SUPPLEMENTAL FIG. 1. Comparison of B. subtilisSP, S. epidermidis RP62a SP-like phage, and COL.

Shown are the schematic diagrams of B. subtilisSP, S. epidermidis RP62a SP-like phage (B), and COL (C). ORFs are colored according to functional categories as defined in the colored boxes. Positions within the respective genomes are indicted as genome coordinates on the ends of each schematic. Matches between B. subtilisSPand S. epidermidis RP62a SP-like phage are based on BLASTP data where SPwas the query and SP-like was in a WU-BLAST-formatted database. Only those ORFs with a percent identity ≥ 35% and p-value of ≤ 1×10-5 were considered significant. Matches were colored based on percent identity as follows: blue, 35-49% identity; brown, 50-59% identity; gold, 60-79% identity; green, 80-89% identity; red, 90-100% identity. Putative transcriptional terminators (red lollypops) were found using the TIGR program TransTerm ( Putative functions of selected COL and the S. epidermidisSP-like phage accompany the locus numbers. Putative functions of all COL and S. epidermidis SP-like phage ORFs and their locus numbers are presented in Supplementary Table 3. Complete DNA sequence and annotation for B. subtilisSP was obtained from GenBank ID AF020713. All B. subtilisSPidentified with a NT prefix are from TIGR annotation.

SUPPLEMENTAL FIG. 2. Comparison of S. aureus and S. epidermidis SSCmec elements and S. epidermidis ATCC SSCpbp4.

Shown are the schematic diagrams of S. hominus SSChominus (A), S. epidermidis RP62a SSCmec-typeII (B), S. epidermidis ATCC12228 SSCpbp4 (C), S. aureus MW2 SSCmec-typeIVa (D), S. aureus COL SSCmec-typeI (E), S aureus N315 SSCmec-typeII (F), and S. aureus 85/2082 SSCmec-typeIII (G). ORFs are colored according to functional categories as defined in the colored boxes. Positions within the respective genomes are indicted as genome coordinates on the ends of each schematic. Matches between the SSC elements are based on BLASTP data where (B) was the query in group (A,B,C), (E) was the query in group (D,E,F) and (F) is the query in group (B,F,G). Only those ORFs with a percent identity ≥ 35% and p-value of ≤ 1×10-5 were considered significant. Matches were colored based on percent identity as follows: blue, 35-49% identity; brown, 50-59% identity; gold, 60-79% identity; green, 80-89% identity; red, 90-100% identity.

Putative functions of selected ORFs accompany the gene locus number. Putative transcriptional terminators (red lollypops) were found using the TIGR program TransTerm ( Putative functions of all ORFs and their locus numbers are presented in Supplementary Table 4. All ORFs with a NTSE or NTSA prefix are from TIGR annotation. Complete DNA sequence and annotation for S. aureus 85/2082 SSCmec-typeIII was obtained from GenBank ID AB047089. Complete DNA sequence and annotation of S. hominus SSChominus (26) was obtained from GenBankID AB063171.

SUPPLEMENTAL FIG. 3. Distribution of NS-SNPs grouped by main role category in S. aureus strains Mu50, N315 and MW2.

On the left Y-axis is displayed the total number of NS-SNPs for each main role category: purple bars, strain Mu50; blue bars, strain N315; green bars, strain MW2. On the right Y-axis is displayed the percentage of NS-SNPs for each role category, from the total number of NS-SNPs: purple diamonds, strain Mu50; blue triangles, strain N315; green diamonds, strain MW2. Pathogenesis, which belongs in the role category of cellular processes, has been separated to demonstrate the high levels of mutations that have occurred in the genes in this role category.

SUPPLEMENTAL FIG. 4. Distribution of NS-SNPs grouped by main role category in S. epidermidis strain ATCC12228.

On the left Y-axis is displayed the total number of NS-SNPs for each main role category: purple bars, strain ATCC12228. On the right Y-axis is displayed the percentage of NS-SNPs for each role category, from the total number of NS-SNPs: purple diamonds, strain ATCC12228.

1