Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

Abstract

Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and individual analyses of locally collinear blocks. Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio logei have been newly sequenced and their genome sequences are documented here.

Results: Phylogenetic results for the 19-taxon datasets show similar levels of collinear subset of dataset incongruence as a previous study of 22 taxa from the sister family Shewanellaceae, while also echoing the strong phylogenetic performance of random subsets of data also shown in this study. Phylogenetic results for both the 19-taxon and 44-taxon datasets corroborate previous hypotheses about the placement of Photobacterium and Aliivibrio within Vibrionaceae and also highlight problems with how Photobacterium is delimited and indicate that it likely should be dissolved into Vibrio to produce a phylogenetic taxonomy. The 19-taxon and 44-taxon trees based on the large chromosome are congruent for the majority of taxa that are present in both datasets. Analyses of the 44-taxon sampling based on the second, small chromosome are quite different from those based on the large chromosome, which is not surprising given the dramatically divergent nature of the small chromosome and the difficulty in postulating primary homologies.

Conclusions: The phylogenetic analyses presented here represent the most comprehensive genome-level phylogenetic analyses in terms of taxa and data. Based on the availability of genome data for many bacterial species on GenBank, many other bacterial groups would also be amenable to similar genome-scale phylogenetic analyses even when present in multiple contigs. The result that collinear subsets of data are incongruent with the concatenated dataset and with each other while random data subsets show very little incongruence echoes the result of previous work on Shewanellaceae. The 44-taxon phylogenetic analysis presented here thus represents the future of phylogenomic analyses in scope and complexity.

Figure 1

Vibrionaceae large chromosome 306 LCB Circular Plot. Circular 306 LCB plot for the Vibrionaceae large chromosome. Each circle represents a genome. From the innermost circle: S. oneidensis, P. profundum, A. salmonicida, A. fischeri ES, A. fischeri MJ, V. anguillarum, V. furnissii, V. cholerae 0395, V. cholerae M66, V. cholerae MJ, V. cholerae El Tor, V. splendidus, V. vulnificus YJ016, V. vulnificus M06, V. vulnificus CMC, V. campbellii, V. sp. EJY3, V. sp. Ex25, V. parahaemolyticus.

Figure 2

Vibrionaceae small chromosome 37 LCB Circular Plot. Circular 37 LCB plot for the Vibrionaceae small chromosome. Each circle represents a genome. From the innermost circle: S. oneidensis, P. profundum, A. salmonicida, A. fischeri ES, A. fischeri MJ, V. anguillarum, V. furnissii, V. cholerae 0395, V. cholerae M66, V. cholerae MJ, V. cholerae El Tor, V. splendidus, V. vulnificus YJ016, V. vulnificus M06, V. vulnificus CMC, V. campbellii, V. sp. EJY3, V. sp. Ex25, V. parahaemolyticus.

Figure 3

Vibrionaceae 19–taxon trees from analysis of concatenated datasets. Topologies resulting from analyses of concatenated 19–taxon datasets. (a) RaxML large chromosome, and both chromosomes concatenated, (b) RaxML small chromosome, (c) TNT large chromosome and both chromosomes concatenated, and (d) TNT small chromosome. Clades are labeled P=Photobacterium clade, C=V. cholerae clade, O=V. orientalis clade, and V=V. vulnificus clade.

Figure 4

Vibrionaceae 19–taxon RaxML tree with support values. Topology resulting from a RaxML analysis of the large chromosome and also both chromosomes concatenated with support values at the nodes. The first number represents the percentage of LCBs of the large chromosome that when analyzed with ML, also contain that particular node. The second number represents the percentage of LCBs on the small chromosome that when analyzed with ML, also contain that particular node.

Figure 5

Vibrionaceae Large Chromosome Trees: 44–Taxon Dataset. Topologies resulting from analysis of the Vbirionaceae large chromosome for all 44 taxa: (a) TNT, (b) RaxML.

Figure 6

Vibrionaceae small chromosome trees: 44–taxon dataset. Topologies resulting from the analysis of the Vibrionaceae small chromosome for all 44 taxa: (a) TNT, (b) RaxML. Clades are labeled P=Photobacterium clade, C=V. cholerae clade, O=V. orientalis clade, and V=V. vulnificus clade.

Figure 7

RAST subsystems Circular Plot. From inner to outer: S. oneidensis, S. costicola, V. gazogenes, G. hollisae, P. damselae, P. profundum, P. angustum, P. sp. SKA34, A. logei, A. salmonicida, A. fischeri ES114, V. nigripulchritudo, V. mediterranei, V. metschnikovii, V. anguillarum, V. furnissii, V. cholerae El Tor, V. mimicus M, V. sp. RC341, V. sp. RC586, V. sp. N418, V. ichthyoenteri, V. scophthalmi, V. sinaloensis, V. corallillyticus, V. brasiliensis, V. orientalis, V. tubiashii, V. splendidus, V. vulnificus CMC, V. campbellii, V. sp. EJY3, V. parahaemolyticus, V. sp. Ex25, V. alginolyticus 12.