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CTDB: an integrated chickpea transcriptome database for functional and applied genomics

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Title CTDB: an integrated chickpea transcriptome database for functional and applied genomics
 
Creator Verma, Mohit
Kumar, Vinay
Patel, Ravi K.
Garg, Rohini
Jain, Mukesh
 
Subject Chickpea
Chickpea Transcriptome Database
 
Description Accepted date: August 10, 2015
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. The CTDB web service is freely available at http://nipgr.res.in/ctdb.html.
The financial support was received from
the Department of Biotechnology, Government of
India, New Delhi, under the Next Generation
Challenge Program on Chickpea Genomics (grant
number BT/PR12919/AGR/02/676/2009 from 2009-
2014).
 
Date 2016-01-25T12:00:21Z
2016-01-25T12:00:21Z
2015
 
Type Article
 
Identifier PLoS One, 10(8): e0136880
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/589
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136880
10.1371/journal.pone.0136880
 
Language en_US
 
Publisher PLOS