RT Journal Article
SR Electronic
T1 Long identical sequences found in multiple bacterial genomes reveal frequent and widespread exchange of genetic material between distant species
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.09.139501
DO 10.1101/2020.06.09.139501
A1 Michael Sheinman
A1 Ksenia Arkhipova
A1 Peter F. Arndt
A1 Bas E Dutilh
A1 Rutger Hermsen
A1 Florian Massip
YR 2020
UL http://biorxiv.org/content/early/2020/06/09/2020.06.09.139501.abstract
AB Horizontal transfer of genomic elements is an essential force that shapes microbial genome evolution. This process occurs via various mechanisms and has been studied in detail for a variety of biological systems. However, a coarse-grained, global picture of horizontal gene transfer (HGT) in the microbial world is still missing. One reason is the difficulty to process large amounts of genomic microbial data to find and characterize HGT events, especially for highly distant organisms. Here, we exploit that HGT between distant species creates long identical DNA sequences in distant species, which can be found efficiently using alignment-free methods. We analyzed over 90, 000 bacterial genomes and thus identified over 100, 000 events of HGT. We further develop a mathematical model to analyze the statistical properties of those long exact matches and thus estimate the transfer rate between any pair of taxa. Our results demonstrate that long-distance gene exchange (across phyla) is very frequent, as more than 8% of the bacterial genomes analyzed have been involved in at least one such event. Finally, we confirm that the function of the transferred sequences strongly impact the transfer rate, as we observe a 3.5 order of magnitude variation between the most and the least transferred categories. Overall, we provide a unique view of horizontal transfer across the bacterial tree of life, illuminating one fundamental process driving bacterial evolution.Competing Interest StatementThe authors have declared no competing interest.