Whole-genome microsynteny-based phylogeny of angiosperms

Tao Zhao (), Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz and Yves Van de Peer ()
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Tao Zhao: State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University
Arthur Zwaenepoel: Ghent University
Jia-Yu Xue: College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University
Shu-Min Kao: Ghent University
Zhen Li: Ghent University
M. Eric Schranz: Biosystematics Group, Wageningen University and Research
Yves Van de Peer: Ghent University

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-021-23665-0

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