BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 we have developed ESTs and stress responsive transcrip- tome of chickpea, as a basis for future transcriptome and proteome comparisons of genetic mutants, pathogen- infected and/or environmentally challenged plants. A total of 6272 high quality ESTs were identified, function- ally annotated, computationally analysed and classified into different functional categories. Of the 2013 Uni- genes, 807 were identified as previously uncharacterized. In addition, we have developed a cDNA based microarray chip and examined the global state of gene expression in the chickpea root during vascular wilt to identify the potential innate immune responsive candidates involved in the complex regulatory network that may function in this organ. These transcriptional signatures often predict previously unknown cellular functions. ESTablished set of pathostress-responsive organ-specific unigenes and the putative differentially expressed genes identified from the present study will provide a foundation for future investi- gation of the expression and function of the genes and proteins to build the interactome map at system level of chickpea and other legumes. In addition, gene mining of these databases, aided by microarray chip, can be used to select candidate genes involved in plant immunity. In the future, it will also be interesting to compare the spatial and temporal transcriptional complexity that underlies organ-specific innate immune response in other multicel- lular organisms. Results Chickpea EST database In an attempt to construct a functional EST dataset for dis- covering subset of genotype dependent, organ specific and extra and intra cellular stimuli responsive genes expressed in chickpea, in this study we have constructed two sup- pression-subtracted cDNA libraries, one from vascular wilt susceptible genotype (JG-62) and the other from resistant genotype (WR-315). The source of RNA for each library was root and collar tissue from the 25-d-old chick- pea seedlings challenged with wilt pathogen, Fusarium oxysporum ciceri race 1, vs control tissue. In total, 6955 ESTs were generated and sequenced from the two libraries out of which 2908 were from susceptible and 4047 from resistant genotypes. Although no chimeric sequence was found but about 9.8% of the sequences were discarded due to low quality of the sequence, short sequence length, Table 2: Sequencing and contigging statistics of chickpea ESTs. Table 1: Chickpea library and EST characterization Sequence reads Failed base calling QC Low quality sequence Short insert sequence No insert E. coli Mitochondrial Total high quality Total 6955 8 214 422 30 0 9 6272 Genotype WR 4047 6 121 246 30 0 1 3643 JG 2908 2 93 176 0 0 8 2629 sequence from other organellar origin or the absence of the insert and the remaining 6272 ESTs were considered for sequence assembly (Table 1). The high quality ESTs that passed the base calling, appropriate length, vector masking and mitochondrial filters were assembled into contigs using CAP3 program [22]. The 6272 high quality sequences had an average read of 366 bp and a cumulative length of 2.29 Mbp. Of the total 6272 ESTs, 1040 were found to be classified as singletons whereas 5232 assem- bled into 973 contigs (Table 2). The additional informa- tion about contigs and singletons is given in additional file 1 and 2 respectively. The redundancy of clones in the contigs ranged from 2 to 230. The total contigs and single- tons comprised a non redundant chickpea unigene (CaU- nigene) set of 2013 different transcripts (see Additional file 3). 3.9% of the unigenes (79) contained more than 10 sequences per contig. Of the total high quality ESTs, 1202 were specific to susceptible genotype whereas 2168 were specific to resistant genotype and 2902 were common to both (Figure 1). The abundance of transcripts, shapes or results in a genotype specific function in response to stim- uli in a given space and time. Absence of chimeras, high percentage of good quality sequences and good average insert size suggested that the libraries were of high quality (Table 1). Functional annotation and classification of chickpea ESTs In order to understand the function of immune-respon- sive ESTs, the entire set of 2013 CaUnigenes were anno- tated on the basis of similarities to the known or putative ESTs in the NCBI database. Using the best hits found by Genotype Total No. of ESTs sequenced Sequencing success per- centagea Good-quality ESTs used for ESTs in contigs EST singletons contiggingb JG-62 2908 WR-315 4047 Total ESTs 6955 90.4 90.0 90.2 2629 3643 6272 2316 2916 5232 313 727 1040 aSequencing success was determined by removing low quality, short insert, no insert and mitochondrial ESTs from the total number of ESTs sequenced. Page 3 of 21 (page number not for citation purposes)