SyMAP Synteny Browser
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Poaceae

We aligned the maps and sequences of several important cereal grasses: Zea mays ("maize") [3,4], Oryza sativa ("rice") [5,6], Brachypodium distachyon [7], and Sorghum bicolor [8].

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, 3D View, 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

    Brachypodium FPC
    Maize FPC
    Brachypodium
    Maize *
    Rice
    Sorghum

   Select All    Select None

Tools
   
Whole genome dot plot of all selected species, with links to 2D.
   
Chromosome 3D, 2D and dot plot of all selected species.
   
Search gene annotations by keyword.
   
Linear display of synteny blocks, with links to 2D.
   
Circular display of synteny blocks.
   
Summary information.

* Only the maize sequence was repeat masked before synteny computation.
We generated putative gene annotation for the maize genome using all maize FLcDNAs from GenBank [9].

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. 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. 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.

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