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Whole-genome microsynteny-based phylogeny of angiosperms

Author

Listed:
  • Tao Zhao

    (State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University
    Ghent University
    Center for Plant Systems Biology, VIB)

  • Arthur Zwaenepoel

    (Ghent University
    Center for Plant Systems Biology, VIB)

  • Jia-Yu Xue

    (College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University
    Institute of Botany, Jiangsu Province and Chinese Academy of Sciences)

  • Shu-Min Kao

    (Ghent University
    Center for Plant Systems Biology, VIB)

  • Zhen Li

    (Ghent University
    Center for Plant Systems Biology, VIB)

  • M. Eric Schranz

    (Biosystematics Group, Wageningen University and Research)

  • Yves Van de Peer

    (Ghent University
    Center for Plant Systems Biology, VIB
    College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University
    University of Pretoria)

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.

Suggested Citation

  • Tao Zhao & Arthur Zwaenepoel & Jia-Yu Xue & Shu-Min Kao & Zhen Li & M. Eric Schranz & Yves Van de Peer, 2021. "Whole-genome microsynteny-based phylogeny of angiosperms," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23665-0
    DOI: 10.1038/s41467-021-23665-0
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    Cited by:

    1. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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