Figure 2. Genetic environments of the C1-M27 clade–specific region of Escherichia coli. All isolates other than the C1-M27 clade isolates had the type A structure in their chromosome (red arrows; gene locus tags shown in the bottom are annotated according to EC958). The C1-M27 clade isolates except 2 isolates (KUN5781 and Ec 24) had the type B structure. A 11,894-bp region (M27PP1; predicted genes shown in light blue arrows) is inserted into the type A structure creating the 7-bp direct repeat (CCGTTCT; yellow triangle). The inserted sequence M27PP1 is identical to a prophage-like genomic island in E. coli PCN033 chromosome (GenBank accession no. CP006632), which had the similar flanking structure (structure C, 98.8% similarity). M27PP1 included phage-like integrase and recombinase. The identical M27PP1 sequence was found in all of the C1-M27 isolates with the use of additional Sanger sequencing. Only the draft genome of IEH71520 had 98.7% coverage to the M27PP1 sequence because of contig discontinuity. KUN5781 and Ec 24 had the type D structure, of which an additional 19,352-bp region (M27PP2) is inserted into the type B structure by creating the same 7-bp direct repeat (yellow triangle). The M27PP2 includes a total of 15,555-bp region (genes shown in orange arrows), which was 88.9% similar to a prophage-like region in γ proteobacterium HdN1 chromosome (GenBank accession no. FP929140) and a following 1,221-bp region is 99.8% similar to ISSen4 (purple box). Code to gene locus tags: 1, 958RS23365; 2, 958RS23370; 3, HDN1F03950; 4, HDN1F03970; 5, HDN1F04000; 6, HDN1F04010; 7, HDN1F04020; 8, HDN1F04030; 9, HDN1F04040; 10, ISSen4; 11, 033RS22420; 12, 033RS22425; 13, 033RS22430; 14, 033RS22440; 15, 033RS22450; 16, 958RS23380.