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SyMAP Version 3
This material is based upon work supported by the National Science Foundation under Grant DBI-0115903.
SyMAP (Synteny Mapping and Analysis Program [1]) is an automated system for identifying and displaying genome synteny alignments. The genomes may be represented either by FPC maps or by ordered draft sequence contigs ("pseudomolecules"). SyMAP v2 computed FPC map to sequence alignments; SyMAP v3 extends v2 to compute sequence to sequence alignments. The SyMAP v2 package is available for download; the v3 distributable is in preparation.

Information about where we obtained these sequences is provided in Resources. Genome annotation has been loaded for rice, arabidopsis, and human, which is viewable from the SyMAP sequence track. MUMmer [2] was used to compute the set of anchors from two sequenced genomes, which is input into SyMAP.

Important: You will need Java version 5 or later for the SyMAP displays. You can check your Java version at http://www.java.com/en/download/installed.jsp and download the latest version.

CONTENTS
Plant Synteny | Plant Self Synteny | Two vs. One Comparisons | FPC Map Synteny | Other Organisms | Resources | References
Plant Synteny
Sorghum & Rice dot plot   synteny blocks   data summary Sorghum bicolor and Oryza sativa diverged ~50 MYA and underwent a whole genome duplication ~70 MYA [3].
Arabidopsis & Rice dot plot   synteny blocks   data summary Arabidopsis thaliana and Oryza sativa diverged ~200 MYA [15].
Arabidopsis & Medicago dot plot   synteny blocks   data summary Medicago truncatula and Arabidopsis thaliana diverged ~90 MYA[14].
Plant Self-Synteny
Arabidopsis dot plot   synteny blocks   data 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 synteny blocks Double alignment to rice, with maize (FPC map) on left, sorghum on right.
FPC Map Synteny
Maize FPC & Rice dot plot   synteny blocks   data summary Zea mays and Oryza sativa diverged ~50 MYA.
Maize FPC & Sorghum dot plot   synteny blocks   data summary Zea mays and Sorghum bicolor diverged ~50 MYA.
S. bicolor FPC & Rice dot plot   synteny blocks   data summary Sorghum bicolor and Oryza sativa diverged ~50 MYA.
S. propinquum FPC & Rice dot plot   synteny blocks   data summary Sorghum propinquum and Oryza sativa diverged ~50 MYA.
Other Organisms
Mouse & Human dot plot   synteny blocks   data summary Homo sapiens and Mus muscula diverged ~80 MYA
Chimp & Human dot plot   synteny blocks   data summary Homo sapiens and Pan Troglodytes diverged ~7 MYA.
Magnaporthe & Neurospora dot plot   synteny blocks   data summary Magnaporthe oryza (grisea) and Neurospora crassa diverged ~500 MYA.
C.briggsae & C.elegans dot plot   synteny blocks   data summary C. briggsae and C. elegans diverged ~100 MYA [9] and are almost indistinguishable morphologically [11].
Button Key
dotplots
block view
summary
C. ELEGANS
Resources
Genus Classification1 Size2 Source3 Refs
Sorghum bicolor Monocot, Poaceae(f) 760 MB Phytozome
Oryza Sativa (japonica) Monocot, Poaceae(f) 430 MB TIGR 5, 6
Arabidopsis thaliana Eudicot, Brassicaceae(f) 119 MB TAIR 7
Medicago truncatula Eudicot, Fabaceae(f) 500 MB Medicago 8
Magnaporthe Oryza (70-15) Ascomycedes(p), Magnaporthaceae(f) 40 MB BROAD 9
Neurospora Crassa Ascomycedes(p), Sordariaceae(f) 43 MB BROAD 10
Caenorhabditis elegans Nematode(p), Rhabditidae(f) 100 MB Wormbase 12
Caenorhabditis briggsae Nematode(f), Rhabditidae(f) 104 MB Wormbase 13
Zea mays (FPC map) Monocot, Poaceae(f) 2.4 GB AGI/AGCOL 16
Sorghum (FPC maps) Monocot, Poaceae(f) 800 Mb PGML/UGA
Mouse Chordata(p), Muridae(f) 2.5 Gb Genbank RefSeq 17
Human Chordata(p), Hominidae(f) 2.9 Gb Genbank RefSeq 18
1Phylum(p), Family(f)    2The classification and sizes were obtained from NCBI    3Download site for sequence and annotation, or FPC map
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References
NB There are many papers on the sequence and evolution of these genomes and we obviously have not listed them all. If you feel a relevant paper has been omitted, please let us know at symap@agcol.arizona.edu.
  1. Soderlund, C., W. Nelson, A. Shoemaker, A. Paterson. 2006. SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Research 16:1159-1168.
  2. Kurtz, S., A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg. 2004. Versatile and open software for comparing large genomes. Genome Biol 5: R12.
  3. Paterson, A.H., J.E. Bowers, and B.A. Chapman. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101: 9903-9908.
  4. The International Rice Genome Sequencing Project. 2005. The map-based sequencing of the rice genome. Nature 436:793-800.
  5. 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.
  6. Ouyang, S., W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-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.
  7. Arabidopsis Sequencing Consortium, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
  8. Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EK, Dwan C, Lamblin AF, Vasdewani J, Mudge J, Cook A, Gish J, Cheung F, Kenton S, Kunau TM, Brown D, May GD, Kim D, Cook DR, Roe BA, Town CD, Young ND, Retzel EF. (2005) Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol. 2005 May;138(1):38-46.
  9. Dean, R.A., N.J. Talbot, D.J. Ebbole, M.L. Farman, T.K. Mitchell, M.J. Orbach, M. Thon, R. Kulkarni, J.R. Xu, H. Pan, et al. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986.
  10. Galagan, J.E., S.E. Calvo, K.A. Borkovich, E.U. Selker, N.D. Read, D. Jaffe, W. FitzHugh, L.J. Ma, S. Smirnov, S. Purcell. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
  11. Coghlan, A. and K.H. Wolfe. 2002. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res 12: 857-867.
  12. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
  13. Stein, L.D., Z. Bao, D. Blasiar, T. Blumenthal, M.R. Brent, N. Chen, A. Chinwalla, L. Clarke, C. Clee, A. Coghlan, et al. 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1: E45.
  14. 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.
  15. Goff, S.A., D. Ricke, T.H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma, 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
  16. Wei, F., E. Coe, W. Nelson, A. Bharti, F. Engler, E. Butler, H. Kim, J. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J. Bowers, A. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund, and R. Wing, Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History. PLoS Genetics 2007 3: e123
  17. Mouse Genome Sequencing Consortium, Initial sequencing and comparative analysis of the mouse genome. 2002. Nature 420, 520-562.
  18. International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome. 2002. Nature 409, 860-921.
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Email comments to: symap@agcol.arizona.edu