Table 1.
Genomes/strains used in this study.
Figure 1.
Neighbour-joining tree inferring phylogenetic relationships of 84 V. cholerae genomes based on 995 orthologous protein-coding genes (954,646 bp).
V. cholerae FL Group is labelled in red and V. cholerae V51 is labelled in blue. Haiti non-O1/non-O139 clinical groups-1 and -2 are further defined by Hasan et al. [6]. Numbers at nodes represent bootstrap values. Nucleotide substitution model is the Kimura-2-parameter. Bar length = 0.002 nucleotide substitutions per site.
Table 2.
ORFs with polymorphisms within the V. cholerae FL group.
Figure 2.
rstR sequences from V. cholerae CP1110.
Sequences are aligned to their most similar homologs extracted from NCBI Genbank database. Nulceotide sequence identity is shown to the right of the last nucleotide aligned for each allele.
Figure 3.
Comparative genomic analysis of Vibrio pathogenicity island 1 (VPI-1).
VPI-1 of the V. cholerae FL Group is the reference sequence in a BLAST alignment with homologs of other Vibrionaceae genomes. Colored squares show degree of similarity.
Figure 4.
Phylogenetic analysis of Vibrio pathogenicity island 1 (VPI-1).
Neighbor-joining tree showing evolutionary relationships of VPI-1. The calculation was based on aligned fragments of 25 orthologous genes (VC0819 to VC0845) comprising ca. 26.9 kb. Bar length = 0.005 substitutions per site.
Figure 5.
Comparative genomic analysis of Vibrio pathogenicity island 2 (VPI-2).
VPI-2 of the V. cholerae FL Group is the reference sequence in a BLAST alignment with homologs of other Vibrionaceae genomes. Colored squares show degree of similarity.
Figure 6.
Phylogenetic analysis of ORFs conserved among all T3SS-positive V. cholerae and closely related species.
Neighbor-joining tree inferred from an alignment of 7 orthologous genes (VCHE25_2738, VCHE25_2741, VCHE25_2742, VCHE25_2744, VCHE25_2745, VCHE25_2749, VCHE25_2754) comprising ca. 5.2 kb. Bar length = 0.05 substitutions per site.
Figure 7.
Phylogenetic analysis of most closely related T3SS.
Neighbor-joining tree inferred from an alignment of 17 orthologous genes (VCHE25_2737 to VCHE25_2742, VCHE25_2745 to VCHE25_2752, and VCHE25_2754) comprising ca. 10.2 kb. Bar length = 0.02 substitutions per site.
Figure 8.
Phylogenetic analysis of sialic acid metabolism region of VPI-2.
Neighbor-joining tree inferred from an alignment of 7 orthologous genes (VC1781 to VC1774) comprising ca. 5.7 kb. Bar length = 0.05 substitutions per site.
Figure 9.
Comparative genomic analysis of Vibrio Seventh pandemic island II-like island.
Vibrio Seventh pandemic II-like island of the V. cholerae FL Group is the reference sequence in a BLAST alignment with homologs of other Vibrionaceae genomes. Colored squares show degree of similarity.
Figure 10.
Structure of the canonical Vibrio Seventh Pandemic island II (VSP-II) and the VSP-II-like element of the V. cholerae FL Group.
Structure of the canonical VSP-II element of V. cholerae N16961 (top), the VSP-II-like element found in the V. cholerae FL Group (middle) based on the annotation in NCBI Genbank, and the homologous locus of insertion of this VSP-II-like element in V. cholerae N16961 (bottom). Sequences homologous to VC0208 and VC0209 in V. cholerae V51 are found on contig NZ_DS179740 at positions 34343 to 34831 and 34897 to 35763. ORFs conserved between the two elements are outlined in red.
Figure 11.
Phylogenetic analysis of Vibrio Seventh pandemic island II-like island.
Neighbor-joining tree inferred from an alignment 8 orthologous ORFs (VC0495, VC0496, VC0504 to VC0506, VC0508 to VC0510) comprising ca. 3.7 kb. Bar represents 0.02 substitutions per site.
Figure 12.
BLAST atlas of V. cholerae FL Group, V. cholerae V51, and V. mimicus MB-451 and V. cholerae N16961 genomes.
V. cholerae N16961 is the reference genome. Genomic islands with the prefix “GI” are described by Chun et al. [12]. SI = superintegron.
Figure 13.
Proposed hypothetical insertions of genomic islands in the V. cholerae V51/V. cholerae FL Group clade.
Figure 14.
Comparative genomic analysis of LPS coding regions.
Reciprocal BLAST analysis of LPS coding region with V. cholerae V51 as a reference.
Figure 15.
Comparative genomic analysis of LPS coding regions.
Reciprocal BLAST analysis of LPS coding region with V. cholerae FL Group as a reference.
Figure 16.
Survival curves of C. elegans challenged with V. cholerae CP1112, CP1114, CP1115, V. cholerae El Tor E7946, Escherichia coli OP50.