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The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes

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Title The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
 
Creator Misra, Gopal
Priya, Piyush
Bandhiwal, Nitesh
Bareja, Neha
Jain, Mukesh
Bhatia, Sabhyata
Chattopadhyay, Debasis
Tyagi, Akhilesh K.
Yadav, Gitanjali
 
Subject Cicer arietinum ICC4958
Clustering
Comparative genomics
Genome browser
Mapping
 
Description Accepted date: 30 October 2014
Background: Availability of the draft nuclear genome sequences of small-seeded desi-type legume crop Cicer
arietinum has provided an opportunity for investigating unique chickpea genomic features and evaluation of
their biological significance. The increasing number of legume genome sequences also presents a challenge for
developing reliable and information-driven bioinformatics applications suitable for comparative exploration of this
important class of crop plants.
Results: The Chickpea Genomic Web Resource (CGWR) is an implementation of a suite of web-based applications
dedicated to chickpea genome visualization and comparative analysis, based on next generation sequencing and
assembly of Cicer arietinum desi-type genotype ICC4958. CGWR has been designed and configured for mapping,
scanning and browsing the significant chickpea genomic features in view of the important existing and potential
roles played by the various legume genome projects in mutant mapping and cloning. It also enables comparative
informatics of ICC4958 DNA sequence analysis with other wild and cultivated genotypes of chickpea, various other
leguminous species as well as several non-leguminous model plants, to enable investigations into evolutionary
processes that shape legume genomes.
Conclusions: CGWR is an online database offering a comprehensive visual and functional genomic analysis of the
chickpea genome, along with customized maps and gene-clustering options. It is also the only plant based web
resource supporting display and analysis of nucleosome positioning patterns in the genome. The usefulness of
CGWR has been demonstrated with discoveries of biological significance made using this server. The CGWR is
compatible with all available operating systems and browsers, and is available freely under the open source
license at http://www.nipgr.res.in/CGWR/home.php.
The CGWR has been developed under the Next Generation Challenge
Program on chickpea genomics (NGCP) funded by the Dept. of
Biotechnology (DBT) of the Govt. of India (Grant No. BT/PR12919/AGR/02/
676/2009). GM and PP were recipients of the senior research fellowship (SRF)
of the DBT, Govt. of India and the CSIR, Govt. of India, respectively, during
the period of work. GY is a recipient of Women’s Excellence Award by
Scientific and Educational Research Board (SERB), Dept. of Science and
Technology (DST), Govt of India. Facilities provided under the Biotechnology
Information System Network (BTISNET) grant of the NIPGR Sub-Distributed
Information center (Sub-DIC) of the DBT, Govt. of India, are gratefully
acknowledged (Grant No. BT/BI/04/069/2006). Useful inputs and ideological
contributions from the members of the CGWR user committee are also
gratefully acknowledged.
 
Date 2015-12-18T06:34:59Z
2015-12-18T06:34:59Z
2014
 
Type Article
 
Identifier BMC Plant Biol., 14: 315
1471-2229
http://172.16.0.77:8080/jspui/handle/123456789/432
http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0315-2
10.1186/s12870-014-0315-2
 
Language en_US
 
Publisher BioMed Central Ltd