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Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Drillon, Guénola, Champeimont, River, Oteri, Francesco, Fischer, Gilles, Carbone, Alessandra·2020·Molecular Biology and Evolution
DOI 10.1093/molbev/msaa114PMC PMC7475045

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Abstract

Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches. PhyChro performance is evaluated on two data sets of 13 vertebrates and 21 yeast genomes by using up to 130,000 and 179,000 breakpoints, respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared with other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in <15 min.

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  • The physical position of homologs offers a second line of evidence that can help overcome challenges posed by WGDs, tandem arrays, heterozygous-duplicated regions, and other genomic complexities.

    “The physical position of homologs offers a second line of evidence that can help overcome challenges posed by WGDs, tandem arrays, heterozygous-duplicated regions, and other genomic complexities (Drillon et al., 2020; Haug-Baltzell et al., 2017; Wang et al., 2012).”

    From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Drillon et al., 2020

    Materials and Methods (Synteny Blocks; Testing the Conservation of Block Adjacencies) uses the positions and adjacency of homologous genes as phylogenetic evidence. The PhyChro Algorithm section says the method is designed to handle duplicated blocks, and Results (Robustness of PhyChro) includes simulated whole-genome duplications. The copy does not establish that this evidence overcomes challenges from tandem arrays or heterozygous-duplicated regions specifically. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Conserved gene order collinearity along local regions of chromosomes can provide evidence of homology and in some cases enable determination of whether two regions diverged as a result of speciation or a large-scale duplication event.

    “Like chromosome-scale synteny, conserved gene order collinearity along local regions of chromosomes can provide evidence of homology, and in some cases enable determination of whether two regions diverged as a result of speciation or a large-scale duplication event (Drillon et al., 2020).”

    From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Drillon et al., 2020

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Metadata

Authors
Drillon, G., Champeimont, R., Oteri, F., Fischer, G., & Carbone, A.
Affiliations
Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative—UMR 7238, Paris, France , Paris,
ORCID
Carbone, Alessandra
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2020-05-08
Volume
37
Issue
9
Pages
2747-2762
ISSN
  • 0737-4038
  • 1537-1719
DOI
10.1093/molbev/msaa114
PMC
PMC7475045
Cited by
46
References
12
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)
Funders
  • Agence Nationale de la Recherche (ANR-10-BLAN-1606-01)
  • Institut Universitaire de France

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