Fig. 1
From: Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis
Prophages are common in sequenced Porphyromonas gingivalis isolates. Phylogenetic relationships among Pg shown on the left (79 strains; 88 leaves, including 3 substrains and 6 strains with independent assemblies), based on concatenated ribosomal protein genes. Relationships among Pg phages shown in midpoint-rooted tree at the top (30 full, 5 partial; “b” suffix indicates version of an “a” phage found in a different assembly of the Pg strain), based on whole genome nucleotide BLAST distance and scaled by VICTOR [28] d0 formula (recommended for nucleic acid datasets). Candidate genus- and species-level clusters are shown for full-length phages in the yellow bars. Three higher-order clades of phages defined by distinct insertion sites in host genomes (by full-length phages only) are highlighted (see color legend). Colored cells in the matrix indicate the assemblies in which each phage was found