US PST-43 may belong to the same clonal lineage as the UK isolates PST-87/7 and PST-08/21. A. Dendrograms illustrating that US isolate PST-43 clustered with the two UK isolates PST-87/7 and PST-08/21. Dendrograms were constructed using the homokaryotic SNP information either in the coding or non-coding regions of the genome from all pair-wise alignments. B. Pair-wise comparison of non-synonymous mutations in synthetic gene sets illustrated that polymorphisms were more apparent when corresponding proteins representing PST-21 and PST-130 were compared against other isolates. Each gene for a given reference was taken in turn and any homokaryotic SNPs incorporated for each isolates mapped. The five genes (one reference gene and four synthetic genes) were then subjected to pair-wise polymorphism and positive selection analysis using Yn00. Circle sizes represent the number of proteins with at least one non-synonymous mutation (green circles) or under positive selection (purple circles). Pair-wise comparisons that showed enrichment in non-synonymous mutations in secreted proteins are illustrated with an orange background. C. The total number of genes determined as absent by mapping the sequence reads from each isolate in turn against every other isolate as a reference was greater for alignments against PST-21 and PST-130 when compared to alignments against PST-43, PST-87/7 and PST-08/21. A similar pattern was also observed when genes encoding predicted secreted proteins were assessed. Total number of genes absent from white to blue (0-482) for full gene complement and white to red (0-14) for secretome.