A branching process for homology distribution-based inference of polyploidy, speciation and loss

Algorithms for Molecular Biology : AMB
Yue ZhangDavid Sankoff

Abstract

The statistical distribution of the similarity or difference between pairs of paralogous genes, created by whole genome doubling, or between pairs of orthologous genes in two related species is an important source of information about genomic evolution, especially in plants. We derive the mixture of distributions of sequence similarity for duplicate gene pairs generated by repeated episodes of whole gene doubling. This involves integrating sequence divergence and gene pair loss through fractionation, using a branching process and a mutational model. We account not only for the timing of these events in terms of local modes, but also the amplitude and variance of the component distributions. This model is then extended to orthologous gene pairs. We apply the model and inference procedures to the evolution of the Solanaceae, focusing on the genomes of economically important crops. We assess how consistent or variable fractionation rates are from species to species and over time.

References

Aug 28, 2007·Nature·Olivier JaillonUNKNOWN French-Italian Public Consortium for Grapevine Genome Characterization
Feb 14, 2008·The Plant Journal : for Cell and Molecular Biology·Eric Lyons, Michael Freeling
May 21, 2010·BMC Genomics·David SankoffQian Zhu
Jul 12, 2011·Nature·UNKNOWN Potato Genome Sequencing ConsortiumRichard G F Visser
Jun 5, 2012·Nature·UNKNOWN Tomato Genome Consortium
Aug 11, 2012·Molecular Plant-microbe Interactions : MPMI·Aureliano BombarelyGregory B Martin
Feb 26, 2014·BMC Genomics·Chunfang ZhengDavid Sankoff
Sep 23, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideki HirakawaHiroyuki Fukuoka
Jun 4, 2016·Nature Plants·Aureliano BombarelyCris Kuhlemeier
Jul 18, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics· Yue ZhangDavid Sankoff
May 11, 2018·BMC Genomics·Yue ZhangDavid Sankoff
Aug 4, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David SankoffHaibao Tang
Dec 24, 2019·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yue ZhangDavid Sankoff

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