BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 ability to enforce successful defenses against invading pathogens. In this study, several genes were identified that are associated with biosynthesis of secondary metabolites. The important enzymes in this category include phenyl ammonia lyase (PAL), chalcone synthase, chalcone iso- merase, and chalcone-flavonone isomerase-1 which were found in both compatible and incompatible interactions. These enzymes are known to modulate plant defense response against invading pathogens and insects [63,64]. Some of the secondary metabolism related genes, for example, squalene epoxidase was found to be specific to susceptible genotype whereas pterocarpan reductase and oxysterol-binding family protein were specific to the resistant one. Other members of this class are caffeic acid O-methyltransferase II, isoflavone 3'-hydroxylase, squalene monooxygenase 2, trans-cinnamate 4-monoox- ygenase and dihydroflavonol reductase. Earlier studies have shown that transgenic rice plants overexpressing dihydroflavonol reductase can provide tolerance to biotic and abiotic stresses [65]. Caffeic acid O-methyltransferase catalyzes a key step in lignin biosynthesis [66], thereby giving protection against pathogen attack. Defense and stress responsive genes Pathogen attack is often accompanied by the accumula- tion of elevated levels of transcripts of disease related pro- teins, the PR genes. The ESTs encoding proteins implicated in stress and defense responses account for 3.18% of the total unigene set. Most dominant candidates among the defense responsive genes were disease resist- ance response protein DRRG49C and PR10. Other genes identified include those encoding chitinase, non-specific lipid transfer proteins, thaumatin and pathogenesis- related protein. The involvement of these proteins in plant defense responses is well known [67]. One of the important observations was that DRRG49C, thaumatin and pathogenesis-related protein were expressed only during incompatible interaction which may lead to increased tolerance to pathogen attack. Also, we found the presence of ESTs encoding proteins like dirigent and harpin-induced 1 in the resistant genotype, implying their role in pathostress response. Dirigent protein has recently been shown to be involved in lignification and hence imparting disease resistance [68]. Many other stress induced proteins, for example, extensin, universal stress proteins, aquaporin, annexin, cold acclimation respon- sive protein BudCAR4 and metallothionien were also identified as more abundant in the resistant genotype implicating their involvement in pathostress response besides their key role in abiotic and other stresses [69,70]. Comparison with other legume genome and EST databases To investigate how many of the chickpea ESTs from this study are highly orthologous to other legume ESTs, we performed a comparative analysis of our CaEST dataset to publicly available dataset comprising ESTs from Arachis hypogea, Cajanus cajan, Pisum sativum, Robinia pseudoaca- cia, Lotus japonicus, Medicago trunculata, Glycine max and Phaseolus vulgaris. Except Phaseolus and Robinia, these data- bases were inclusive of root ESTs. The highest number of common orthologous ESTs was found to be present in Pisum sativum, although, Cajanus cajan and Arachis hypogea also showed higher similarity with CaUnigenes. The per- centage of chickpea ESTs that matched to Pisum sativum was 88.8% and 79.43% at DNA sequence identity of  80% and 90%, respectively. A total of 87.6% and 83% Cajanus cajan ESTs and 85.89% and 55.54% of Arachis ESTS were common with CaUnigenes. Chickpea and Pisum show close phylogenetic affliations, both being representatives of galegoid, a group of cool season leg- umes [71] and is reflected in their sequence similarities. However, high sequence similarity with Arachis and Caja- nus came as a surprise since these legumes are phylogenet- ically distant relatives of Cicer and belong to tropical season legumes (phaseoloid). The comparative analysis of chickpea ESTs with that of Glycine max showed homology of 80.32% and 31.54%. Interestingly, Medicago and Lotus showed more divergent trend with only 58.02% and 30.50% and 43.31% and 14.25% ESTs respectively, hav- ing counterpart in CaUnigene set. A recent phylogenetic study based on penalized likelihood analysis [72] indi- cated that Medicago, Lotus and Cicer are closer and fall in the same galegoid clade, however, the divergence/differ- ence in the pattern of ESTs may be attributed to the fact that gene expression is shaped by cellular environment besides ecological niche of the corresponding organism. Chickpea ESTs showed lesser homology with Robinia pseu- doacacia and was about 12% and 3.92% at DNA sequence identity of 80% and 90%, respectively. This can be due to the fact that Robinia is a perennial tree while chickpea is an annual herb. Detailed comparative analysis of ESTs is shown in Table 3. Thus the current study documents sub- stantial conservation as well as genome divergence amongst legume crops and in future can facilitate cross species analysis of gene function. Identification of chickpea specific transcripts and enrichment of CaEST In an attempt to identify the genotype-specific transcript signatures in chickpea, we performed a blast analysis of CaUnigene. Of the total 2013 CaUnigenes, about 18.22% sequences that belong to NSH group represented poten- tial chickpea specific sequences. To verify whether these sequences were indeed chickpea specific, TBLASTX was used for comparing them to the EST_others database. Nearly 64% of the NSH class of CaEST dataset did not show any significant match thereby confirming that these ESTs represent unique chickpea sequences. Thus this data- set represents 234 novel chickpea specific ESTs, which were never reported earlier. Further, we compared our Page 8 of 21 (page number not for citation purposes)