Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
- Netherlands Cancer Institute, Netherlands
- Utrecht University, Netherlands
- Max Planck Institute for Molecular Genetics, Germany
- 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
Article and author information
Author details
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.
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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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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