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.
Highlights
Microbial genomes are subject to loss and gain of genetic material from other microorganisms (Boto, 2010; Puigboet al., 2014), via a variety of mechanisms: conjugation, transduction, and transformation, collectively known as horizontal gene transfer (HGT) (Soucy et al, 2015; GarcıaAljaro et al, 2017)
We identified HGT events between distant bacterial taxa by detecting long exact sequence matches shared by pairs of genomes belonging to different genera
We developed a computationally efficient method to identify recent HGT events
Summary
Microbial genomes are subject to loss and gain of genetic material from other microorganisms (Boto, 2010; Puigboet al., 2014), via a variety of mechanisms: conjugation, transduction, and transformation, collectively known as horizontal gene transfer (HGT) (Soucy et al, 2015; GarcıaAljaro et al, 2017). Gene acquisition via HGT can provide microbes with adaptive traits that confer a selective advantage in particular conditions (Koonin, 2016; Massey and Wilson, 2017) and eliminate deleterious mutations, resolving the paradox of Muller’s ratchet (Takeuchi et al, 2014). Other methods are based on discrepancies between gene and species distances, that is, surprising similarity between genomic regions belonging to distant organisms that cannot be satisfactorily explained by their conservation
Sign-in/Register to view highlights & summary 
Published Version
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
