The fate of horizontally acquired genes: rapid initial turnover followed by long-term persistence

A major driver of bacterial evolution is horizontal gene transfer (HGT), the acquisition of genes from other strains or species. Transfers between closely related taxa are more likely to succeed, while the pervasive deletion bias of bacterial genomes drives frequent turnover of horizontally acquired genes. However, whether the rate of gene loss after acquisition is constant across lineages or time remains unclear. Here, we analyze a comprehensive dataset of bacterial genomes to infer the frequency, distribution, and retention of inter-phylum HGT events. The retention of inter-phylum gene transfers is highly skewed, with only a small subset of bacterial genomes accounting for the majority of such events. Most transferred genes are lost rapidly. Those genes that survive the initial purging are retained over long periods, are biased toward functions such as transport and metabolism, and have larger numbers of protein-protein interactions.