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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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SyMAP multiple chromosome 3D view and dot plot. (a) On the left panel, the reference chromosome is selected by clicking its number, which highlights the regions of all other chromosomes that have shared synteny blocks. Selecting the body of chromosomes on the left adds them to the 3D view. Selecting them a second time removes them from the 3D display. The 3D display on the right can be rotated, zoomed and moved in order to inspect the syntenic relations. Red ribbons represent un-inverted synteny blocks, green ribbons are inverted (although, as SyMAP detects imperfect synteny, each may contain small regions of the opposite type). (b) Selecting the ‘Dotplot’ button brings up the dot plot for the same set of chromosomes as shown in the 3D display. The black arrows have been added to point to the inverted and un-inverted blocks discussed in the text.
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Figure 2: SyMAP multiple chromosome 3D view and dot plot. (a) On the left panel, the reference chromosome is selected by clicking its number, which highlights the regions of all other chromosomes that have shared synteny blocks. Selecting the body of chromosomes on the left adds them to the 3D view. Selecting them a second time removes them from the 3D display. The 3D display on the right can be rotated, zoomed and moved in order to inspect the syntenic relations. Red ribbons represent un-inverted synteny blocks, green ribbons are inverted (although, as SyMAP detects imperfect synteny, each may contain small regions of the opposite type). (b) Selecting the ‘Dotplot’ button brings up the dot plot for the same set of chromosomes as shown in the 3D display. The black arrows have been added to point to the inverted and un-inverted blocks discussed in the text.

Mentions: To further investigate this set of chromosomes, the ‘Chromosome 3D and 2D’ option was selected from the project manager; this leads to 3D, 2D and dot-plot display options for multiple chromosomes. On the left side of Figure 2a, rice-1 was selected as the reference chromosome, which automatically highlights maize-3,6,8 and sorghum-3,9. All five of these chromosomes were then selected, which aligned them in the 3D figure, as shown on the right side of Figure 2a. By selecting the ‘Dotplot’ button, the dot-plot view was displayed for the same set of chromosomes (Figure 2b). Anchor chains that slope from lower left to upper right are inversions, for example, the segment in the upper corner of (rice-1, maize-3). Scanning vertically from this block, it can be seen that maize-6 does not have the segment and maize-8 has the segment but it is not inverted; sorghum-3 has the segment inverted and sorghum-8 has the un-inverted segment.Figure 2.


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

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

SyMAP multiple chromosome 3D view and dot plot. (a) On the left panel, the reference chromosome is selected by clicking its number, which highlights the regions of all other chromosomes that have shared synteny blocks. Selecting the body of chromosomes on the left adds them to the 3D view. Selecting them a second time removes them from the 3D display. The 3D display on the right can be rotated, zoomed and moved in order to inspect the syntenic relations. Red ribbons represent un-inverted synteny blocks, green ribbons are inverted (although, as SyMAP detects imperfect synteny, each may contain small regions of the opposite type). (b) Selecting the ‘Dotplot’ button brings up the dot plot for the same set of chromosomes as shown in the 3D display. The black arrows have been added to point to the inverted and un-inverted blocks discussed in the text.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: SyMAP multiple chromosome 3D view and dot plot. (a) On the left panel, the reference chromosome is selected by clicking its number, which highlights the regions of all other chromosomes that have shared synteny blocks. Selecting the body of chromosomes on the left adds them to the 3D view. Selecting them a second time removes them from the 3D display. The 3D display on the right can be rotated, zoomed and moved in order to inspect the syntenic relations. Red ribbons represent un-inverted synteny blocks, green ribbons are inverted (although, as SyMAP detects imperfect synteny, each may contain small regions of the opposite type). (b) Selecting the ‘Dotplot’ button brings up the dot plot for the same set of chromosomes as shown in the 3D display. The black arrows have been added to point to the inverted and un-inverted blocks discussed in the text.
Mentions: To further investigate this set of chromosomes, the ‘Chromosome 3D and 2D’ option was selected from the project manager; this leads to 3D, 2D and dot-plot display options for multiple chromosomes. On the left side of Figure 2a, rice-1 was selected as the reference chromosome, which automatically highlights maize-3,6,8 and sorghum-3,9. All five of these chromosomes were then selected, which aligned them in the 3D figure, as shown on the right side of Figure 2a. By selecting the ‘Dotplot’ button, the dot-plot view was displayed for the same set of chromosomes (Figure 2b). Anchor chains that slope from lower left to upper right are inversions, for example, the segment in the upper corner of (rice-1, maize-3). Scanning vertically from this block, it can be seen that maize-6 does not have the segment and maize-8 has the segment but it is not inverted; sorghum-3 has the segment inverted and sorghum-8 has the un-inverted segment.Figure 2.

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