Evolutionary dynamics of genome structure and content among closely related bacteria

Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of E. coli ST131, which likely shared a common ancestor around one hundred years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6000 core genome mutations. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2000 structural changes within the accessory genome, i.e. one structural change for every 3 core genome mutations. 63% of loci with structural diversity could be resolved into individual gain and loss events with ten-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in bacterial genomes are likely deleterious and only persist for a short time before being removed by purifying selection.