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

Sheinman, M., Arkhipova, K., Arndt, P. F., Dutilh, B. E.., Hermsen, R., & Massip, F. (2021). Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife, 10: e62719. doi:10.7554/eLife.62719.

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 Creators:
Sheinman, Michael 1, 2, Author
Arkhipova, Ksenia 1, Author
Arndt, Peter F.3, Author              
Dutilh, Bas E .1, Author
Hermsen, Rutger 1, Author
Massip, Florian 4, 5, Author
Affiliations:
1Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands, ou_persistent22              
2Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands, ou_persistent22              
3Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              
4Berlin Institute for Medical Systems Biology, Max Delbruck Center, Berlin, Germany, ou_persistent22              
5Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, Villleurbanne, France, ou_persistent22              

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 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 three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.

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Language(s): eng - English
 Dates: 2021-06-132021-06-14
 Publication Status: Published online
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 Identifiers: DOI: 10.7554/eLife.62719
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Title: eLife
Source Genre: Journal
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Publ. Info: Cambridge : eLife Sciences Publications
Pages: - Volume / Issue: 10 Sequence Number: e62719 Start / End Page: - Identifier: ISSN: 2050-084X
CoNE: https://pure.mpg.de/cone/journals/resource/2050-084X