Figure 3

Phylogenetic relationships of 206 Clostridium perfringens genomes. (A) A maximum-likelihood (ML) phylogeny computed from the core genome SNPs using RAxML. Branch colouration denotes bootstrap values as described in the legend. Red colour coding at the tips of the tree indicate strains represented by closed genomes. The five major phylogroups are highlighted on the ML tree with boxes numbered I to V according to phylogroups described in the text. Strains’ origins and toxin types are plotted next to the ML tree. Bar plots represent the percentages of insertion sequences and the total size of the strains’ genomes, respectively. Genome size reported for closed genomes includes the chromosome and extrachromosomal elements. The presence (violet colour) or absence (white colour) of conjugation locus (tcp) in each strain is shown. The phylogenetic position of the historic Darmbrand strain is highlighted with a horizontal dotted line. The phylogenetic tree was visualized using iTOL ⁸¹ (B) SplitsTree phylogenetic network based on 63,036 unique SNP sites in the core genome of 206 C. perfringens strains with phylogroups highlighted. (C) The numbers of pairwise SNP distances between strains within each of the five phylogroups and between phylogroups are depicted. The plot was generated in R ⁸⁷ and edited in Adobe Photoshop CS5 (www.adobe.com/photoshop).