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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.

Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G - BMC Plant Biol. (2014)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

ABSTRACT

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.

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The CGWR home page containing an outline of its features and capabilities. Insets depict typical outcomes of BLAST and Mapping and clustering runs showing links to genome browser for visualization of the gene or cluster of interest on the chickpea genome.
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Fig2: The CGWR home page containing an outline of its features and capabilities. Insets depict typical outcomes of BLAST and Mapping and clustering runs showing links to genome browser for visualization of the gene or cluster of interest on the chickpea genome.

Mentions: The Tools menu of CGWR comprises a simple user-friendly GUI that enables rapid scanning and extraction of desired regions of the genome as well as pairwise alignments with user specified sequences, for identification of paralogs and orthologs. Various options are available to users from this pull down menu, including SSR Search, BLAST, CDS, Protein and Keyword Search, as shown in FigureĀ 2.Figure 2


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

Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G - BMC Plant Biol. (2014)

The CGWR home page containing an outline of its features and capabilities. Insets depict typical outcomes of BLAST and Mapping and clustering runs showing links to genome browser for visualization of the gene or cluster of interest on the chickpea genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4307184&req=5

Fig2: The CGWR home page containing an outline of its features and capabilities. Insets depict typical outcomes of BLAST and Mapping and clustering runs showing links to genome browser for visualization of the gene or cluster of interest on the chickpea genome.
Mentions: The Tools menu of CGWR comprises a simple user-friendly GUI that enables rapid scanning and extraction of desired regions of the genome as well as pairwise alignments with user specified sequences, for identification of paralogs and orthologs. Various options are available to users from this pull down menu, including SSR Search, BLAST, CDS, Protein and Keyword Search, as shown in FigureĀ 2.Figure 2

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

ABSTRACT

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.

Show MeSH