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 colline...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.展开更多
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.)+1 种基金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)。
文摘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.
