Verma, M. and Kumar, V. and Patel, R.K. and Garg, R. and Jain, M.
(2015)
CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics.
PLOS ONE, 10 (8).
pp. 1-10.
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Abstract
Chickpea is an important grain legume used as a rich source of protein in human diet. The
narrow genetic diversity and limited availability of genomic resources are the major constraints
in implementing breeding strategies and biotechnological interventions for genetic
enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database
(CTDB), which provides the comprehensive web interface for visualization and easy
retrieval of transcriptome data in chickpea. The database features many tools for similarity
search, functional annotation (putative function, PFAM domain and gene ontology) search
and comparative gene expression analysis. The current release of CTDB (v2.0) hosts transcriptome
datasets with high quality functional annotation from cultivated (desi and kabuli
types) and wild chickpea. A catalog of transcription factor families and their expression profiles
in chickpea are available in the database. The gene expression data have been integrated
to study the expression profiles of chickpea transcripts in major tissues/organs and
various stages of flower development. The utilities, such as similarity search, ortholog identification
and comparative gene expression have also been implemented in the database to
facilitate comparative genomic studies among different legumes and Arabidopsis. Furthermore,
the CTDB represents a resource for the discovery of functional molecular markers
(microsatellites and single nucleotide polymorphisms) between different chickpea types.
We anticipate that integrated information content of this database will accelerate the functional
and applied genomic research for improvement of chickpea.
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