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Whole-genome microsynteny-based phylogeny of angiosperms

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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. Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.
Keywords
General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry, GENE-ORDER, EARLY DIVERSIFICATION, MAXIMUM-LIKELIHOOD, NUCLEAR GENES, LAND PLANTS, EVOLUTION, REVEALS, REARRANGEMENTS, INTROGRESSION, ORIGIN

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MLA
Zhao, Tao, et al. “Whole-Genome Microsynteny-Based Phylogeny of Angiosperms.” NATURE COMMUNICATIONS, vol. 12, no. 1, 2021, doi:10.1038/s41467-021-23665-0.
APA
Zhao, T., Zwaenepoel, A., Xue, J.-Y., Kao, S.-M., Li, Z., Schranz, M. E., & Van de Peer, Y. (2021). Whole-genome microsynteny-based phylogeny of angiosperms. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-23665-0
Chicago author-date
Zhao, Tao, Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz, and Yves Van de Peer. 2021. “Whole-Genome Microsynteny-Based Phylogeny of Angiosperms.” NATURE COMMUNICATIONS 12 (1). https://doi.org/10.1038/s41467-021-23665-0.
Chicago author-date (all authors)
Zhao, Tao, Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz, and Yves Van de Peer. 2021. “Whole-Genome Microsynteny-Based Phylogeny of Angiosperms.” NATURE COMMUNICATIONS 12 (1). doi:10.1038/s41467-021-23665-0.
Vancouver
1.
Zhao T, Zwaenepoel A, Xue J-Y, Kao S-M, Li Z, Schranz ME, et al. Whole-genome microsynteny-based phylogeny of angiosperms. NATURE COMMUNICATIONS. 2021;12(1).
IEEE
[1]
T. Zhao et al., “Whole-genome microsynteny-based phylogeny of angiosperms,” NATURE COMMUNICATIONS, vol. 12, no. 1, 2021.
@article{8712580,
  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. Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.}},
  articleno    = {{3498}},
  author       = {{Zhao, Tao and Zwaenepoel, Arthur and Xue, Jia-Yu and Kao, Shu-Min and Li, Zhen and Schranz, M. Eric and Van de Peer, Yves}},
  issn         = {{2041-1723}},
  journal      = {{NATURE COMMUNICATIONS}},
  keywords     = {{General Biochemistry,Genetics and Molecular Biology,General Physics and Astronomy,General Chemistry,GENE-ORDER,EARLY DIVERSIFICATION,MAXIMUM-LIKELIHOOD,NUCLEAR GENES,LAND PLANTS,EVOLUTION,REVEALS,REARRANGEMENTS,INTROGRESSION,ORIGIN}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{14}},
  title        = {{Whole-genome microsynteny-based phylogeny of angiosperms}},
  url          = {{http://doi.org/10.1038/s41467-021-23665-0}},
  volume       = {{12}},
  year         = {{2021}},
}

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