SynMap: Difference between revisions

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Please refer to the appropriate images for this discussion, or you can regenerate this analysis [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.]  This example shows a whole genome syntenic dotplot comparison of ''Arabidopsis thaliana'' (At) and ''Arabidopsis lyrata'' (Al).  These taxa diverged from one another ~5MYA <ref name="lysak2006>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.
Please refer to the appropriate images for this discussion, or you can regenerate this analysis [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.]  This example shows a whole genome syntenic dotplot comparison of ''Arabidopsis thaliana'' (At) and ''Arabidopsis lyrata'' (Al).  These taxa diverged from one another ~5MYA <ref name="lysak2006>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.
</ref> and share two sequential whole genome duplications events <ref name=bowers2003>Bowers JE, Chapman BA, Rong JK, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003;422:433–438.</ref> since the divergence of their lineage with ''Carica papaya'''s lineage <ref name=ming2008>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.</ref>.  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 [[inversion]]s, gene [[transposition]] events, and other genomic changes.
</ref> and share two sequential whole genome duplications events <ref name=bowers2003>Bowers JE, Chapman BA, Rong JK, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003;422:433–438.</ref> since the divergence of their lineage with ''Carica papaya'''s lineage <ref name=ming2008>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.</ref>.  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 [[inversion]]s, gene [[transposition]] events, and other genomic changes. In addition, duplicated genes that are retained (as well as surrounding non-coding sequence) will diverge from one another.  Coding sequence divergence can be measured by synonymous changes (Ks), and a population of contemporaneously created syntenic genes pairs from a whole genome duplication event will create characteristic peaks in a histogram of Ks values <ref name=blank2004>Blanc, G., and K. H. Wolfe. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678</ref>


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.
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.

Revision as of 19:33, 28 August 2009

Overview

Specifying genomes

DAGChainer options

SynMap options

Calculating and displaying synonymous/non-synonymous (kS, kN) data

Interacting with results

Example Results

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 here.
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.
Syntenic dotplot and synonymous substitution histogram of Chromosome 1 of Arabidopsis thaliana and Arabidopsis lyrata. Syntenic gene pairs were identified by DAGChainer, and colored based on their synonymous substitution rate as calculated by CodeML. Syntenic regions derived from speciation (orthologs) or from the shared whole genome duplication events (alpha and beta) are labeled. These images were generated by SynMap and can be viewed at generated by SynMap at http://toxic.berkeley.edu/CoGe//diags/Arabidopsis_lyrata/Arabidopsis_thaliana_thale_cress/html/3068_8.CDS-CDS.blastn.dag_geneorder_D20_g10_A5.scaffold_1-1.w600.ks.html

Please refer to the appropriate images for this discussion, or you can regenerate this analysis here. 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. In addition, duplicated genes that are retained (as well as surrounding non-coding sequence) will diverge from one another. Coding sequence divergence can be measured by synonymous changes (Ks), and a population of contemporaneously created syntenic genes pairs from a whole genome duplication event will create characteristic peaks in a histogram of Ks values [4]

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.


  1. ↑ 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.
  2. ↑ Bowers JE, Chapman BA, Rong JK, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003;422:433–438.
  3. ↑ 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.
  4. ↑ Blanc, G., and K. H. Wolfe. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678
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