Fig. 3.

ΔPtoH ratio and replication modes of induced S. Tm LT2^p22 prophages determined by high-throughput sequencing. (a) ΔPtoH ratio of each gene in mitomycin C-induced (n=3) S. Tm LT2^p22 cultures shown as mean l₂fc. The fold change in read coverage for each gene was evaluated using the DESeq2 package. Statistical significance required both a significant change of read coverage between induced and control cultures (Wald test; p value<0.05 after Benjamin Hochberg correction) and a l₂fc higher than one standard deviation of the mean l₂fc of all non-prophage genes. Data points in plots represent all protein-coding S. Tm LT2^p22 genes and are shown in orange if the l₂fcs were statistically significant (otherwise in grey). The l₂fcs along the S. Tm LT2^p22 genome resemble a one-sided and a two-sided tent-like shape around the genomic locations of the phages p22 (1,213,987-1,255,756) and FELS-1 (1,849,458-1,892,188). The grey dashed lines indicate the locations of the prophages Gifsy-2 and Gifsy-1. Detailed views of the genomic locations of the prophages p22 (b), Fels-1 (c) and Fels-2 (d). Mean OPR counts in induced (red) and control (dark purple) cultures are shown in the upper panel. Each bar represents the normalised mean count of OPRs that were aligned within the shown regions. The individual OPR counts per sample were normalised by the sample-specific median insert coverage of 10 single-copy MGs to yield OPR counts per cell before the overall mean OPR counts was calculated. The lower panel shows the patterns of the ΔPtoH ratio for each prophage and adjacent host regions. Orange data points with grey borders denote the genes containing the packaging site pac for p22 and cos for Fels-1