Characterisation and distribution of SNPs in ST313 lineage I and lineage II.

<p><b>A</b>. Unrooted maximum likelihood tree showing relationships between lineage I (blue), lineage II (red) and gastroenteritis-associated isolates (grey polygons). Size of polygons represents numbers of taxa in the clade. Representative isolates from each group are highlighted within each clade. Scale bar indicates substitutions per variable site. Numbers in light grey boxes indicate parental branches leading to the respective ST313 lineages as shown in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003611#pntd.0003611.t001" target="_blank">Table 1</a>. Text boxes indicate selected degraded genes (pseudogenes—light green and deletions—light blue occurring on the respective branches). Re-used with permission from Okoro <i>et al</i>., Nat Genet. 2012. 44(11): 1215–21. doi: <a href="http://dx.doi.org/10.1038/ng.2423" target="_blank">10.1038/ng.2423</a>. List of degraded complement for strain D23580 is adapted from Kingsley <i>et al</i>., 2009. <b>B. Distribution of prophage elements and <i>Salmonella</i> pathogenicity islands in ST313 lineage I and II</b>. Top left panel represents concatenated phage sequences from strains D23580 (‘BTP’), SL1344 (‘SL’) and DT104 (‘DT’). Top right panel represents concatenated sequences of coding and non-coding sequences of SPI-1 to SPI-22 and CSS4 island. Sequence reads mapping to the complete feature length is represented as a heatmap. Green colour indicates >90% (high) coverage; light green indicates >30% but <90% coverage; and white indicates <30% (low) coverage. Isolate order in lineages I and II on left hand panel although not to scale, is according to phylogenetic positioning in 1A. <b>C</b> Distribution of phages and SPIs in selected non-ST313 isolates.