Evolution of gene repertoire and genome structure in bacteria

Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet, in contrast to the core genome where diversification is readily described by mutations and homologous recombination, the dynamics of accessory genome evolution are very poorly understood. To determine mode and tempo of evolution of genome content and structure, we constructed a pan-genome graph of ~200 closely related Escherichia coli ST131 genomes. Within this diversity, we estimate around 2,000 structural changes within the accessory genome corresponding to roughly one structural change for every three core genome substitutions. Furthermore, we show that the dominant mode of structural evolution is gains due to insertion sequences and prophage integration. Our results suggest a very broad distribution of rates at which genome structure and and content evolve. Some loci seem to saturate in diversity over a few decades, while synteny is conserved over millions of years.