SyMAP Synteny Browser
SyMAP (Synteny Mapping and Analysis Program) is an automated system for identifying and displaying genome synteny alignments. The genomes may be represented either by FPC maps or by sequenced chromosomes (pseudomolecules).

This project has been funded in part by the National Science Foundation #0115903.
        Current developments are funded by USDA NRI #0214643.

If you use results from this page in a publication or website, please reference:
        Soderlund et al. 2006, Genome Research 16:1159 (download).

     

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

Note:
We recently upgraded to SyMAP v3.0 (available for download soon) with its new 3D functionality. Please contact us at symap@agcol.arizona.edu if you encounter any problems.

Button Key
3D view
dot plot
block view
circular map
summary
Plant Synteny
Sorghum & Rice 3D   dot plot   synteny blocks   circle   summary Sorghum bicolor and Oryza sativa diverged ~45 MYA and underwent a whole genome duplication ~70 MYA [3].
Arabidopsis & Rice 3D   dot plot   synteny blocks   cirlce   summary Arabidopsis thaliana and Oryza sativa diverged ~200 MYA [15].
Arabidopsis & Medicago 3D   dot plot   synteny blocks   circle   summary Medicago truncatula and Arabidopsis thaliana diverged ~90 MYA [14].
Plant Self-Synteny
Arabidopsis 3D   dot plot   synteny blocks   circle   summary Arabidopsis thaliana has undergone at least two rounds of duplication with the most recent being ~112 MYA [7]. (Note that MUMmer characteristics prevent off-diagonal alignments from being found in the self-alignments of chromosomes).
Two vs. One Comparisons
Maize, Sorghum vs. Rice 3D   synteny blocks Double alignment to rice, with maize (FPC map) on left, sorghum on right.
FPC Map Synteny
Maize FPC & Rice 3D   dot plot   synteny blocks   circle   summary Zea mays and Oryza sativa diverged ~45 MYA.
Maize FPC & Sorghum 3D   dot plot   synteny blocks   circle   summary Zea mays and Sorghum bicolor diverged ~11 MYA.
S. bicolor FPC & Rice 3D   dot plot   synteny blocks   circle   summary Sorghum bicolor and Oryza sativa diverged ~45 MYA.
S. propinquum FPC & Rice 3D   dot plot   synteny blocks   circle   summary Sorghum propinquum and Oryza sativa diverged ~45 MYA.
Other Organisms
Mouse & Human 3D   dot plot   synteny blocks   circle   summary Homo sapiens and Mus muscula diverged ~80 MYA
Chimp & Human 3D   dot plot   synteny blocks   circle   summary Homo sapiens and Pan Troglodytes diverged ~7 MYA.
Magnaporthe & Neurospora 3D   dot plot   synteny blocks   circle   summary Magnaporthe oryza (grisea) and Neurospora crassa diverged ~200 MYA.
C.briggsae & C.elegans 3D   dot plot   synteny blocks   circle   summary C. briggsae and C. elegans diverged ~100 MYA [9] and are almost indistinguishable morphologically [11].