RC586-GI-1 are located on the large chromosome and islets-3 and 4, and GIs-9, -10, -20, and -61 are located on the small chromosome (see Additional file 12). The VSP-I island is located at the homologous insertion locus for VSP-I (VOA_002906-VOA_002918) in V. cholerae strains, but is a variant of the canonical island having a deletion in VC0175 (deoxycytidylate deaminase-related protein) and 90% sequence similarity to the canonical island. Vibrio sp. RC586 also encodes five sequences with homology to the CTXΦ attachment site, with four of them being tandemly arranged on the putative large chromosome (VOA_000105-VOA_000126). At these loci are four elements

with high similarity ZD1839 in vivo (82 and 81% AAI) to the RS1Φ phage-like elements (rstA1 and rstB1) of V. cholerae SCE264 [33] and 97 to 100% nucleotide identity to the RS1Φ-like elements in V. cholerae TMA21, TM11079-80, VL426, and 623-39, reported by Chun et al. [17] to be GI-33 (Figure 3). RS1Φ is a satellite phage related to CTXΦ and assists in integration and replication of the CTXΦ [34, 35]. However, these V. cholerae strains were either CTXΦ-negative or encode a CTXΦ on the other chromosome, while encoding sequences with high similarity to

rstA, and rstB of RS1Φ, RS1-type sequences [33]. Immediately upstream of the rstA1-like sequence is an hypothetical protein and immediately downstream of this rstB1-like sequence is an hypothetical learn more protein with 52% identity with that of Colwellia psychrerythraea 34H, and Protein tyrosine phosphatase a sequence with 99% similarity to an end-repeat (ER) region and an intergenic region (ig) of CTXΦ (Figure 3). This region may represent a novel phage containing ORFs with similarity to the RS1Φ satellite phage and ER and ig-1 regions with high similarity to CTXΦ. Absence of an integrase in this region suggests it may integrate into the genome via XerCD tyrosine recombinases, as does CTXΦ. All putative

genomic islands shared by V. cholerae and Vibrio sp. RC586 are listed in Additional file 12. Figure 3 RS1Φ-like elements located at CTXΦ attachment sites on the large chromosomes of Vibrio sp. RC586 and Vibrio sp. RC341 and the canonical RS1Φ of V. cholerae. SHK = sensor histidine kinase, HP = hypothetical protein, ER = end repeat, ig = intergenic region. Vibrio sp. RC341 putatively encodes 14 sequences that are characteristic of genomic islands and islets that are also found in V. cholerae (see Additional file 11). VSP-I and -II and GIs-1 to 4, 33, and islets-1 to 5 are located on the large chromosome, while GI-9 and 10 are located on the small chromosome (see Additional file 11). These GIs were described by Chun et al. [17] and two are single copies of VSP-I (VCJ_003466 to VCJ_003480) and VSP-II (VCJ_000310 to VCJ_000324). Neither of the VSP islands was present in their entirety, compared to 7th pandemic V. cholerae strains. Similar to the VSP-I variant in Vibrio sp. RC586, the variant in Vibrio sp. RC341 has a deletion of VC0175.