SyMAP Synteny Browser
Home | Software | Team | AGCoL | Contact | Relevant links

We aligned the maps and sequences of several important cereal grasses: Zea mays ("maize") [1,2], Oryza sativa ("rice") [3,4], Brachypodium distachyon [5], Sorghum bicolor [6], and Foxtail Millet [7].

Synteny Tools

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.


Sequenced genomes
B. distachyon (brachypodium)
Z. mays (maize) *
S. italica (foxtail millet)
O. sativa (rice)
S. bicolor (sorghum)
FPC projects (physical map)
B. distachyon (brachypodium)
Z. mays (maize)

Select All   Select None


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.

*Maize V2 repeat-masked pseudomolecules, with annotation supplemented by full-length cDNA [8].

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

  1. Schnable P, et al. 2009. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326 (5956), 1112.
  2. Wei, F, Coe E, Nelson W, Bharti A, Engler F, Butler E, Kim H, Goicoechea JL, Chen M,Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers J, Paterson A, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, and Wing RA. 2007. Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History. PLoS Genet 3:e123.
  3. Ouyang, S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibafud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, and Buell CR. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-887.
  4. The International Rice Genome Sequencing Project. 2005. The map-based sequencing of the rice genome. Nature 436:793-800.
  5. Gu YQ, Ma Y, Huo N, Vogel JP, You FM, Lazo GR, Nelson WM, Soderlund C, Dvorak J, Anderson OD, Luo MC. 2009. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 2009, 10:496.
  6. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature. 457(7229):551-6.
  7. Not published yet, released under Ft. Lauderdale terms. See Phytozome information page.
  8. Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E, Morrow D, Fernandes J, Walbot V, and Yu Y. 2009. Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs. PLoS Genet 5(11): e1000740.

Brachpodium distachyon (FPC map): UC Davis
Zea mays (FPC map): AGI/AGCoL
Brachypodium distachyon: Phytozome
Zea mays B73, v2:
Oryza sativa (japonica): MSU
Sorghum bicolor Sorbi1: Phytozome
Foxtail millet Phytozome