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Fig. 1 | Genome Medicine

Fig. 1

From: Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA

Fig. 1

Epidemiology of S. pneumoniae GPSC12. A Evolutionary reconstruction of GPSC12. The left panel shows a recombination-corrected maximum-likelihood phylogeny of GPSC12, with branch lengths in point mutations per genome. The branches coloured red have been truncated to a length of 250 point mutations; the unmodified tree is shown in Additional file 1: Fig. S2, and can be interactively visualised using Microreact (https://microreact.org/project/gpsc12-recombination-dynamics). The adjacent columns describe the distribution of genetic characteristics across the collection, with one row per isolate, according to the legend at the bottom of the panel. The leftmost column assigns isolates to clades; the next column displays whether the unmodified csRNA3 or phage-modified csRNA3L was detected in the isolate; the next column shows whether attBOXC is intact or disrupted by a prophage insertion; and the rightmost column shows whether a ϕOXC141-like prophage is present in the isolate. The right panel shows the distribution of inferred recombination events across the strain using a grid in which each row corresponds to an isolate, and each column a base in the reference genome, the annotation of which is displayed across the top. The recombination events are coloured red if they were reconstructed as occurring on an internal branch, and therefore are shared by multiple isolates through common descent, or blue if they were reconstructed on a terminal branch, and are therefore unique to a single isolate. B, C Recombination dynamics within GPSC12. The extent of recombination inferred to occur within each clade is quantified as the ratio of base substitutions introduced by recombination, relative to the number occurring through point mutation (r/m), in B, and as the number of recombination events relative to point mutations (ρ/m) in C

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