WGDI:A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes  

作　　者：Pengchuan Sun Beibei Jiao Yongzhi Yang Lanxing Shan Ting Li Xiaonan Li Zhenxiang Xi Xiyin Wang Jianquan Liu 

机构地区：[1]Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering,College of Life Sciences,Sichuan University,Chengdu,China [2]Center for Genomics and Bio-computing,North China University of Science and Technology,Tangshan,Hebei,China [3]State Key Laboratory of Grassland Agro-Ecosystem,College of Ecology,Lanzhou University,Lanzhou,China

出　　处：《Molecular Plant》2022年第12期1841-1851,共11页分子植物（英文版）

基　　金：This work was supported equally by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000);the National Natural Science Foundation of China(grant numbers 31590821 and 91731301 to J.L.and 32070669to X.W.);the National Key Research and Development Program of China(2017YFC0505203 to Z.X.);also by the Fundamental Research Funds for the Central Universities(SCU2019D013 and 2020SCUNL207)and theNational High-Level Talents Special Support Plan(10 Thousand People Plan)。

摘　　要：Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

关 键 词：WGDI POLYPLOIDY COLLINEARITY inference of hierarchical and event-related gene collinearity ancestral chromosome karyotype 

分 类 号：Q94[生物学—植物学]