Genome sequencing and comparative genomics

The 05HAS68 S. suis genome was sequenced and assembled using the routine random shotgun method [12]. Prediction of putative coding sequences (CDSs) and gene annotation were done using the NCBI’s Microbial Genome Annotation Tools and Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/browse/reference/). The predictions and the slices were then searched against the NCBI Entrez Protein Cluster database (https://www.ncbi.nlm.nih.gov/proteinclusters/browse/stats/) as well as proteins from all complete microbial genomes. The genome sequence feature information was visualized using the CGView genome visualization program ([13] http://stothard.afns.ualberta.ca/). Annotation was supplied from both sets and supplemented with information from the Conserved Domain Database (https://www.ncbi.nlm.nih.gov/cdd) and from Clusters of Orthologous Groups [14]. The protein sets of strains 98HAH33, P1/5 and 05HAS68 were compared using FASTA3. The sequence alignment was produced by Mauve Genome software [14] and the phylogenetic tree was built using CLC Genomics Workbench 3.2 software (https://www.qiagenbioinformatics.com/genomics/). Comparison of S. suis genome structures was done as follows: pair wise comparisons of the P1/7, 05ZYH33 and 05HAS68 displayed chromosomes was done using the Artemis Comparison Tool (ACT) [15, 16] and a dot matrix was used to show the relatedness of genome sequences generated with MUMmer [17]. The 05HAS68, 98HAH33, 05ZYH33 and P1/7 CRISPR defense systems were analyzed using CRT1.1 software [18]. Identification of the bacterial CRISPR-associated proteins (Cas) adjacent to the CRISPR loci and comparative analysis of proteins from putative prophages, viruses (bacteriophage and viruses of archaea), and plasmid-like sequences was done using the Non-Redundant GenBank databases (https://www.ncbi.nlm.nih.gov/genbank/).