Branching Out to Speciation in a Model of Fractionation: The Malvaceae

被引：1

作者：

Zhang, Yue ^{[1
]}

Zheng, Chunfang ^{[1
]}

Islam, Sindeed ^{[1
]}

Kim, Yong-Min ^{[2
]}

Sankoff, David ^{[1
]}

机构：

[1] Univ Ottawa, Dept Math & Stat, Ottawa, ON K1S 2C3, Canada

[2] Korea Res Inst Biosci & Biotechnol, Korean Bioinformat Ctr, Daejeon 34141, South Korea

来源：

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | 2021年 / 18卷 / 05期

基金：

加拿大自然科学与工程研究理事会;

关键词：

Bioinformatics; Genomics; Fractionation; Phylogeny; Trajectory; Biological system modeling; Computational modeling; Whole genome duplication; fractionation; branching process; gene pair similarity distribution; Malvaceae; durian; GENOME SEQUENCE; DRAFT GENOME; ARABIDOPSIS; EVOLUTION; GENES;

D O I：

10.1109/TCBB.2019.2955649

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1875 / 1884

页数：10

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