Fig. 3.—

Phylogenetic relationship of PaLoc accessory genes. Phylogenies of the PaLoc accessory genes (A) tcdR and (B) tcdE, which encode a positive regulator and a putative holin gene, respectively. The A⁻B⁺ tcdR gene (from strain AI27, marked with asterisk) clustered closest to the A⁺B⁺ lineage (A) was a hybrid of the two sequences suggesting it derived from a recombination event (data not shown). The putative holin gene present in the PaLoc of clade 5 A⁻B⁺ strains is distantly related to that found in the other clades (B), suggesting it was gained via allelic exchange with another source. Strain labels are shown in supplementary figure S2, Supplementary Material online.