Draft genome sequence of Vibrio diabolicus isolated from the starlet sea anemone Nematostella vectensis

TL;DR

This paper presents the complete genome sequence of a Vibrio diabolicus strain isolated from a sea anemone, aiding in understanding host-bacteria interactions.

Contribution

The paper provides the first full genome sequence of Vibrio diabolicus NVE-VD1 from Nematostella vectensis.

Findings

The Vibrio diabolicus strain was isolated from the starlet sea anemone Nematostella vectensis.

The full genome sequence is reported, supporting future studies on host-microbe interactions.

Abstract

Nematostella vectensis has grown as a model organism for investigating host–bacteria interactions. Here, we report the full genome of Vibrio diabolicus NVE-VD1, an isolate from N. vectensis from the South Carolina Baruch Estuarine Reserve.

Figures

Phylogenetic tree of Vibrio diabolicus NVE-VD1 single-copy genes. The single-copy genes of the clade were identified with Orthofinder v2.4.0 and aligned with MUSCLE. The maximum-likelihood tree was constructed in IQTREE2 v2.1.2 and visualized in FigTree v1.4.4.

Tables

TABLE 1. Genome metrics for Vibrio diabolicus NVE-VD1 including sequenced reads, assembly statistics, and genome completeness

	Vibrio diabolicus
Raw reads	23,441,293
Trimmed reads	16,975,243
	Unicycler
Statistics without reference	Scaffolds
# contigs	93
Largest contig	1,863,922
Total length	5,117,331
N50	1,302,326
N75	849,246
L50	2
L75	3
GC (%)	44.75
Mismatches
# N’s	575
# N’s per 100 kbp	9.77
CDS	4,541
rRNA	10
tRNA	98
tmRNA	1
CheckM
Completion	100.00
Contamination	3.67

Full text

ANNOUNCEMENT

Nematostella vectensis was collected from tidally restricted pools on Goat Island located in the South Carolina Baruch Estuarine Reserve in June 2018 (33°19′50.6″N 79°12′04.2″W). Anemones were then transported to the University of North Carolina at Charlotte (Charlotte, NC, USA). Homogenized anemone was serially diluted and plated on marine broth (24.72 g L^−1^ NaCl, 0.78 g L^−1^ KCl, 1.36 g L^−1^ CaCl_2_, 4.66 g L^−1^ MgCl_2_, 6.30 g L^−1^ MgSO_4_, 0.36 g L^−1^ NaHCO_3_, 10 g L^−1^ peptone, 3 g L^−1^ yeast extract, and 15 g L^−1^ agar) plates. A distinct colony was isolated and struck at minimum three times on fresh media to ensure a pure isolate. The isolate was then grown in marine broth and pelleted by centrifugation for DNA extraction and sequencing at Omega Bioservices. DNA was extracted with the Mag-Bind Universal Pathogen DNA Kit (Omega Bio-tek, M4024-00) and quality-checked by PicoGreen (ThermoFisher) and NanoDrop. The library was prepared by the KAPA HyperPrep for WGS (Roche, KR0961) and sequenced on the Illumina HiSeq X Ten (PE 2 × 150).

Paired-end read files were quality-checked with FastQC v0.11.9 (1). A total of 23,441,293 reads were generated from the sequencing run (Table 1). The raw reads were then adapter-clipped and quality-trimmed using Trimmomatic v0.39, which resulted in 16,975,243 remaining reads (2). Next, the trimmed reads were assembled with Unicycler v0.5.0 for de novo assembly (3). The final assembly metrics were assessed using Quast v5.0.2 (4) and CheckM v1.2.2 (5) to determine genome completeness and identify any potential contamination. The genome was subsequently annotated with PROKKA v1.14.6, using the options --genus Vibrio and –mincontiglen 500 (6). Next, orthogroups containing 1,309 single-copy genes identified with Orthofinder v2.4.0 were aligned using option -A muscle (7). ModelFinder determined that the best-fit model according to the Bayesian Information Criterion was LG+F+R6 (8). This alignment was used to generate a maximum likelihood phylogenetic tree in IQTREE2 v2.1.2, with 1,000 bootstraps (9). This tree was then visualized in FigTree v1.4.4. Lastly, taxonomic ranks were predicted with NCBI’s PGAP build 6771, using the –taxcheck-only option (10). The Vibrio isolate described here was predicted to be Vibrio diabolicus, based on the phylogenetic distance of single-copy orthologs (Fig. 1). The constructed maximum-likelihood tree places this isolate in a monophyletic clade with Vibrio diabolicus. We designate this isolate Vibrio diabolicus strain NVE-VD1. The reference isolate sharing the most genetic similarity with V. diabolicus NVE-VD1 was Vibrio chemaguriensis with an Average Nucleotide Identity of 98.136% (NCBI accession number ASM1227570).

Phylogenetic tree of Vibrio diabolicus NVE-VD1 single-copy genes. The single-copy genes of the clade were identified with Orthofinder v2.4.0 and aligned with MUSCLE. The maximum-likelihood tree was constructed in IQTREE2 v2.1.2 and visualized in FigTree v1.4.4.

The final assembly was 5,117,331 bp, with a GC content of 44.75%. There were 93 contigs, where the L50 was 2 and N50 was 1,302,326 bp. Interestingly, we found that 309 genes were duplicated, including stress/resistance proteins, secretion system genes, transporter genes, and motility/adhesion genes. These duplications may allow for additional flexibility in the interactions the bacteria have with the host.