SyMAP Synteny Browser
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Rosaceae + Curcurbiteae

This page shows alignments of the Apple v1.0 [1] and Peach v1.0 [2] genomes to each other, as well as self-alignments of each. Cucumber scaffolds larger than 100kb have also been aligned.

Important: The data below are preliminary and not to be used in any publication. Peach v1.0 is in preliminary release under the Fort Lauderdale agreement and may not be used for chromosome-scale published analyses. We are posting this data pursuant to our commitment to support Rosaceae comparative genomics, under USDA NIFA grant #0214643.

Apple v1.0 was not presented as pseudomolecules, due to high heterozygosity [1]; however, chromosome co-ordinates for the contigs were provided, and we used this information to construct approximate pseudomolecules for the purpose of synteny comparison. Based on the discussion of [1], we expect that these pseudomolecules will have errors in the vicinity of hemizygous loci of 1kb or larger, and also that many open reading frames may not be complete. These problems should not disrupt a synteny alignment, although there may be discrepancies with gene annotation in a close-up view of the affected regions.

Synteny Tools

Instructions:
Select one or more species of interest from the left and then click a tool button on the right.
The first three tools, Dot Plot, Java Explorer, and Gene Search can be used with any number of selected species.
The remaining tools are only be available when one (self-alignment) or two species are selected.

Species

Sequenced genomes
M. domestica (apple)
P. persica (peach)
F. vesca (strawberry)
Draft-sequenced genomes
C. sativis (cucumber)*

Select All  Select None

    Tools


Whole genome dot plot of all selected species, with links to 2D.

Dynamic circular view + 2D + dotplot, for all selected species.

Search gene annotations **NEW enhanced interface**

Linear display of synteny blocks, with links to 2D.

Circular display of synteny blocks.

Summary information and table of blocks.

* Scaffolds larger than 100kb, ordered against peach. The Java Explorer is not available for this genome.

Important:
SyMAP requires the Java Runtime Environment (JRE) version 5 or later.
Click here to check your Java installation and upgrade if necessary.

References
  1. Velasco, R, et al. 2009. The Genome of the Domesticated Apple (Malus x domestica Borkh.) Nature Genetics 42, 833–839. 2010.
  2. International Peach Genome Initiative (http://www.rosaceae.org/node/365)
  3. Shulaev, V., et al. The genome of woodland strawberry (Fragaria vesca). Nature genetics 43, 109-116. 2010
Resources

Peach v1.0, Apple v1.0: Genome Database for Rosaceae