Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio

Abstract

In the genomic era phylogenetic relationship among prokaryotes can be inferred from the core orthologous genes (OGs) or proteins in order to elucidate their evolutionary history and current taxonomy should benefits of that. The genus Salinivibrio belongs to the family Vibrionaceae and currently includes only five halophilic species, in spite the fact that new strains are very frequently isolated from hypersaline environments. Species belonging to this genus have undergone several reclassifications and, moreover, there are many strains of Salinivibrio with available genomes which have not been affiliated to the existing species or have been wrongly designated. Therefore, a phylogenetic study using the available genomic information is necessary to clarify the relationships of existing strains within this genus and to review their taxonomic affiliation. For that purpose, we have also sequenced the first complete genome of a Salinivibrio species, Salinivibrio kushneri AL184^T, which was employed as a reference to order the contigs of the draft genomes of the type strains of the current species of this genus, as well as to perform a comparative analysis with all the other available Salinivibrio sp. genomes. The genome of S. kushneri AL184^T was assembled in two circular chromosomes (with sizes of 2.84 Mb and 0.60 Mb, respectively), as typically occurs in members of the family Vibrionaceae, with nine complete ribosomal operons, which might explain the fast growing rate of salinivibrios cultured under laboratory conditions. Synteny analysis among the type strains of the genus revealed a high level of genomic conservation in both chromosomes, which allow us to hypothesize a slow speciation process or homogenization events taking place in this group of microorganisms to be tested experimentally in the future. Phylogenomic and orthologous average nucleotide identity (OrthoANI)/average amino acid identity (AAI) analyses also evidenced the elevated level of genetic relatedness within members of this genus and allowed to group all the Salinivibrio strains with available genomes in seven separated species. Genome-scale attribute study of the salinivibrios identified traits related to polar flagellum, facultatively anaerobic growth and osmotic response, in accordance to the phenotypic features described for species of this genus.

Keywords: Salinivibrio; Salinivibrio kushneri; complete genome; genomics; halophilic bacteria; hypersaline environments; phylogenomics; synteny.

FIGURE 1

Dot plots displaying the comparison of assembled contig 1 (A) and contig 2 (B) of Salinivibrio kushneri AL184^T against itself. The enlarged images of the dot plots show that both ends of each contig are identical and, therefore, demonstrate that they constitute two circular chromosomes.

FIGURE 2

Graphical circular map of the chromosome I (A) and choromosome II (B) of S. kushneri AL184^T. From the outer to inner chromosomal rings: (1) predicted CDSs transcribed in a clockwise direction; (2) predicted CDSs transcribed in a counterclockwise direction; (3) GC content in a 1,000-bp sliding window; (4) GC skew (C-G/G+C) in a 1,000-bp sliding window; (5) rRNAs (red), tRNAs (yellow), ribosomal proteins (blue), flagellum and flagellar motility genes (green), compatible solute synthesis genes (gray), compatible solute transporters (black), and anaerobic respiration-related genes (purple).

FIGURE 3

Pairwise alignment of locally collinear blocks (LCBs) between large (A) and small (B) chromosomes of S. kushneri AL184^T and those of S. costicola subsp. costicola LMG 11651^T, S. costicola subsp. alcaliphilus DSM 16359^T, S. proteolyticus DSM 19052^T, S. sharmensis DSM 18182^T, and S. siamensis JCM 14472^T. Blue bands represents LBC > 100 Kb and gray bands LCB < 100 Kb.

FIGURE 4

Salinivibrio large (87 LCBs) (A) and small (30 LCBs) (B) chromosomes circular plots. Each circle represents a genome. From the outer most circle: S. kushneri AL184^T, S. costicola subsp. costicola LMG 11651^T, S. costicola subsp. alcaliphilus DSM 16359^T, S. proteolyticus DSM 19052^T, S. sharmensis DSM 18182^T, and S. siamensis JCM 14472^T. LCBs in the same color are shared by all six strains, with the exception of LCBs in black which are shared by less than the six strains.

FIGURE 5

Maximum-likelihood phylogenomic tree based on the concatenation of 776 single copy core genes showing the relationships among 45 Salinivibrio strains whose genomes are available. Bootstrap values ≥ 70% are shown at the nodes. Bar, 0.02 nt changes per position.

FIGURE 6

Progression of the pan-genome (red) and core-genome (blue) of the 45 Salinivibrio genomes based on protein (A) and gene (B) sequences.