Tree2GD: a phylogenomic method to detect large-scale gene duplication events

被引：9

作者：

Chen, Duoyuan ^{[1
]}

Zhang, Taikui ^{[1
,2
,3
]}

Chen, Yamao ^{[1
]}

Ma, Hong ^{[2
,3
]}

Qi, Ji ^{[1
]}

机构：

[1] Fudan Univ, Sch Life Sci, Inst Plant Biol, State Key Lab Genet Engn, Shanghai 200433, Peoples R China

[2] Penn State Univ, Dept Biol, Eberly Coll Sci, University Pk, PA 16802 USA

[3] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA

来源：

BIOINFORMATICS | 2022年 / 38卷 / 23期

基金：

中国国家自然科学基金; 中国博士后科学基金;

关键词：

WHOLE-GENOME DUPLICATIONS; EVOLUTIONARY SIGNIFICANCE; PROVIDES INSIGHTS; MODEL SELECTION; POLYPLOIDY; ANCESTOR; PHYLOTRANSCRIPTOMICS; ALIGNMENT;

D O I：

10.1093/bioinformatics/btac669

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy. Results: Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses. Application of Tree2GD on 2 datasets, 12 metazoan genomes and 68 angiosperms, successfully identifies all reported whole-genome duplication events exhibited by these species, showing effectiveness and efficiency of Tree2GD on phylogenomic analyses of large-scale gene duplications.

引用

页码：5317 / 5321

页数：5

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