The genome structure of the ST28 <i>S</i>. <i>suis</i> strain NSUI002.

<p>The following information on the NSUI002 genome is shown from the innermost circle: protein-coding genes transcribed clockwise (1^st track, blue) and counterclockwise (2^nd, blue), common genes that were shared among NSUI002 and all ST28 <i>S</i>. <i>suis</i> isolates, transcribed clockwise (3^rd, green) and counterclockwise (4^th, green), MGEs (5^th, black), and genes in the <i>cps</i> gene cluster (6^th, yellow). The common genes in which synonymous and nonsynonymous mutations were detected are shown in the 7^th (purple) and 8^th (gray) tracks, respectively. The outermost bar graph for the common genes in the 9^th track (red) shows the number of pairs in which nonsynonymous mutations were detected. No common gene exhibited a number of pairs more than 15, the maximum value of the graph.</p

The proportion of each pair classified by number of mutations.

<p>The number of mutations was calculated in each of 26 pairs, and its distribution is shown in ST1 and ST28 isolates as a percentage of pairs, as follows: gray bars for pairs with 0–5 mutations, blank bars for 6–20, dotted bars for 21–100, and filled bars for 101–300. Percentages are shown in ST1 and ST28 clones when genes on MGEs are excluded from the calculation.</p

<i>S</i>. <i>suis</i> isolates from Japan used in this study.

<p><i>S</i>. <i>suis</i> isolates from Japan used in this study.</p

Geographic location of porcine farms examined and results of encapsulated and unencapsulated <i>S</i>. <i>suis</i> isolates.

<p>(A) The map shows the northern east area of the main island of Japan from which <i>S</i>. <i>suis</i> was isolated in the present study. The farms are indicated by the following symbols: blank circles and blank triangles: encapsulated and unencapsulated <i>S</i>. <i>suis</i>, respectively, were exclusively isolated, and filled circles: encapsulated and unencapsulated <i>S</i>. <i>suis</i> were both isolated. The farm identifiers (alphabetical characters) and sample Nos. of endocarditis samples are indicated along the above symbols. The map was publicly available from the Geospatial Information Authority in Japan. (B) The heat map shows the encapsulation traits of 24 <i>S</i>. <i>suis</i> isolates in each of 59 endocarditis samples, with the following colors: blue for encapsulated, and red for unencapsulated isolates. Untypeable isolates in serotype-specific PCR are indicated by blanks. Encapsulated and unencapsulated isolates were exclusively from 31 (Nos. 27–57) and 2 (Nos. 58 and 59) endocarditis samples, respectively. Sample Nos. 1 to 26 were hereafter used as the No. of the pair of encapsulated and unencapsulated isolates.</p

A phylogenetic tree for 26 encapsulated and 26 unencapsulated <i>S</i>. <i>suis</i> isolates.

<p>The tree was constructed using the maximum parsimony method for genome-wide SNPs in 52 <i>S</i>. <i>suis</i> isolates. The 52 isolates analyzed were composed of 26 encapsulated and unencapsulated isolate pairs from 17 porcine farms, indicated by the following symbols: blank circles for encapsulated, and filled circles for unencapsulated isolates, with pair Nos. and farm identifiers (colored rectangles) along with the symbols. The isolates were separately clustered into two STs, ST1 and ST28; a detailed tree structure in each ST is shown as an enlarged tree. Several ends of the enlarged tree in ST28 are further enlarged. Seventeen colors are used to show distribution of farms in the tree. Only the bootstrap values >50% are indicated on the branches.</p

Nonsynonymous mutations and indels in the <i>cps</i> gene cluster between encapsulated and unencapsulated <i>S</i>. <i>suis</i> isolates in 26 pairs.

<p>The genetic organization of the <i>cps</i> gene cluster (from <i>cps2A</i> to <i>cps2S</i>) is shown as a sequence of the arrows located by transcriptional directions with the identifiers such as “A” for “<i>cps2A</i>”. The mutations between encapsulated and unencapsulated isolates in each pair are shown along with the genetic map, with the following symbols: red circles for nonsynonymous mutations, blue triangles for insertions, and gray rectangles for deletions along with the nucleotide length of the mutations.</p