Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792

Abstract

Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The aim of this work was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78 %) than to those of the other closely related species Vibrio owensii (67 %), Vibrio rotiferianus (63 %) and Vibrio campbellii (59 %). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA-DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. The pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. BLASTP atlases were created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…This example demonstrated the promise of SNP genotyping technology for analysis of genetic relationships in veterinary and environmental microorganisms. A comparison of genome regions in Vibrio harveyi and related species with the shrimp pathogen V. harveyi (CAIM 1792) demonstrated its higher similarity to those of other V. harveyi strains than to those of the other closely related species V. owensii, V. rotiferianus and V. campbellii (Espinoza-Valles et al, 2015). The SNP trees showed that V. harveyi is the most conserved of the four species studied, and V. campbellii may be divided into at least three subspecies.…”

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

“…The presence of a pan-genome is associated with increased intra-species diversity, environment/host adaptations, and differentiations in pathogenic mechanisms (Tettelin et al, 2008 ). Several pan-genomic studies exist for different fish microorganisms, including marine pathogens such as Aeromonas salmonicida (Vincent and Charette, 2017 ), the Alteromonas ssp genus (López-Pérez and Rodriguez-Valera, 2016 ), and Vibrio harveyi (Espinoza-Valles et al, 2015 ). To define the entire core- and pan-genomes of an organism, a large quantity of fully sequenced genomes is essential.…”

Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade

“…Such data have aided the study of phylogenomics 2 3 21 and the identification of diagnostic features in Vibrio species 22 . A recent study of V. harveyi compared the genome of this species with those of three other related ones 21 . Nevertheless, a detailed genomic analysis of the frequently misidentified pathogen V. campbellii is still absent.…”

“…By applying genome-wide data, microbial taxonomy can be established via (1) average nucleotide identity (ANI) among sequences between two genomes 23 , and (2) the phylogeny of concatenated single copy orthologues, such as a core genome tree 2 21 . ANI ≥ 95% against type strains has become a commonly accepted definition of species 3 24 .…”