Natarajan et al. BMC Genomics 2010, 11:606 http://www.biomedcentral.com/1471-2164/11/606 Page 6 of 14 Figure 3 Phylogenetic analysis. Phylogenetic trees were generated using the DNA sequences coding for (a) beta-keto acyl ACP synthase II, (b) omega-3-fatty acid desaturase, and (c) beta-keto acyl ACP synthase I from J. curcas, R. communis, G.max, A. hypogaea, B. napus, H. annuus and V. vinifera. Clone IDs (for J. curcas) and Genbank accession numbers were given in the parentheses. When enzymes for glycine betaine biosynthesis are expressed in plants that do not naturally produce glycine betaine, they accumulate little glycine betaine, because their endogenous choline supply is inadequate [49,50]. These plants may require overexpression of phos- phoethanolamine N-methyltransferase to overproduce choline. Overexpression of Na+/H+ antiporter from Pen- nisetum glaucum conferred high level of salinity toler- ance in transgenic Brassica [51] and overexpression of E. coli trehalose-6-phosphate synthase gene conferred drought and salt tolerance in rice [52]. The stress related unigenes identified in the current study include the genes coding for phosphoethanolamine N-methyltransferase, Na+/H+ antiporter, trehalose-6-phosphate synthase, glu- tathione peroxidase, glutathione s-transferase, spermidine synthase, ethylene-responsive transcription factors, ascor- bate peroxidase, late embryogenesis abundant proteins, aquaporin, and salt tolerance protein. The genes that code for the enzymes involved in differ- ent metabolic pathways are very important for genetic manipulation in jatropha. Several genes involved in diverse metabolic pathways such as phospholipids bio- synthesis, flavanol synthesis, glycolysis, TCA cycle, HMP shunt, glycogenesis were identified from the current study. Other important genes identified from this study are ferritin, mevalonate kinase, lipoxygenase, glutamate decarboxylase, ent-kaurenoic acid oxidase, cinnamoyl- CoA reductase, zeta-carotene desaturase, gibberellin 2-oxidase, lipoic acid synthetase and beta-carotene hydro- xylase. The unigenes also included 208 gene families with 3 or more genes. There were 15 families with more than 10 genes and a highest number of 46 members were identified in serine-threonine kinase gene family. Other gene families included glucan endo-1,3-beta-glucosidase precursor, aspartic proteinase nepenthesin-1 precursor, calmodulin binding protein, F-Box family protein, WD- repeat protein, pentatricopeptide repeat-containing pro- tein, cytochrome P450 etc. Genes with unknown functions BLASTX results showed that 40.4% of J. curcas unigenes (2836) are having significant similarity with genes that code for unknown, hypothetical and putative proteins. This is significantly higher than 13 to 25% unknown genes reported in arabidopsis, citrus and oil palm [12,53,54]. It was found that 2.8% of J. curcas unigenes