BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 Table 3: Comparative matching of CaESTs to the ESTs of other legume databases. Gene indices Identity >80% Identity>90% Arachis hypogea Cajanus cajan Pisum sativum Robinia pseudoacacia Lotus japonicus Medicago trunculata Glycine max phaseolus vulgaris 1686 (83.75) 1764 (87.6) 1788 (88.8) 245 (12.17) 872 (43.31) 1168 (58.02) 1617 (80.32) 928 (46.10) 1118 (55.54) 1729 (85.89) 1599 (79.43) 79 (3.92) 287 (14.25) 614 (30.50) 635 (31.54) 234 (11.62) The chickpea ESTs isolated in this study were compared to other legume databases like Arachis hypogea, Cajanus cajan, Pisum sativua, Robinia psedoacacia, Lotus japonicus, Medicago trunculata, Glycine max and Phaseolus vulgaris collected from NCBI and TIGR gene indices. The criteria for stand alone BLASTN were (1) exact match = 11; (2) e-value cutoff 1e-5; and (3) identity > 80% and 90% at DNA sequence level. CaUnigenes with the earlier reported ESTs of chickpea. TBLASTX with e-value cutoff of 10-10 showed that 532 uni- genes from the CaUnigene set of 2013 had a significant match, while the remaining 1483 did not have any coun- terpart. Thus, 73.67% of our CaUnigenes represent new chickpea genes yet unidentified. Full length sequencing of these unigenes and their expression analyses may provide further insight into the species-specific functions of these genes. Comparative stress responsive transcriptome reveals canonical and non-canonical genes Although a number of studies have catalogued stress- responsive genes against different environmental condi- tions into various functional classes, comparative genom- ics of stress-responsive transcriptome is still lacking. To investigate the comparative biology of stress-responsive transcriptome at organismal level with the currently avail- able data, we compared the CaUnigenes with previously reported stress-responsive genes from other organisms. We classified genes known to be involved in multi-stress responses as ubiquitous, while those found to be specific to Fusarium infection were categorized as canonical. All other genes, which have never been implicated in any stress, were designated as noncanonical (Figure 3A). We found that around 516 genes are ubiquitous, suggesting broad similarities in stress responses across most of the organisms and confirming cross communicating path- ways playing role in different kinds of stresses. However, only 41 genes were found to be canonical all of which showed an overlap with ubiquitous class. A significantly large number of genes (649) were found to be noncanon- ical. This difference in the pattern of immune-responsive root transcriptome may be attributed to the fact that the gene expression in an organism is shaped by the cellular environment and the epigenetic factors. Metabolism was FCwioigtmhurpeear3laiteirveknaonawlynsisstroefscshrieclkapteda sgterneess responsive genes Comparative analysis of chickpea stress responsive genes with earlier known stress related genes. (A) Venn represents the overlap between ubiquitous, canonical and non canonical genes and the numbers signify unique and common stress responsive genes. (B) Expression pattern and prevalence of functional classes within the three groups. Each bar represents the number of genes in the respective func- tional class. one of the most abundant functional class in all the three groups (Figure 3B), suggesting that any stress response results in the alteration of the metabolic pathways of an organism. A few of the metabolic enzymes found to be expressed in response to multiple stresses represented in the ubiquitous category included S-adenosylmethionine decarboxylase, glyceraldehyde 3-phosphate dehydroge- nase, methionine sulfoxide reductase, and copper amine oxidase [38,73-75]. Cell signaling related genes also formed an important class that included leucine-rich repeat receptor-like kinase and multiple bridging factor among others [76,77]. As expected, many canonical genes belonged to functional class of cellular redox, defense and signaling; included Cationic peroxidase 2, chitinase and 14-3-3 protein [78]. Our data on immune responsive tran- scriptome and comparative analysis thereof provide evi- dence for molecular diversity vs. commonality in gene expression profile at organismal level. The comparative Page 9 of 21 (page number not for citation purposes)