SynMap: Difference between revisions
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==Example Results== | ==Example Results== | ||
[[Image:Master_3068_8.CDS-CDS.blastn_geneorder_D20_g10_A5.w2000.ks.png|thumb|right|600px|Syntenic dotplot between ''Arabidopsis thaliana'' and ''Arabidopsis lyrata''. Syntenic gene pairs identified by DAGChainer have been colored based on their synonymous rate change as calculated by CODEML. Results can be regenerated [http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=3068;dsgid2=8;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder;ks=1;autogo=1 here]. ]] | [[Image:Master_3068_8.CDS-CDS.blastn_geneorder_D20_g10_A5.w2000.ks.png|thumb|right|600px|Syntenic dotplot between ''Arabidopsis thaliana'' and ''Arabidopsis lyrata''. Syntenic gene pairs identified by DAGChainer have been colored based on their synonymous rate change as calculated by CODEML. Results can be regenerated [http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=3068;dsgid2=8;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder;ks=1;autogo=1|here]. ]] | ||
[[Image:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png|thumb|right|600px|Histogram of synonymous rate change data for syntenic gene pairs between Arabidopsis thaliana and Arabidopsis lyrata. The two obvious peaks in the distribution are from syntenic gene pairs (syntelogs) derived from the speciation of these two taxa and from their shared most recent whole genome duplication event, known as alpha.]] | [[Image:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png|thumb|right|600px|Histogram of synonymous rate change data for syntenic gene pairs between Arabidopsis thaliana and Arabidopsis lyrata. The two obvious peaks in the distribution are from syntenic gene pairs (syntelogs) derived from the speciation of these two taxa and from their shared most recent whole genome duplication event, known as alpha.]] | ||
Revision as of 18:14, 28 August 2009
Overview
Specifying genomes
DAGChainer options
SynMap options
Calculating and displaying synonymous/non-synonymous (kS, kN) data
Interacting with results
Example Results
Please refer to the appropriate images for this discussion, or you can regenerate this analysis [2] This example shows a whole genome syntenic dotplot comparison of Arabidopsis thaliana (At) and Arabidopsis lyrata (Al). These taxa diverged from one another ~5MYA [1] and share two sequential whole genome duplications events [2] since the divergence of their lineage with Carica papaya's lineage [3]. Each whole genome duplication event creates a contemporaneous copy of every chromosome and all the genetic information they contain. However, over evolutionary time, these duplicated homeologous chromosomes are fractionated, undergo rearrangement and inversions, gene transposition events, and other genomic changes.
Shared whole genome duplication events can be detected through syntenic dotplot analysis (spacial analysis of gene order) and through synonymous change rate (kS) historgrams (temporal analysis of coding sequence divergence) for putative homologous gene pairs. SynMap can combine these approaches and can identify collinear sets of putatively homologous genes (spatial detection of synteny), calculate kS values for these syntelogous gene pairs pairs, and use those kS values to generate a color-metric histogram and paint the syntelogs the appropriate color on the dotplot. This combination of temporal and spatial syntenic analysis creates a final image that permits the rapid visual identification and evaluation of shared whole genome duplication events.
- ↑ Lysak MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proceedings of the National Academy of Sciences of the United States of America. 2006 Mar 28;103(13):5224-5229.
- ↑ Bowers JE, Chapman BA, Rong JK, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003;422:433–438.
- ↑ Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452:991–996. doi: 10.1038/nature06856.