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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

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Title 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
 
Creator Ashraf, Nasheeman
Ghai, Deepali
Barman, Pranjan
Basu, Swaraj
Gangisetty, Nagaraju
Mandal, Mihir K
Chakraborty, Niranjan
Datta, Asis
Chakraborty, Subhra
 
Subject chickpea
genotype
transcriptome
sequence tags
plant immunity
stress-responsive
 
Description 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.
 
Date 2013-11-12T09:25:41Z
2013-11-12T09:25:41Z
2009
15 September 2009
 
Type Article
 
Identifier BMC Genomics, 10: 415
http://hdl.handle.net/123456789/104
 
Language en
 
Publisher BioMed Central