SyMAP Synteny Browser
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Fabaceae, et al.

We aligned the sequences of several model and agricultural plant species: two varieties of Arabidopsis (thaliana [1] and lyrata), Vitis vinifera ("common grape vine") [4], Medicago truncatula [2], Glycine max ("soybean") [5], and Populus trichocarpa ("poplar") [6].

Arabidopsis is a model plant species and A. thaliana the first plant genome to be fully sequenced. Poplar is the first tree to be fully sequenced. Medicago, a model legume, and soybean, an important legume food crop, diverged an estimated 50 million years ago [3]. Grape is an important agricultural crop.

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, 3D View, Gene Search, and Dot Plot 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

    A. lyrata *
    A. thaliana
    Grape
    Medicago
    Poplar
    Soybean

   Select All    Select None

Tools
   
Open a three-dimensional display of synteny block alignments.
   
Search gene annotations by keyword.
   
Open a dot plot display showing individual hits and syteny block alignments.
   
Open a linear display of synteny block alignments.
   
Open a circular display of synteny block alignments.
   
Display summary information.

* Draft sequence, only the eight largest scaffolds.

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. Arabidopsis Sequencing Consortium, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
  2. Cannon SB, et al. Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol. 2005 May;138(1):38-46.
  3. Hee Shin, J., et al. 2008. The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula. BMC Plant Biology 8:133.
  4. Jaillon, O., et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467.
  5. Mudge, J., S.B. Cannon, P. Kalo, G.E. Oldroyd, B.A. Roe, C.D. Town, and N.D. Young. 2005. Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol 5: 15.
  6. Tuskan GA, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006 Sep 15; 313(5793):1596-604.
  7. Arabidopsis lyrata v1: Phytozome (JGI)
  8. Arabidopsis thaliana v9: TAIR
  9. Medicago truncatula v3.0: Medicago.org
  10. Populus trichocarpa v1.1: JGI
  11. Glycine max v1.01: Phytozome (JGI)
  12. Vitis vinifera Sep. 2007: Genoscope