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

Elife. 2021 Jun 14;10:e62719. doi: 10.7554/eLife.62719.


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.

Keywords: alignment-free method; antibiotic resistance; computational biology; genome evolution; horizontal gene transfer; infectious disease; microbiology; power law; systems biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / classification
  • Archaea / genetics
  • Bacteria* / classification
  • Bacteria* / genetics
  • Evolution, Molecular*
  • Gene Transfer, Horizontal / genetics*
  • Genome, Archaeal / genetics
  • Genome, Bacterial / genetics*
  • Genomics
  • Sequence Alignment
  • Sequence Analysis, DNA

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.