Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

  1. Michael Sheinman  Is a corresponding author
  2. Ksenia Arkhipova
  3. Peter F Arndt
  4. Bas Dutilh
  5. Rutger Hermsen  Is a corresponding author
  6. Florian Massip  Is a corresponding author
  1. Netherlands Cancer Institute, Netherlands
  2. Utrecht University, Netherlands
  3. Max Planck Institute for Molecular Genetics, Germany
  4. Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine,, Germany

Abstract

Horizontal Gene Transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93 481 bacterial genomes identified 138 273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than 3 orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.

Data availability

Results of the analysis are provided as supplementary files

The following previously published data sets were used

Article and author information

Author details

  1. Michael Sheinman

    Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
    For correspondence
    mishashe@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
  2. Ksenia Arkhipova

    Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  3. Peter F Arndt

    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1762-9836
  4. Bas Dutilh

    Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  5. Rutger Hermsen

    Science faculty, Biology Department, Utrecht University, Utrecht, Netherlands
    For correspondence
    r.hermsen@uu.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4633-4877
  6. Florian Massip

    Evolutionary and Cancer Genomics, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine,, Berlin, Germany
    For correspondence
    florian.massip@mdc-berlin.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5855-0935

Funding

Netherlands Organisation for Scientific Research (Vidi grant 864.14.004)

  • Ksenia Arkhipova
  • Bas Dutilh

H2020 European Research Council (Consolidator Grant 865694: DiversiPHI)

  • Bas Dutilh

Fondation pour la Recherche Médicale (SPE201803005264)

  • Florian Massip

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Richard A Neher, University of Basel, Switzerland

Publication history

  1. Received: September 3, 2020
  2. Accepted: June 13, 2021
  3. Accepted Manuscript published: June 14, 2021 (version 1)
  4. Version of Record published: July 9, 2021 (version 2)

Copyright

© 2021, Sheinman et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Michael Sheinman
  2. Ksenia Arkhipova
  3. Peter F Arndt
  4. Bas Dutilh
  5. Rutger Hermsen
  6. Florian Massip
(2021)
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
eLife 10:e62719.
https://doi.org/10.7554/eLife.62719
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