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

eLife

Florian Massip¹  Peter F Arndt²  Ksenia Arkhipova³  Rutger Hermsen³  Bas E Dutilh³  Michael Sheinman⁴ 

[1] Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany;Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France;Max Planck Institute for Molecular Genetics, Berlin, Germany;Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands;Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands;Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands;

关键词: horizontal gene transfer;    alignment-free method;    antibiotic resistance;    power law;    genome evolution;    Other;   

DOI  :  10.7554/eLife.62719

来源: eLife Sciences Publications, Ltd

【 摘 要 】

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.

【 授权许可】

CC BY