Fig 2. Sliding window analysis of single-nucleotide polymorphism (SNP) distribution, recombination analysis and phylogenetic relationships among S. suis ST25 strains.

A) In a group of 23 North American strains (defined as North American variant 1, NA V1 Strains) SNPs were distributed across the genome of the reference strain. Sliding windows were created using R-software and custom scripts and a window of 5 kbp. B) In a group of 19 North American strains (NA V2 Strains), SNPS distribution was non-random, and an overabundance of polymorphisms was identified between positions 1 to 1.035 Mbp of the NSUI060 genome. C) In all 8 Thai strains, SNP distribution was non-random, with two distinct peaks (positions ~740 kbp to ~760 kbp and ~790 kbp to ~860 kbp of the reference genome) showing overabundance of SNPs. D) SNP distribution in a single Canadian strain (NSUI069) also identified overabundance of SNPs in discrete areas of the reference genome. E) The left panel depicts results of Bayesian analysis of recombination for 51 ST25 S. suis strains. The colored bars denote recombination events identified for each strain relative to the core ST25 genome. The coloring of the bars at a specific genomic location reflects the clustering of the recombination events into groups, and is unrelated to other bars at distant genomic locations. The right panel shows a Neighbor-joining phylogenetic tree constructed using 3,023 non redundant SNP loci identified among all ST25 S. suis strains relative to the core ST25 genome devoid of areas having undergone recombination. The different clades are indicated by the different colors used to label strain names, circles represent strains that were isolated from a swine host, and triangles represent strains that were isolated from a human host. Variants defined by sliding window analysis are also indicated.