Comparative genomics of Vibrio toranzoniae strains

Abstract

Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade, originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at genome level among strains, as well as to determine their phylogeny. For this purpose, whole genomes were sequenced by different technologies and the resulting sequences corrected. Genomes were annotated and compared with different online tools. Furthermore, the study of core and pan genome was examined, and the phylogeny was inferred. The content of the core genome ranged from 2,953 to 2,766 genes and that of the pangenome from 6,278 to 6,132, depending on the tool used. The comparison revealed that although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI higher than 97%,notable differences were found related to motility, capsule synthesis, iron acquisition system or mobile genetic elements. The phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle, but that of the pangenome pointed out certain geographical isolation in the same growing area. The study led to a reclassification of some isolates formerly described as V. toranzoniae and manifested the importance of cured deposited sequences to proper phylogenetic assignment.

Keywords: Vibrio toranzoniae; genome sequencing; phylogenomics; virulence genes.

Figure 1

Values of OrthoANI for the strains of study.

Figure 2

Phylogenetic tree of the core genome of V. toranzoniae and V. kanaloae strains.

Figure 3

Pangenome analysis of V. toranzoniae strains. (A) Partition of the OMCL pangenomic matrix into shell, cloud, soft-core, and core compartments; (B) Estimate size of core genome.

Figure 4

Phylogenomic tree based on pangenomic matrix of V. toranzoniaestrains.