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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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Related in: MedlinePlus

Typical display of the chickpea genome browser in the region of the first LG. Four main areas can be seen on the top left side of the upper panel panel, namely, Search, Overview, Region and Details. The topmost ‘Search’ section identifies the exact genomic range displayed in the browser (see ‘Landmark’ textbox on top left corner). The area highlighted in sky-blue shades in both of next two sections, namely, ‘Overview’ and ‘Region’, is expanded in the remaining browser view. Accordingly, the current example (‘Details’ section) represents a 10 kbp stretch within 3 Mbp region of CA LG 1. The 3 Mbp region has about 11 gene models (see yellow bands in ‘Region’ Section), of which only two lie within the expanded Details section (see yellow bands in Annotation track). Annotation of the gene models can be seen by clicking the annotation bands in the expanded section, in the form of a pop-up box, as shown here. In this image, seven genomic tracks have been toggled on, including retrotransposons, nucleosome states, and the transcriptome. Users can select additional tracks from over forty-eight options in the present CGWR build, as shown in the lower left panel.
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Fig5: Typical display of the chickpea genome browser in the region of the first LG. Four main areas can be seen on the top left side of the upper panel panel, namely, Search, Overview, Region and Details. The topmost ‘Search’ section identifies the exact genomic range displayed in the browser (see ‘Landmark’ textbox on top left corner). The area highlighted in sky-blue shades in both of next two sections, namely, ‘Overview’ and ‘Region’, is expanded in the remaining browser view. Accordingly, the current example (‘Details’ section) represents a 10 kbp stretch within 3 Mbp region of CA LG 1. The 3 Mbp region has about 11 gene models (see yellow bands in ‘Region’ Section), of which only two lie within the expanded Details section (see yellow bands in Annotation track). Annotation of the gene models can be seen by clicking the annotation bands in the expanded section, in the form of a pop-up box, as shown here. In this image, seven genomic tracks have been toggled on, including retrotransposons, nucleosome states, and the transcriptome. Users can select additional tracks from over forty-eight options in the present CGWR build, as shown in the lower left panel.

Mentions: The genome browser is one of the primary capabilities of the CGWR. Currently, the May 2013 assembly is available; the next freeze of the assembly will be made accessible as soon as it is released, in the near future. Figure 5 shows the default browser display i.e. the first 10 kbp data on the first Chickpea pseudomolecule LG1, although users can select any of the eight LGs from the pull-down list in the Data Source, and positional information can also be typed into the landmark or position box on the top left corner, e.g., Ca_LG_1 for the whole of chromosome 1 and Ca_LG_2:1..10,000 for the region from position 1 to 10,000 on chromosome 2. The region expanded in the browser will be highlighted in pale blue in the Overview section as shown in Figure 5. For the unassembled scaffolds, users can select Ca_LG_0 from the pull down data source list in the Search section, and type the name and position of the desired scaffold. Zooming and scrolling controls help to narrow or broaden the displayed chromosomal range to focus on the exact region of interest. Default browser display can be altered as desired by using track controls offered at the bottom of the browser enabled through the ‘configure tracks’ button, where about fifty different tracks are available to choose from, as shown in Figure 5.Figure 5


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)

Typical display of the chickpea genome browser in the region of the first LG. Four main areas can be seen on the top left side of the upper panel panel, namely, Search, Overview, Region and Details. The topmost ‘Search’ section identifies the exact genomic range displayed in the browser (see ‘Landmark’ textbox on top left corner). The area highlighted in sky-blue shades in both of next two sections, namely, ‘Overview’ and ‘Region’, is expanded in the remaining browser view. Accordingly, the current example (‘Details’ section) represents a 10 kbp stretch within 3 Mbp region of CA LG 1. The 3 Mbp region has about 11 gene models (see yellow bands in ‘Region’ Section), of which only two lie within the expanded Details section (see yellow bands in Annotation track). Annotation of the gene models can be seen by clicking the annotation bands in the expanded section, in the form of a pop-up box, as shown here. In this image, seven genomic tracks have been toggled on, including retrotransposons, nucleosome states, and the transcriptome. Users can select additional tracks from over forty-eight options in the present CGWR build, as shown in the lower left panel.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Typical display of the chickpea genome browser in the region of the first LG. Four main areas can be seen on the top left side of the upper panel panel, namely, Search, Overview, Region and Details. The topmost ‘Search’ section identifies the exact genomic range displayed in the browser (see ‘Landmark’ textbox on top left corner). The area highlighted in sky-blue shades in both of next two sections, namely, ‘Overview’ and ‘Region’, is expanded in the remaining browser view. Accordingly, the current example (‘Details’ section) represents a 10 kbp stretch within 3 Mbp region of CA LG 1. The 3 Mbp region has about 11 gene models (see yellow bands in ‘Region’ Section), of which only two lie within the expanded Details section (see yellow bands in Annotation track). Annotation of the gene models can be seen by clicking the annotation bands in the expanded section, in the form of a pop-up box, as shown here. In this image, seven genomic tracks have been toggled on, including retrotransposons, nucleosome states, and the transcriptome. Users can select additional tracks from over forty-eight options in the present CGWR build, as shown in the lower left panel.
Mentions: The genome browser is one of the primary capabilities of the CGWR. Currently, the May 2013 assembly is available; the next freeze of the assembly will be made accessible as soon as it is released, in the near future. Figure 5 shows the default browser display i.e. the first 10 kbp data on the first Chickpea pseudomolecule LG1, although users can select any of the eight LGs from the pull-down list in the Data Source, and positional information can also be typed into the landmark or position box on the top left corner, e.g., Ca_LG_1 for the whole of chromosome 1 and Ca_LG_2:1..10,000 for the region from position 1 to 10,000 on chromosome 2. The region expanded in the browser will be highlighted in pale blue in the Overview section as shown in Figure 5. For the unassembled scaffolds, users can select Ca_LG_0 from the pull down data source list in the Search section, and type the name and position of the desired scaffold. Zooming and scrolling controls help to narrow or broaden the displayed chromosomal range to focus on the exact region of interest. Default browser display can be altered as desired by using track controls offered at the bottom of the browser enabled through the ‘configure tracks’ button, where about fifty different tracks are available to choose from, as shown in Figure 5.Figure 5

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
Related in: MedlinePlus