Core genes can have higher recombination rates than accessory genes within global microbial populations

Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. However, quantifying the impact of homologous recombination on different gene classes, which is critical to understanding how selection acts on variation to shape species diversity and genome structure, remains challenging due to the complex phylogenetic relationships of bacterial genomes. Here, we apply a non-phylogenetic approach to infer homologous recombination rates in the core and accessory genome (genes present in all strains and only a subset of strains, respectively) using >100,000 whole genome sequences from 12 microbial species. By sampling discrete sets of sequence clusters, we find global gene pools are remarkably interconnected despite biogeographic boundaries, which has implications for how population structure influences evolutionary trajectories. We show that in a majority of species, core genes have shorter coalescence times and higher recombination rates than accessory genes, and that gene frequency is often positively correlated with recombination. Our results indicate that homologous recombination may play a key role in increasing the efficiency of selection in critical gene classes.