Integrated synteny- and similarity-based inference on the polyploidization-fractionation cycle.

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Yue ZhangDavid Sankoff

Abstract

Whole-genome doubling, tripling or replicating to a greater degree, due to fixation of polyploidization events, is attested in almost all lineages of the flowering plants, recurring in the ancestry of some plants two, three or more times in retracing their history to the earliest angiosperm. This major mechanism in plant genome evolution, which generally appears as instantaneous on the evolutionary time scale, sets in operation a compensatory process called fractionation, the loss of duplicate genes, initially rapid, but continuing at a diminishing rate over millions and tens of millions of years. We study this process by statistically comparing the distribution of duplicate gene pairs as a function of their time of creation through polyploidization, as measured by sequence similarity. The stochastic model that accounts for this distribution, though exceedingly simple, still has too many parameters to be estimated based only on the similarity distribution, while the computational procedures for compiling the distribution from annotated genomic data is heavily biased against earlier polyploidization events-syntenic 'crumble'. Other parameters, such as the size of the initial gene complement and the ploidy of the various events g...Continue Reading

References

Mar 11, 2006·Molecular Biology and Evolution·Jake K ByrnesWen-Hsiung Li
Sep 5, 2007·Molecular Biology and Evolution·Milan J A van Hoek, Paulien Hogeweg
Feb 14, 2008·The Plant Journal : for Cell and Molecular Biology·Eric Lyons, Michael Freeling
Jun 10, 2009·Journal of Bioinformatics and Computational Biology·Chunfang ZhengDavid Sankoff
Feb 26, 2014·BMC Genomics·Chunfang ZhengDavid Sankoff
Sep 1, 2017·Annals of Botany·Carlos M Vicient, Josep M Casacuberta
Oct 11, 2017·Nature Genetics·Bin Tean TehPatrick Tan
May 11, 2018·BMC Genomics·Yue ZhangDavid Sankoff
Aug 4, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David SankoffHaibao Tang
Nov 6, 2018·Plant Physiology·Jinpeng WangZhiyan Xi
Aug 8, 2019·Algorithms for Molecular Biology : AMB·Yue ZhangDavid Sankoff

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