Eighteen repeat types of CRISPR/Cas detected in this study and their distribution among <i>Porphyromonas</i> species with their corresponding <i>cas</i> types.

<p>In each (CRISPR-associated) <i>cas</i> type, the presence or absence of each repeat type is shown for each <i>Porphyromonas</i> species by a black/white box. The boxes on the right side of the <i>cas</i> type name show the presence or absence of each <i>cas</i> type, regardless of repeat type. Representative genetic organization of CRISPR arrays and <i>cas</i> genes is shown for each repeat type with the name of <i>Porphyromonas</i> species. Two genetic organizations are shown if two representatives are hard to regard as the same organization in a particular type. The CRISPR arrays are indicated by yellow boxes. The CDSs are indicated by arrows, and CDSs of the predicted <i>cas</i> genes are colored, as described in the Materials and Methods section. The broken arrows indicate <i>cas</i> genes that are untypable using our criteria. All genetic elements are proportional to their nucleotide lengths, except for the CRISPR arrays.</p

Microbial species whose genomic regions were targeted by <i>Porphyromonas</i> CRISPR spacers.

<p>Microbial species whose genomic regions were targeted by <i>Porphyromonas</i> CRISPR spacers.</p

The number of potential targets in the NCBI Nucleotide Collection and in the <i>Porphyromonas</i> genomes, and dissection of the latter group by focusing on the locational relationships between the CRISPR spacer and its potential targets.

<p>(A) The number of potential targets of the <i>Porphyromonas</i> CRISPR arrays in the NCBI Nucleotide Collection and in the <i>Porphyromonas</i> genomes are shown in the left and right bar charts, respectively. In each chart, the numbers are presented, based on the number of mismatches. The numbers for the <i>Porphyromonas</i> genomes are excluded from the chart for the NCBI Nucleotide Collection. (B) The Venn diagram shows the relationships among spacers having intraspecies or interspecies targets and endogenous or exogenous targets. Two circles for spacers with endogenous and exogenous targets are overlapped on the left side to form one large population of spacers with intraspecies targets. This circle is overlapped with one circle on the right for spacers with interspecies targets. For instance, the number 33 indicates spacers with both endogenous and exogenous targets but without any interspecies targets. (C) The relationships between CRISPR spacers and their potential targets in <i>Porphyromonas</i> species. The left side presents the name of species with CRISPR arrays, and the lower axis shows species with potential targets of the CRISPR spacers in the genomes of the species on the left. The presence or absence of potential targets is indicated by blue or gray, respectively, and those that are targeted by CRISPR spacers of the same species are indicated by red.</p

Function of <i>Porphyromonas</i> genomic regions where CRISPR targets are located.

<p>Function of <i>Porphyromonas</i> genomic regions where CRISPR targets are located.</p

A schematic view of the locational relationships between CRISPR spacers and their potential targets.

<p>Endogenous interference of <i>Porphyromonas</i> CRISPR/Cas is supposed for the CRISPR spacer and its target, both of which are in the same species A. Exogenous interference is supposed for the spacer in the species A and its target that is introduced from another cell of the species A by the mechanisms such as natural transformation and conjugation. These endogenous and exogenous interferences are referred to as intraspecies interference in this paper. Interspecies interference is supposed for the spacer in the species A and its target introduced from the species B.</p

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