Phylogenomics and the flowering plant tree of life

作     者：Cen Guo Yang Luo Lian-Ming Gao Ting-Shuang Yi Hong-Tao Li Jun-Bo Yang De-Zhu Li Cen Guo;Yang Luo;Lian-Ming Gao;Ting-Shuang Yi;Hong-Tao Li;Jun-Bo Yang;De-Zhu Li

作者机构：Germplasm Bank of Wild SpeciesKunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China Lijiang Forest Diversity National Observation and Research StationKunming Institute of BotanyChinese Academy of SciencesLijiang 674100China Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunming 650201China 

出 版 物：《Journal of Integrative Plant Biology》 (植物学报（英文版）)

年 卷 期：2023年第65卷第2期

页      面：299-323页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 090102[农学-作物遗传育种] 

基　　金：supported by the Priority Research Program of the Chinese Academy of Sciences (CAS) (Grant No.XDB31000000) Large-scale Scientific Facilities of the CAS (Grant No.2017LSF-GBOWS-2) 

主　　题：angiosperms hybridization incomplete lineage sorting orthology inference phylogenetic conflicts reduced representation sequencing whole-genome sequencing whole-genome duplication 

摘      要：The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic *** the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new *** the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is *** review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower *** also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of ***,we discuss promising avenues for future plant phylogenomic studies.