On the origins of a Vibrio species

Abstract

Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.

Figure 1

Phylogenetic tree of the 16S rRNA gene extracted from 32 sequenced Vibrio genomes listed in Table 1. Environmental V. cholerae lacking the cholera enterotoxin genes are highlighted in bright green, whilst pathogenic V. cholerae genomes are in dark green. Further colouring was used for species for which two genomes are represented

Figure 2

Pan-genome family clustering of the 32 Vibrio genome sequences. The two plots represent weighted values for genes present in at least 90% of the genomes (stabilome) or genes found in only a few (two to four) genomes (mobilome). The colours highlighting the species are the same as in Fig. 1

Figure 3

Pan- and core genome plot of the 32 Vibrionaceae genomes. The colours highlighting species are the same as in Fig. 1

Figure 4

BLAST matrix of the 32 Vibrionaceae genomes. The colours highlighting the species are the same as in Fig. 1. Since the reciprocal similarity (reported as percent) is not readable at this resolution, every matrix cell is coloured using the scales as indicated. The bottom row identifies hits (other than hits-to-self) found within a genome. Four matrix cells reporting high pairwise similarities are outlined; their numbers are specified in the text

Figure 5

BLAST atlas with V. cholerae strain N16961 as a reference strain, showing chromosomes 1 (top) and 2 (bottom). The best BLAST hits identified with genes from N16961 in the other V. cholerae genomes are represented in dark red, for the location as it appears in N16961. Blast hits in the other genomes are shown in various colours as indicated to the right. Major areas conserved in V. cholerae but not in other Vibrionaceae are identified as gap B, gap C, gap D and gap F in green; areas that are found in toxigenic V. cholerae only are marked black as gap A, gap E and gap G. The superintegron on chromosome 2 of V. cholerae is also indicated