Phylogenetic Relationship Among Brackishwater
Vibrio Species.
Evol Bioinform Online 2020;
16:1176934320903288. [PMID:
32214789 PMCID:
PMC7065438 DOI:
10.1177/1176934320903288]
[Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae
in hatcheries. Among the Vibrio species, Vibrio
parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii,
Vibrio harveyi, Vibrio alginolyticus, and Vibrio
anguillarum are often associated with diseases in finfish and
shellfish of brackishwater ecosystem. Accurate species differentiating methods
for the organisms present in an ecosystem are required for precise
classification of the species and to take steps for their management.
Conventional methods like 16s rRNA phylogeny and multilocus sequence typing
(MLST) have often failed to correctly identify Vibrio species.
This has necessitated a comprehensive investigation on methodologies available
to distinguish Vibrio species associated with brackishwater
aquaculture system. To achieve this, 35 whole genomes belonging to 7
Vibrio species were subjected to phylogenetic analysis
based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and
single-nucleotide polymorphisms. In addition, genome-based similarity indices
like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH)
were computed as confirmatory tests to verify the phylogenetic relations. There
were some misclassifications occurred regarding phylogenetic relations based on
16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous
genes produced accurate species-level clustering. Study reveals that the species
identification based on whole genome-based estimates or genome-wide variants are
more precise than the ones done with single or subset of genes.
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