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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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Genome maps of various chickpea gene families. (A) Flavonoids (B) Chickpea-specific gene models (C) DNA Transposons - RC Helitrons (D) R-genes. In each panel, vertical bars represent the eight distinct chickpea pseudomolecules (LGs), while individual members of respective gene families are marked in red horizontal lines on each bar, corresponding to genomic locations.
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Fig3: Genome maps of various chickpea gene families. (A) Flavonoids (B) Chickpea-specific gene models (C) DNA Transposons - RC Helitrons (D) R-genes. In each panel, vertical bars represent the eight distinct chickpea pseudomolecules (LGs), while individual members of respective gene families are marked in red horizontal lines on each bar, corresponding to genomic locations.

Mentions: Of the 640 unique gene models identified to be associated with the metabolism of flavonoids in chickpea, those that could be mapped to the eight distinct pseudomolecules have been depicted in Figure 3A, and the highest number of flavonoid gene models were found clustered on pseudomolecule 3. Such a tendency to cluster was not observed for gene models predicted to be associated with carotenoid metabolism (data available on CGWR website under Maps menu). Each gene or cluster can be analyzed in detail by clicking on the respective bar on the map image. For example, the top three flavonoid genes on LG-3 fall into one cluster that can be clicked to see full details of each member of the cluster, including gene name, functional annotation, gene ontology, TF binding sites, and complete sequence. More information can be noted by clicking the link that connects each gene or cluster to the CGWR genome browser. Our analysis across the entire plant kingdom revealed 9990 legume specific gene models and 2751 chickpea specific gene models in the chickpea genome and panel B of Figure 3 shows the mapped subset of the chickpea specific genes. Further, the putative resistance related gene models (R-genes) as identified through screening of the chickpea unigene set were also mapped and these appear to reside throughout the chickpea genome, although clustering may occur within the specific conserved classes that R-genes were assigned during the analysis (Figure 3D). Almost one third of chickpea genome repeats were identified to be various kinds of transposable elements, a majority of which represented retrotransposons and about 5% constituted DNA transposons. Of the latter group, Figure 3C shows the mapped RC helitrons, i.e. transposons that are thought to replicate by a rolling circle mechanism, and it can be seen that they are interspersed all over the chickpea genome and clustered in a few regions. It is notable that several types of LINEs and other gene families also appear to be clustered on the chickpea genome and it may be interesting to find out whether the clustering occurs in other legume genomes as well. This possibility can be queried within the CGWR by using a combination of the browser and tools menu as described in the following sections.Figure 3


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)

Genome maps of various chickpea gene families. (A) Flavonoids (B) Chickpea-specific gene models (C) DNA Transposons - RC Helitrons (D) R-genes. In each panel, vertical bars represent the eight distinct chickpea pseudomolecules (LGs), while individual members of respective gene families are marked in red horizontal lines on each bar, corresponding to genomic locations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Genome maps of various chickpea gene families. (A) Flavonoids (B) Chickpea-specific gene models (C) DNA Transposons - RC Helitrons (D) R-genes. In each panel, vertical bars represent the eight distinct chickpea pseudomolecules (LGs), while individual members of respective gene families are marked in red horizontal lines on each bar, corresponding to genomic locations.
Mentions: Of the 640 unique gene models identified to be associated with the metabolism of flavonoids in chickpea, those that could be mapped to the eight distinct pseudomolecules have been depicted in Figure 3A, and the highest number of flavonoid gene models were found clustered on pseudomolecule 3. Such a tendency to cluster was not observed for gene models predicted to be associated with carotenoid metabolism (data available on CGWR website under Maps menu). Each gene or cluster can be analyzed in detail by clicking on the respective bar on the map image. For example, the top three flavonoid genes on LG-3 fall into one cluster that can be clicked to see full details of each member of the cluster, including gene name, functional annotation, gene ontology, TF binding sites, and complete sequence. More information can be noted by clicking the link that connects each gene or cluster to the CGWR genome browser. Our analysis across the entire plant kingdom revealed 9990 legume specific gene models and 2751 chickpea specific gene models in the chickpea genome and panel B of Figure 3 shows the mapped subset of the chickpea specific genes. Further, the putative resistance related gene models (R-genes) as identified through screening of the chickpea unigene set were also mapped and these appear to reside throughout the chickpea genome, although clustering may occur within the specific conserved classes that R-genes were assigned during the analysis (Figure 3D). Almost one third of chickpea genome repeats were identified to be various kinds of transposable elements, a majority of which represented retrotransposons and about 5% constituted DNA transposons. Of the latter group, Figure 3C shows the mapped RC helitrons, i.e. transposons that are thought to replicate by a rolling circle mechanism, and it can be seen that they are interspersed all over the chickpea genome and clustered in a few regions. It is notable that several types of LINEs and other gene families also appear to be clustered on the chickpea genome and it may be interesting to find out whether the clustering occurs in other legume genomes as well. This possibility can be queried within the CGWR by using a combination of the browser and tools menu as described in the following sections.Figure 3

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