Genetic Diversity Among Subspecies Revealed by Analysis of Complete Genome Sequences.

comprises four subspecies that contain both human and veterinary pathogens. At the inception of this study, twenty-eight genomes had been annotated as RefSeq genomes, facilitating direct comparisons. These genomes represent strains from around the world and provided a unique opportunity to examine genome dynamics in this species. Each genome was confirmed to be classified correctly based on SNP genotyping, nucleotide identity and presence/absence of repetitive elements or other typing methods. The subspecies () genome size and organization was remarkably consistent, averaging 4.8 Mb with a variance of only 29.6 kb among the 13 strains. Comparing recombination events along with the larger genome size and variance observed among subspecies () and subspecies () strains (collectively termed non-) suggests horizontal gene transfer occurs in non-, but not in strains. Overall, subspecies could be divided into two major sub-divisions, with the type II (bovine strains) clustering tightly on one end of a phylogenetic spectrum and strains clustering more loosely together on the other end. The most evolutionarily distinct strain was an ovine strain, designated Telford, which had >1,000 SNPs and showed large rearrangements compared to the bovine type II strains. The Telford strain clustered with strains as an intermediate between type II and . SNP analysis and genome organization analyses repeatedly demonstrated the conserved nature of versus the mosaic nature of non- strains. Finally, core and pangenomes were developed for and non- strains. A total of 80% genes belonged to the core genome, while only 40% of non- genes belonged to the non- core genome. These genomes provide a more complete and detailed comparison of these subspecies strains as well as a blueprint for how genetic diversity originated.