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Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology 2023年第2期65卷 299-323页

作者： Cen Guo Yang Luo Lian-Ming Gao Ting-Shuang Yi Hong-Tao Li Jun-Bo Yang De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China Lijiang Forest Diversity National Observation and Research Station Kunming Institute of BotanyChinese Academy of SciencesLijiang 674100China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650201China

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.

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

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