Phylogenetic Relationship Among Brackishwater Vibrio Species

Abstract

Vibriosis is one of the major diseases of concern to the aquaculture.1 Several Vibrio spp. of harveyi clade such as Vibrio parahaemolyticus, Vibrio alginolyticus, Vibrio harveyi, Vibrio owensii, and Vibrio campbellii infect farmed aquatic animals.2 They affect both fish and shrimp in marine environment and brackishwater aquaculture. Vibrio harveyi infections result in 80% to 100% mortality during the early larval stages and inflict huge economic losses to shrimp hatcheries.3 Vibrio parahaemolyticus is another opportunistic pathogen, which devastated the shrimp aquaculture sector in Southeast Asia in recent years by causing acute hepatopancreatic necrosis disease (AHPND), also called as early mortality syndrome (EMS).4 Due to the outbreak of AHPND, Thailand lost about 7% of production in 2012, Vietnam experienced USD7.2 million losses and Mexico lost USD118 million.5 Diagnosis of vibrios is done by phenotypic or polymerase chain reaction (PCR) tests for identification of these bacteria at species level. Accurate identification of species is difficult with the conventional phenotypic methods. Often, the 16s rRNA sequencing also fail to correctly identify Vibrio species. In such a scenario, application of bioinformatics tools can aid in differenti-ating these pathogenic strains.6 Vibrios are Gram-negative bacteria in the family Vibrionaceae under the phylum Gammaproteobacteria and are found abundantly in marine environments.7 Genome of vibrios contains 2 chromosomes, of which chromosome 1 is longer than chromosome 2 and is about two-thirds of total genome regarding its length. The longer chromosome carries housekeeping genes, while the smaller one has accessory genes.8,9 The GenBank (https://www.ncbi.nlm.nih.gov/) consists of 88 complete genomes of vibrio species as on April 2019.

Recent advances in next-generation sequencing made it possible to study the phylogenetic relations of targeted organisms more accurately at genome level using in silico approaches. Several whole genomes of Vibrio spp. sequenced from different laboratories located around the globe were deposited at GenBank and made readily available for reanalysis studies. Present study aims at finding appropriate methods for differentiating and finding evolutionary distances of Vibrio spp. that are more commonly found in brackishwater ecosystem with the available complete genomes and modern bioinformatics tools.