气候变化领域集成服务门户(CCPortal): Whole-genome microsynteny-based phylogeny of angiosperms

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DOI	10.1038/s41467-021-23665-0
	Whole-genome microsynteny-based phylogeny of angiosperms
	Zhao T.; Zwaenepoel A.; Xue J.-Y.; Kao S.-M.; Li Z.; Schranz M.E.; Van de Peer Y.
发表日期	2021
卷号	12 期号:1
英文摘要	Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny—the conservation of local gene content and order—is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our ‘microsynteny-based’ tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships. © 2021, The Author(s).
语种	英语
scopus关键词	angiosperm; data set; empirical analysis; genome; maximum likelihood analysis; numerical model; phylogenetics; phylogeny; simulation; article; female; magnoliid; maximum likelihood method; monocot; network analysis; nonhuman; phylogeny; Saxifragales; sequence alignment; simulation; synteny; angiosperm; biological model; classification; genetics; molecular evolution; multigene family; plant gene; plant genome; synteny; Liliopsida; magnoliids; Magnoliophyta; Saxifragales; Evolution, Molecular; Genes, Plant; Genome, Plant; Magnoliopsida; Models, Genetic; Multigene Family; Phylogeny; Synteny
来源期刊	Nature Communications
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/251552
作者单位	State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Center for Plant Systems Biology, VIB, Ghent, Belgium; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China; Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
推荐引用方式 GB/T 7714	Zhao T.,Zwaenepoel A.,Xue J.-Y.,et al. Whole-genome microsynteny-based phylogeny of angiosperms[J],2021,12(1).
APA	Zhao T..,Zwaenepoel A..,Xue J.-Y..,Kao S.-M..,Li Z..,...&Van de Peer Y..(2021).Whole-genome microsynteny-based phylogeny of angiosperms.Nature Communications,12(1).
MLA	Zhao T.,et al."Whole-genome microsynteny-based phylogeny of angiosperms".Nature Communications 12.1(2021).