaceae. Next to castor, most of the unigenes showed similarity with genes from grape (Vitis vinifera) that belongs to the family Vitaceae. Phylogenetic analy- sis using 10 selected ESTs by including orthologs from five oilseed crops and V. vinifera also revealed that J. curcas is closely related to R. communis followed by V. vinifera (Figure 3, data shown for 3 genes). This asso- ciation is totally unexpected according to the morpholo- gical system of classification [33] in which Jatropha belongs to monochlamideae whereas Vitis belongs to polypetalae. However, more recent Angiosperm Phylo- geny Group Classifications, APGII and APGIII [34,35], which are based on cladistic analysis of larger data sets involving DNA sequences or other forms of systematic data show many contradictory relationships [36]. According to these classifications, the malpighiales (Euphorbiaceae) and Vitales (Vitaceae) are placed much closer under a major core eudicots clade, Rosids. Our data based on coding genes corroborate the APG classi- fication with regard to Jatropha and Vitis. Genes for oil biosynthesis and b-oxidation Recently jatropha seed oil is widely used for biodiesel production as an alternative renewable energy source. It is important to undertake genetic improvement of this crop to increase oil content, to modify the oil composi- tion, to remove toxic compounds, to increase drought tolerance etc. Seed oil content in brassica and arabidop- sis has been increased by the overexpression of diacyl glycerol acyl transferase, lysophosphatidic acid acyltrans- ferase, and glycerol-3-phosphate acyltransferase [37-39]. Seed oil composition has been changed in soybean by using mutant 3-Keto-acyl-ACP synthase II gene which increases the 16-carbon fatty acids and decreases 18- carbon fatty acids [40]. Silencing of stearoyl-ACP desa- turase has dramatically increased the content of satu- rated fatty acid (stearic acid) from 1.2% to 32% in brassica [41]. Therefore, it is possible that increased oil content and specialized seed oil composition can be achieved in jatropha also, provided the genes involved in rate limiting steps of oil biosynthesis pathway are cloned. Important oil biosynthesis genes identified in the present study include the genes involved in fatty acid biosynthesis in plastids (carboxyl transferase of ACCase b subunit, biotin carboxyl carrier protein of ACCase, malonyl-CoA:ACP transacylase, 3-keto acyl ACP reductase, beta-keto acyl ACP synthase I, beta- keto acyl ACP synthase II and acyl carrier protein), desaturation of fatty acids (ω-3-fatty acid desaturase and ω-6-fatty acid desaturase), hydrolysis of fatty acids from acyl-ACP (acyl ACP thioesterase A), activation and transport of free fatty acids to endoplasmic reticulum (long chain acyl-CoA synthetase, acyl -CoA binding protein) and serial incorporation of activated fatty acids to the glycerol backbone to form triacylglycerol or oil (glycerol-3-phosphate acyl transferase, lysophosphatidic acid acyl transferase). Some of these genes are being