Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity

We report 6272 gene sequences of immune-response pathway that would provide genotype-dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of a CaUnigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non-cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome.Our study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis of CaEST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt.Living cells have evolved to perceive and integrate different 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 intergenomic comparisons, gene discovery, generation of single nucleotide polymorphisms (SNPs), cloning of genes from MStag peptide sequences, transcript pattern characterization, identifying splice variants, erroneous annotatio