SyMAP Synteny Browser
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Poaceae

We aligned the sequences of several important cereal grasses: Zea mays ("maize") [6], Oryza sativa ("rice") [8], Brachypodium distachyon [2], and Sorghum bicolor [5].

Grasses (Poaceae) exceed all other plant families in ecological dominance and economic importance. Grass subfamilies diverged from a common ancestor 50 to 80 million years ago [1], with the cereals diverging 45 to 47 million years ago [3]. Despite their relatively recent divergence, grass genomes have very different characteristics such as number of chromosomes, ploidy, and size.

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

    Brachypodium FPC
    Maize FPC
    Brachypodium
    Maize *
    Rice
    Sorghum

   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.

* 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 [7].

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. Charles M, Tang H, Belcram H, Paterson A, Gornicki P, Chalhoub B. 2009. Sixty Million Years in Evolution of Soft Grain Trait in Grasses: Emergence of the Softness Locus in the Common Ancestor of Pooideae and Ehrhartoideae, after their Divergence from Panicoideae. Molecular Biology and Evolution 26(7):1651-1661.
  2. 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.
  3. Kumar S, Mohan A, Balyan HS, Gupta PK. 2009. Orthology between genomes of Brachypodium, wheat and rice. BMC Research Notes 2:93.
  4. Ouyang, S., W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibafud-Nissen, R.L. Malek, Y. Lee, L. Zheng, J. Orvis, B. Haas, J. Wortman, and C.R. Buell. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-887.
  5. 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.
  6. Schnable P, et al. 2009. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326 (5956), 1112.
  7. Soderlund C, et al. 2009. Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs. PLoS Genet 5(11): e1000740.
  8. The International Rice Genome Sequencing Project. 2005. The map-based sequencing of the rice genome. Nature 436:793-800.
  9. The Rice Chromosome 3 Sequencing Consortium 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res 15: 1284-1291.
  10. Wei F, et al. 2007. Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History. PLoS Genet 3:e123.
  11. Brachpodium distachyon (FPC map): UC Davis
  12. Zea mays (FPC map): AGI/AGCoL
  13. Brachypodium distachyon: Phytozome
  14. Zea mays B73: AGI
  15. Oryza sativa (japonica) TIGR5: TIGR
  16. Sorghum bicolor Sorbi1: Phytozome