Branching out to speciation in a model of fractionation: the malvaceae

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Title
Branching out to speciation in a model of fractionation: the malvaceae
Author(s)
Y Zhang; C Zheng; S Islam; Yong Min Kim; D Sankoff
Bibliographic Citation
IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 5, pp. 1875-1884
Publication Year
2021
Abstract
Fractionation is the genome-wide process of losing one gene per duplicate pair following whole genome doubling (WGD). An important type of evidence for duplicate gene loss is the frequency distribution of similarities between paralogous gene pairs in a genome or orthologous gene pairs in two species. We extend a previous branching process model for fractionation, originally accounting for paralog similarities, to encompass the distribution of ortholog similarities, after multiple rounds of whole genome doubling and fractionation, with the speciation event occurring at any point. We estimate the fractionation rates during all the inter-event periods in each lineage of the plant family Malvaceae. We suggest a major correction of the phylogenetic position of the durian sub-family, and discover a new triplication event in this lineage.
Keyword
Whole genome duplicationFractionationBranching processGene pair similarity distributionMalvaceaeDurian
ISSN
1545-5963
Publisher
IEEE
DOI
http://dx.doi.org/10.1109/TCBB.2019.2955649
Type
Article
Appears in Collections:
Division of Research on National Challenges > Plant Systems Engineering Research > 1. Journal Articles
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