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, Dot Plot, Explorer, and Gene Search can be used with any number of selected species.
The remaining tools require one (self-alignment) or two selected species.

Species

Sequenced genomes
A. thaliana
V . vinifera (grape)
M. trunculatus (medicago)
P. trichocarpa (poplar)
G. max (soybean)
B. rapa
Draft-sequenced genomes
A. lyrata *
C. papaya (papaya) **

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.

* Draft sequence, only the eight largest scaffolds.
** Scaffolds larger than 1M, ordered by reference to grape. 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. 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