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Cited by 35Genome Rearrangement AlgorithmsChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes

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Nakatani, Yoichiro, McLysaght, Aoife·2017·Bioinformatics
DOI 10.1093/bioinformatics/btx259PMC PMC5870716
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Abstract

Motivation: It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Results: Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate. Conclusions: We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history. Availability and implementation: The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip, and the software written in Java is available upon request. Supplementary information: Supplementary data are available at Bioinformatics online.

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  • Comparison of chromosome-scale genomes across vertebrates has clarified the timing and consequences of ancient whole-genome duplications that led to extant vertebrate genomes, supporting Ohno's hypothesis.

    “Comparison of chromosome-scale genomes across vertebrates has clarified the timing and consequences of the ancient whole-genome duplications (WGDs) that led to extant vertebrate genomes (59–65), supporting Ohno's (66) hypothesis.”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [64]

    The Introduction describes ancient WGDs and their proposed effects on present-day genomes, while Results §4.2 compares vertebrate genomes and refines the reconstruction of chromosome changes around the teleost WGD. The cited paper therefore supports the comparison and evolutionary-consequences portions of the claim, but it does not itself clarify the timing of the ancient vertebrate WGDs. The separate citation (66), not this paper, is attached to Ohno’s hypothesis. (LLM, conf=0.82)

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Cites

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Research works printed but not linked: 30

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Sorted by citations

Authors
Nakatani, Y., & McLysaght, A.
Affiliations
Trinity College Dublin (IE)
Corresponding author
  • Nakatani, Yoichiro
  • McLysaght, Aoife
ORCID
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2017-07-12
Volume
33
Issue
14
Pages
i369-i378
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btx259
PMC
PMC5870716
OpenAlex
W2734843587
Cited by
35
References
3
Citations by year
2026: 8 · 2025: 2 · 2024: 2 · 2023: 4 · 2022: 2 · 2021: 5 · 2020: 5 · 2019: 4 · 2018: 3
FWCI
2.13
Type
journal article
Language
en
Open access
Licence
Locations
  • Bioinformatics (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Arrow@dit (Dublin Institute of Technology) (acceptedVersion)
  • Trinity's Access to Research Output (TARA) (Trinity College Dublin) (submittedVersion, cc-by-nc-sa)
Funders
European Research Council (309834)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
whole-genome duplication, ancestral genome reconstruction, macrosynteny, orthologs, teleost genomes, genome rearrangement, gene loss, variational inference, vertebrate evolution
MeSH terms
Algorithms, Animals, Bayes Theorem, Chromosomes, Humans, Models, Genetic, Phylogeny, Software, Vertebrates, Genome, Evolution, Molecular, Gene Order, Genomics

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