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

作者机构：Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River EngineeringCollege of Life SciencesSichuan UniversityChengduChina Center for Genomics and Bio-computingNorth China University of Science and TechnologyTangshanHebeiChina State Key Laboratory of Grassland Agro-EcosystemCollege of EcologyLanzhou UniversityLanzhouChina 

出 版 物：《Molecular Plant》 (分子植物（英文版）)

年 卷 期：2022年第15卷第12期

页      面：1841-1851页

核心收录：

学科分类：0710[理学-生物学] 071001[理学-植物学] 07[理学] 

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) 

主　　题：WGDI polyploidy collinearity inference of hierarchical and event-related gene collinearity ancestral chromosome karyotype 

摘      要：Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on *** clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate *** 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 *** 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 ***,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype *** toolkit is freely available at GitHub(https://***/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.