Additional file 1: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Table S1. P. freudenreichii strains used in this study. Table S2. Average nucleotide identities of P. freudenreichii phages. (DOCX 71 kb

Additional file 4: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S3. Genome organization of phage G4. See Additional file 2: Figure S1 for details. (PDF 185 kb

Additional file 5: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S4. Genome organization of phage E1. See Additional file 2: Figure S1 for details. (PDF 152 kb

Additional file 2: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S1. Genome organization of phage B22. Predicted genes are shown as boxes either above or below the genome corresponding to rightwards- and leftwards-transcription, respectively. The gene numbers are shown within each colored box and its phamily number is shown above with the number of phamily members shown in parentheses; coloring reflects the phamily assignment. Grouping of genes into phamily of related sequences and map generation was performed using Phamerator (30) and the database ‘Actinobacteriophage_685’. Putative gene functions are listed above the genes. (PDF 164 kb

Additional file 7: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S6. Phylogenetic tree of tandemly repeated genes in P. freudenreichii phages. The four Cluster BW phages all encode two copies of related genes that are tandemly repeated in Doucette, B22, and E6, but which are separated by 17 genes in G4. The Cluster BV phage Anatole contains a single copy of this gene. Genes duplicated in one genome (e.g. Doucette 38 and 39) are more distantly related (51% aa identity) that with the corresponding gene in another genome (e.g. Doucette gp39 and B22 gp38 share 93% aa identity). Sequences were aligned using ClustalX and the tree drawn using NJPlot. Bootstrap values from 1000 iterations are shown. (PDF 22 kb

Additional file 6: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S5. Genome organization of phage B3. See Additional file 2: Figure S1 for details. (PDF 159 kb

Additional file 3: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S2. Genome organization of phage E6. See Additional file 2: Figure S1 for details. (PDF 161 kb

Genome maps of Mycobacteriophage BAKA.

<p>The annotated map of BAKA is represented as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069273#pone-0069273-g003" target="_blank">Figure 3</a>.</p

HNH endonuclease insertion regions.

<p><b>A</b>. Regions including <i>lysA</i> genes showing insertion of a free-standing HNH endonuclease into Courthouse upstream of <i>lysA</i>. <b>B</b>. LysA region of Optimus and Omega, showing two different predicted HNH endonucleases, Optimus gp51 and Omega gp51. <b>C</b>. Sequence alignment of Courthouse and Thibault shows a precise insertion of predicted HNH endonuclease. <b>D</b>. Sequence alignment of Optimus and Omega, showing the HNH insertion site.</p

HNH endonuclease phamilies in Cluster J phages.

<p><b>A</b>, <b>B</b>. Pham circles for phams 3687 (A) and 6944 (B). Phage names are organized by cluster/subcluster sequentially in a clockwise direction around the edge of the circle. Phages containing a gene within each pham are connected by an arc in blue (BLASTP) or red (ClustalW). Cirlces were drawn using Phamerator and thresholds of 32% identity and an E value of 10^-50 for ClustalW and BlastP respectively. <b>C</b>, <b>D</b>. Phylogenetic trees of pham 3687 genes (C) and pham 6944 genes (D). Trees were generated using ClustalW multisequence alignments and neighbor-joining. Trees were drawn using NJPlot. Phages are color coded to designate cluster assignment, as shown in the key.</p