Duckweed v. Duckweed: Difference between revisions
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Self-self sytnenic analyses of duckweed has strong evidence for at least one whole genome duplication event. In addition, this may be a hexaploidy event or two sequential tetraploidy events. The [[Ks]] value estimates of syntenic gene pairs, which may be used to differentiate sequential whole genome duplication events (as seen in [[Syntenic comparison of Arabidopsis thaliana and Arabidopsis lyrata | Arabidopsis]]), does not work with Duckweed. This is likely due to the [[Plant genome CDS GC content | high GC content of its coding sequence]]. If duckweed has undergone a recent [[GC content shift]], then all synonymous substitution rate estimates are suspect as not being neutral. | |||
[[File:Screen Shot 2012-03-21 at 6.40.51 PM.png|thumb|800px|center|Syntenic dotplot of self-self with Duckweed. Minimum of 5 genes to call a region syntenic. Results may be regenerated at: http://genomevolution.org/r/4mtn]] | [[File:Screen Shot 2012-03-21 at 6.40.51 PM.png|thumb|800px|center|Syntenic dotplot of self-self with Duckweed. Minimum of 5 genes to call a region syntenic. Results may be regenerated at: http://genomevolution.org/r/4mtn]] | ||
Revision as of 12:19, 22 March 2012
Self-self sytnenic analyses of duckweed has strong evidence for at least one whole genome duplication event. In addition, this may be a hexaploidy event or two sequential tetraploidy events. The Ks value estimates of syntenic gene pairs, which may be used to differentiate sequential whole genome duplication events (as seen in Arabidopsis), does not work with Duckweed. This is likely due to the high GC content of its coding sequence. If duckweed has undergone a recent GC content shift, then all synonymous substitution rate estimates are suspect as not being neutral.
