Prophages integrating into prophages: A mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli
Fig 2
Variation in the prophage content at the ompW, attB in PPompW, and yecE loci in STEC O145:H28.
In the left panel, an ML tree of 64 O145:H28 strains is shown. Completely sequenced strains are indicated in bold (plasmids were not finished for strain 2015C-3125). The tree was constructed based on the recombination-free SNPs (3,277 sites) identified on the conserved chromosome backbone (3,961,936 bp in total length) by RAxML using the GTR gamma substitution model [43]. The reliabilities of the tree’ s internal branches were assessed using bootstrapping with 1,000 pseudoreplicates. Along with the tree, the geographic and ST/clade information of strains, the presence or absence of prophages at three loci (ompW, attB in PPompW, and yecE) and the types of prophages at the attB in PPompW and yecE loci are shown. Prophages sequenced in this study and those in the finished genomes are indicated by asterisks and daggers, respectively. Note that the attB in PPompW sequence is missing from the PPompWs of strains EH2246 and 12E109; a deletion in the latter stain was detected in its draft genome assembly. The bar indicates the mean number of nucleotide substitutions per site. In the right panel, the patterns of the prophage content at the three loci are schematically presented. Strains showing each pattern are also indicated in the left panel by diagrams. For more details about the T3SS effector set, see Fig 3 and main text. Note that we detected recombination between the Stx2a phage at attB in PPompW and a prophage present at the ydfJ locus that induced a large chromosome inversion in strains 10942 and 499. In strain EH1910, an inversion appeared to have occurred by the recombination between PPompW and a prophage at ydfJ.