Phylogenetic tree.

<p>Branch lengths are proportional to the total number of SNPs, which are indicated above or below the branches. Genomes sequenced in this study are in bold face. The genomic groups (I–VII) and plasmid types are denoted as described <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085417#pone.0085417-Beare1" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085417#pone.0085417-Glazunova1" target="_blank">[26]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085417#pone.0085417-Hornstra1" target="_blank">[28]</a>. CanSNP markers are depicted in red (C.1–C.15) and the corresponding MST markers are depicted in grey. The genomes Cb109, Cb175 and Z3055 became available after the time of assay design resulting in four new branches (C.12 to C.15). Although not included in this work, it demonstrates that the systematics of canSNPs easily can be extended when new genomes become available. The ancestral and derived state for C.1 and C.2 could not be determined due to the lack of sequence from a near neighbor (a root). Therefore, we could only design one assay C.1 that could be on either the C.1 or C.2 branches.