BMC Genomics Research article 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 Nasheeman Ashraf, Deepali Ghai, Pranjan Barman, Swaraj Basu, Nagaraju Gangisetty, Mihir K Mandal, Niranjan Chakraborty, Asis Datta and Subhra Chakraborty* BioMed Central Open Access Address: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India Email: Nasheeman Ashraf - nasheemanashraf9@gmail.com; Deepali Ghai - deepalighai@yahoo.com; Pranjan Barman - pranjan.barman@rediffmail.com; Swaraj Basu - basu_swaraj@rediffmail.com; Nagaraju Gangisetty - gnraju_gn@rediffmail.com; Mihir K Mandal - mkm96@rediffmail.com; Niranjan Chakraborty - nchakraborty@hotmail.com; Asis Datta - asisdatta@hotmail.com; Subhra Chakraborty* - subhrac@hotmail.com * Corresponding author Published: 5 September 2009 BMC Genomics 2009, 10:415 doi:10.1186/1471-2164-10-415 This article is available from: http://www.biomedcentral.com/1471-2164/10/415 Received: 11 February 2009 Accepted: 5 September 2009 © 2009 Ashraf et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses on Fusarium wilt responsive gene expression in chickpea. Results: 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. Conclusion: 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. Page 1 of 21 (page number not for citation purposes)