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SyMAP v3.4: a turnkey synteny system with application to plant genomes.

Soderlund C, Bomhoff M, Nelson WM - Nucleic Acids Res. (2011)

Bottom Line: These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice.The software may be used from a website or standalone for the best performance.A project manager is provided to organize and automate the analysis of multi-genome groups.

View Article: PubMed Central - PubMed

Affiliation: BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA. cari@agcol.arizona.edu

ABSTRACT
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.

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Related in: MedlinePlus

SyMAP multiple genome dot plot. The reference chromosomes are listed across the top. Synteny blocks are outlined in blue and the dots are anchors. Each cell represents a comparison between the two respective chromosomes, e.g. cell (1,3) represents the comparison between rice-1 and maize-3. Anchor chains that slope from lower left to upper right represent inversions. The Filters button brings up a menu of filters that can be applied; for this example, the filter was set to show only the anchors that are part of a synteny block. The black arrows have been added to point to the upper right corner of the duplications discussed in the text.
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Figure 1: SyMAP multiple genome dot plot. The reference chromosomes are listed across the top. Synteny blocks are outlined in blue and the dots are anchors. Each cell represents a comparison between the two respective chromosomes, e.g. cell (1,3) represents the comparison between rice-1 and maize-3. Anchor chains that slope from lower left to upper right represent inversions. The Filters button brings up a menu of filters that can be applied; for this example, the filter was set to show only the anchors that are part of a synteny block. The black arrows have been added to point to the upper right corner of the duplications discussed in the text.

Mentions: Figure 1 shows the whole-genome dot plot of the three genomes, where the 12 rice chromosomes are the reference (listed across the top) and are aligned to the 10 maize and 10 sorghum chromosomes (listed on the left side). The synteny blocks are enclosed in blue boxes with anchors shown as dots. As discussed in Wei et al. (44), a rice chromosome may share synteny blocks with up to four maize chromosomes, where two are ‘primary’ (from the recent maize duplication) and two are ‘secondary’ (from the ancient grass duplication). The dot plot provides visual evidence, for example, scanning down the vertical cells under rice-1, it shares synteny blocks with maize-3,6,8 and sorghum-3,9. Maize-3,8 have stronger synteny with rice-1 (more anchors) compared to maize-6, which provides evidence that maize-3,8 are the primary syntenic chromosomes; there is only one obvious secondary syntenic chromosome, which is maize-6. Scanning horizontally from these five chromosomes, they all share synteny blocks with rice-5, where maize-6 and sorghum-9 have stronger synteny than maize-3,8 and sorghum-3.Figure 1.


SyMAP v3.4: a turnkey synteny system with application to plant genomes.

Soderlund C, Bomhoff M, Nelson WM - Nucleic Acids Res. (2011)

SyMAP multiple genome dot plot. The reference chromosomes are listed across the top. Synteny blocks are outlined in blue and the dots are anchors. Each cell represents a comparison between the two respective chromosomes, e.g. cell (1,3) represents the comparison between rice-1 and maize-3. Anchor chains that slope from lower left to upper right represent inversions. The Filters button brings up a menu of filters that can be applied; for this example, the filter was set to show only the anchors that are part of a synteny block. The black arrows have been added to point to the upper right corner of the duplications discussed in the text.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105427&req=5

Figure 1: SyMAP multiple genome dot plot. The reference chromosomes are listed across the top. Synteny blocks are outlined in blue and the dots are anchors. Each cell represents a comparison between the two respective chromosomes, e.g. cell (1,3) represents the comparison between rice-1 and maize-3. Anchor chains that slope from lower left to upper right represent inversions. The Filters button brings up a menu of filters that can be applied; for this example, the filter was set to show only the anchors that are part of a synteny block. The black arrows have been added to point to the upper right corner of the duplications discussed in the text.
Mentions: Figure 1 shows the whole-genome dot plot of the three genomes, where the 12 rice chromosomes are the reference (listed across the top) and are aligned to the 10 maize and 10 sorghum chromosomes (listed on the left side). The synteny blocks are enclosed in blue boxes with anchors shown as dots. As discussed in Wei et al. (44), a rice chromosome may share synteny blocks with up to four maize chromosomes, where two are ‘primary’ (from the recent maize duplication) and two are ‘secondary’ (from the ancient grass duplication). The dot plot provides visual evidence, for example, scanning down the vertical cells under rice-1, it shares synteny blocks with maize-3,6,8 and sorghum-3,9. Maize-3,8 have stronger synteny with rice-1 (more anchors) compared to maize-6, which provides evidence that maize-3,8 are the primary syntenic chromosomes; there is only one obvious secondary syntenic chromosome, which is maize-6. Scanning horizontally from these five chromosomes, they all share synteny blocks with rice-5, where maize-6 and sorghum-9 have stronger synteny than maize-3,8 and sorghum-3.Figure 1.

Bottom Line: These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice.The software may be used from a website or standalone for the best performance.A project manager is provided to organize and automate the analysis of multi-genome groups.

View Article: PubMed Central - PubMed

Affiliation: BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA. cari@agcol.arizona.edu

ABSTRACT
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.

Show MeSH
Related in: MedlinePlus