BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 Background Living cells have evolved to perceive and integrate differ- ent signals from their surroundings and to respond by modulating the appropriate gene expression. Expressed sequence tags (ESTs) provide an invaluable resource for analysis of gene expression associated with specific organs, growth conditions, developmental processes and responses to various environmental stresses [1-3]. It bridges the gap between the genome sequences and gene function. ESTs have been useful for intra- and interge- nomic comparisons, gene discovery, generation of single nucleotide polymorphisms (SNPs), cloning of genes from MStag peptide sequences, transcript pattern characteriza- tion, identifying splice variants, erroneous annotations in the genome database and incomplete prediction of gene structure [4,5]. Further, the transcriptome of cells and organs comprise a focused set of transcripts that fulfills discrete but varied cellular functions. The analyses of organ specific transcriptome provide additional informa- tion about localization of gene function and pathway compartmentalization. Whereas the transcriptome research is quite advanced in animals, yeast, bacteria and reference plants like Arabidopsis and rice [6-10] there is relatively less information in crop plants. Legumes are valuable agricultural and commercial crops that serve as important nutrient sources for human diet and animal feed. About one third of human nutrition comes from legumes and in many developing countries, legumes serve as the only source of protein. Many second- ary metabolites in legumes have been implicated in defense and are of particular interest as novel pharmaceu- ticals [11]. Five tribes constitute the family fabaceae, of which one representative genus each from four tribes have been used to generate ESTs [4,12,13]. However, the tribe ciceri having a single genus Cicer, remained as the under- studied legume. Chickpea, the most important member of the genus Cicer, represents the world's third important pulse crop. It is grown on about 10 mha area worldwide and the global production exceeds 8 million tons [14]. In many water-deficient regions of the world, it serves as an important protein-rich food and an increasingly valuable traded commodity. Chickpea has one of the highest nutri- tional compositions of edible legume and does not con- tain any specific major anti-nutritional factor, rather it is used in herbal medicine. Despite the importance of chick- pea in the study of plant evolution, its role in nutritional requirement in humans, and stress adaptation, nothing is known about the genes responsible for these traits-prima- rily because it is recalcitrant to genetic analysis. Unlike genetically tractable plants such as tomato, maize and Arabidopsis, chickpea produces a limited number of seeds. Furthermore, its genome is large (732 Mbp) as compared to Arabidopsis (125 Mbp). Consequently, chickpea has remained outside the realm of both modern genome- sequencing initiatives and large scale functional genomics studies. Currently available completely annotated plant genome sequences make it possible to study the genomes of agriculturally important genetically complex crop plants such as chickpea by comparing the ESTs derived from them. Only very recently, attention has been given from both genomics and proteomics perspect to this important food legume [15-19]. Because of its evolution- ary position as a key node within legumes as well as its nutritional and medicinal significance to humans, chick- pea is ideally suited for genomic prospecting. Transcriptional programs that regulate development and stress response are exquisitely controlled in space and time. Elucidating these programs that underlie develop- ment is essential to understand the acquisition of cell and tissue identity. Root in higher plants is a highly organized structure that plays a key role in nutrient acquisition and water uptake besides its primary function of mechanical support to the plant. Nevertheless, it is essentially the entry point for the soil borne pathogens into the plant body. Of the soil borne root pathogen, vascular wilt is the most important disease. Vascular wilt caused by Fusarium is ubiquitous evolutionarily and effects crop plants across families. In particular, chickpea wilt, is widespread in occurrence and on an average causes substantial loss of 10 to 15% in production every year worldwide. During the infection process the fungus invades roots and spreads systemically through the host's vascular system, breaking down the cell walls to form gels that block the plant's transport system thereby causing yellowing and wilting symptoms. In general, the wilt symptoms appear as chlo- rotic spots on the lower leaves followed by discoloration and necrosis. Vascular discoloration occurs from the roots to the young stems, followed by a yellowing and wilting of the leaves before final necrosis [20]. When uprooted the stem is split vertically and internal discoloration is vis- ible in pith and xylem [21]. The susceptible genotypes take less than 25 days for wilting whereas the resistant ones do not show any symptoms of wilting upto 60 days. In the present study, two genotypes JG-62 and WR-315 were used which are known to be susceptible and resistant to Fusarium wilt, respectively. The localization of the fun- gus was limited in the resistant cultivar while extensive colonization occurs in susceptible one by fourth to fifth day post infection. Externally the extent of mycelial colo- nization is manifested in the form of browning of the roots after 72 hours in the susceptible genotype while no such discoloration is evident in the resistant one. To understand the regulatory networks and metabolic pathways governing genotype-specific cellular responses towards different signals, we have initiated ESTablishing CaUnigene dataset and a genome-wide analysis of gene expression in this food legume. As a first step towards this, Page 2 of 21 (page number not for citation purposes)