Fig. 2: Genomic description, phylogenetic context, and shared protein orthologues of study strains.

The 20 complete genomes for A E. coli; B KpSC; C S. aureus; D S. pyogenes are illustrated. For each, the composition of the genome is illustrated as bubbles, with the chromosome represented by the largest bubble, with key features annotated, and the smaller bubbles representing plasmids, the size of which is a semi-quantitative representation of the plasmid size. The ___location of each genome in the respective phylogenetic trees for each species is illustrated; the tree representing all complete genomes for the species available in GenBank as of June 2020, and constructed using Mashree v1.1.2 based on the distance calculated from 50,000 k-mers. Clonal Groups (CG) and Clonal Complexes (CC) of interest for the species are annotated. Adjacent to each tree is an UpSet plot and a pie chart, illustrating the results of hierarchical protein orthologue clustering, performed with pirate v1.0.2. Predicted protein-coding sequences were clustered at five thresholds of amino acid identity (50%, 60%, 70%, 80%, 90%). The distribution of all orthologue clusters represented in a species at these thresholds is indicated in the pie chart. The sharing of orthologue clusters amongst the respective genomes (in various combinations or in isolation) is shown in the UpSet plot, ordered based on the frequency and coloured to match the genomes as illustrated in the phylogenetic trees. Asterisks (*) indicate the orthologue clusters that are conserved within a species (i.e., the ‘core’ cluster for each species). The corresponding list of core orthologue clusters is detailed in Supplementary Data 1 (E. coli), 2 (KpSC), 3 (S. aureus), and 4 (S. pyogenes). Combinations with less than ten shared orthologue clusters are not shown.