Draft genome sequence data of Vibrio harveyi VH1 isolated from a diseased tiger grouper, Epinephelus fuscoguttatus, cultured in Malaysia.

Vibriosis accounts for 66.7% of diseases reported in groupers' cultures and affects almost all stages of growth. The disease could lead up to mortality up to 50% mortality, and it was reported that high stocking density and poor fish handling were among the factors that contributed to the disease dissemination. V. harveyi has been reported to be among the causative agent and has caused acute mortality in cage groupers. In this study, we report the genome of V. harveyi VH1 isolated from a diseased tiger grouper Epinephelus fuscoguttatus, reared in a cage farm located in the coastal area of Langkawi.

Specification Table

Value of the Data

The draft genome of Vibrio harveyi VH1, isolated from cultured marine fish (E. fuscoguttatus) will be useful for further research on the virulence gene transfer of V. harveyi and Vibrio spp. in general.

Data on the genome sequence of Vibrio harveyi VH1 can be used for comparative genomic studies with other Vibrio spp. disease isolates from other places.

Data on the genome sequence of Vibrio harveyi VH1 could be used to identify and characterize important virulence factors that contribute to the pathogenesis.

Data is useful for the bioinformatician and bacteriologist to better understand the genetic features of Vibrio harveyi VH1 and novel insights about its key virulence determinants.

Data Description

The draft genome of V. harveyi strain VH1 was reported in this finding. The draft genome assembly of V. harveyi strain VH1 has a length of 6,094,415 bp and a GC content of 44.8% (Fig. 1). The paired-end reads were assembled de novo into three huge contigs using Canu 1.6 with error and mismatch correction (N50, 3,675,737 bp). Annotation of the draft genome with RAST (Rapid Annotation using Subsystem Technology) 2.0 identified 416 subsystems, 8763 coding sequences (CDS), and 161 total RNAs in the genome (Table 2). 108 coding sequences involves in virulency, diseases, and defense which inclusive of bacteriocins productions, ribosomally synthesized antibacterial peptides, and resistance to antibiotics (Fig. 2). Four coding sequences were found to have identity with phages, prophages, transposable elements and plasmids [1], [2], [3], [4].

Fig. 1

Circular map of the V. harveyi VH1 genome. From the outermost circle to the center: CDSs on forward strand (including tRNA, rRNA and mRNA), open reading frame (ORF), Contigs, GC skew+ and GC skew-, GC content, BLAST results, and the marker of genome size is the innermost circle.

Table 2

Genome features of V. harveyi VH1.

Attribute	Description
Genome size (bp)	6,094,415 bp
G+C content (%)	44.8%
CDS (coding sequences)	8763
rRNA number	37
tRNA number	124
Genbank accession	JAAIKJ000000000
BioSample acession	SAMN14091020
BioProject acession	PRJNA606422

Fig. 2

The subsystem category distribution of V. harveyi VH1 based on the SEED viewer RAST.

Besides that, 219 coding sequences involved in motility and chemotaxis, 120 coding sequences involved in regulation and cell signaling, 139 coding sequences involved in stress response, and 158 coding sequences involved in cell respiration. The genome sequence of V. harveyi VH1 serves as an additional genomic resource for comparative genomic studies of other V. harveyi strains that infected marine fish (Fig. 2).

Experimental Design, Materials and Methods

V. harveyi strain VH1 was isolated from the skin lesion samples originated from a male diseased tiger grouper Epinephelus fuscoguttatus, reared in a cage farm located in the coastal area of Langkawi, Malaysia (Table 1). The V. harveyi isolate was cultured and maintained in thiosulfate-citrate-bile salts (TCBS) (Oxoid) agar and tryptone soy broth (TSB) (Oxoid), supplemented with NaCl (1.5% w/v) at 30 °C. A TCBS agar is a selective medium for enteropathogenic Vibrio spp. When cultured on TCBS agar, the colonies of pathogenic V. harveyi strain VH1 appeared as yellow colonies. Genomic DNA of V. harveyi VH1 was extracted from the culture using the DNA kit (Thermo Fisher Scientific). Sequencing library was prepared using the Rapid Barcoding Kit (SQK-RBK001) (Oxford Nanopore Technologies, Oxford, UK) as per instruction in the manual provided by the manufacturer. The library was then loaded to a MinION R9 flow cell (FLO-MIN106) (Oxford Nanopore Technologies, Oxford, UK), and the sequencing analysis was performed using MinKNOW software version 1.7.14. Fast5s from Nanopore sequencing were basecalled with ONT Albacore Sequencing Pipeline software version 2.0.2 and reads passing the internal test were used for subsequent analysis [5]. Porechop 0.2.2 (https://github.com/rrwick/Porechop) was used for debarcoding and adaptor trimming. Nanopore reads were assembled using Canu 1.6 [6]. For Nanopore-only assembly, output contigs were polished using Nanopolish software version 0.8.1 (https://github.com/jts/nanopolish). Contigs from Canu 1.6 were manually closed based on the assembly graph with Bandage software version 0.8.1 [7].

Table 1

General information and genome sequencing project information of V. harveyi VH1.

Items	Description
Classification	Domain	Bacteria
	Phylum	Proteobacteria
	Class	Gammaproteobacteria
	Order	Vibrionales
	Family	Vibrionaceae
	Genus	Vibrio
	Species	Vibrio harveyi
Gram stain	Negative
Cell shape	Rod-shaped
Pigmentation	Non-pigmented
Sporulation	Non-sporulating
Optimum temperature	25 °C
Salinity	30 ppt
Oxygen	Aerobic
MIGS Data
Submitted to NCBI	GenBank
Investigation type	Bacteria
Project Name	Genome of Vibrio harveyi VH1
Collection date	May 2017
Longitude and Latitude	6°13′16.1"N 99°46′07.5"E
Geographic location name	Langkawi, Kedah, Malaysia
Environment biome	Coastal area
Environment feature	Cage farm
Environment material	Water
Depth	3.0-5.0 m
Biotic relationship	Free living

Ethics Statements

The study was conducted according to the guidelines by the Animal Care and Use Committee Universiti Putra Malaysia (UPM/IACUC/AUP-R078/2019). All animal experiments are reported in compliance with the ARRIVE guidelines and carried out in accordance with the U.K. Animals (Scientific Procedures) Act, 1986 and associated guidelines, EU Directive 2010/63/EU for animal experiments, or the National Institutes of Health guide for the care and use of Laboratory animals (NIH Publications No. 8023, revised 1978).

CRediT Author Statement

The authors here declare their individual contributions:

Md. Ali Amatul-Samahah: Writing – original draft and editing; Aslah Mohamad: Investigation and writing; Nurhidayu Al-saari: Investigation and writing; Mohd Zamri-Saad: Validation and reviewing; Mohamad Noor Amal Azmai: Validation and reviewing; Mohd Termizi Yusof: Validation and reviewing; Ina-Salwany Md.Yasin: Validation, reviewing, editing & supervision; Mami Tanaka: Investigation, data curation, software & validation; Sayaka Mino: Data curation, software, validation & investigation; Tomoo Sawabe: Software, validation, investigation & supervision.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Subject	Biology
Specific subject area	Microbiology, Genomics, Biotechnology
Type of data	Table, figures
How the data were acquired	The draft genome sequence was processed using MinION instrument, Oxford Nanopore Technology, UK.
Data format	Raw, analyzed and deposited
Description of data collection	Vibrio harveyi VH1 was isolated from the skin lesion samples originated from a cultured tiger grouper (Epinephelus fuscoguttatus) in Malaysia. Genomic DNA extraction and sequencing were performed.
Data source location	Vibrio harveyi VH1 was isolated from the skin lesion samples originated from a cultured tiger grouper (Epinephelus fuscoguttatus) in a cage farm located in the coastal area of Langkawi, Kedah, Malaysia (latitude and longitude: 6°13′16.1″N 99°46′07.5″E). Vibrio harveyi VH1 genome was analyzed at the Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia (latitude and longitude: 2° 59′ 59.1684″ N, 101° 43′ 21.918″ E).
Data accessibility	Data are publicly available at NCBI GenBankhttps://www.ncbi.nlm.nih.gov/nuccore/JAAIXX000000000https://www.ncbi.nlm.nih.gov/biosample/SAMN14091020https://www.ncbi.nlm.nih.gov/bioproject/PRJNA606422
Related research article	Y.K. Chin, M.Y. Ina-Salwany, M. Zamri-Saad, M.N.A. Amal, A. Mohamad, J.Y. Lee, S. Annas & N. Al-saari, Efficacy of bath vaccination with a live attenuated Vibrio harveyi against vibriosis in Asian seabass fingerling, Lates calcarifer, Disease of Aquatic Organism 137: 167-173 (2020). https://doi.org/10.3354/dao03435