Draft genome sequences of Tenacibaculum finnmarkense isolates from diseased Atlantic salmon (Salmo salar) in Chilean farms

TL;DR

This paper presents draft genome sequences of a pathogen found in diseased Atlantic salmon in Chile, aiming to help develop better diagnostic and prevention tools for aquaculture.

Contribution

The study provides the first draft genome sequences of Tenacibaculum finnmarkense isolates from Chilean aquaculture.

Findings

Draft genome sequences of Tenacibaculum finnmarkense isolates from diseased Atlantic salmon in Chile were reported.

The findings aim to support the development of genome-based diagnostic tools and prevention strategies for aquaculture.

Abstract

We report the draft genome sequences of Tenacibaculum finnmarkense isolates from diseased Atlantic salmon (Salmo salar) in Chile, providing initial insights into the genomics of this pathogen. Currently, limited data exist on Chilean isolates to aid in the development of genome-based diagnostic tools, typing methods, and/or prevention strategies for aquaculture applications.

Tables

TABLE 1. Tenacibaculum finnmarkense isolate genomes released to the NCBI

Strain	SRA	Accession no.	No. of readsa	Total length (bp)b	Completenessc	Genome coverage	Contaminationc	Contigsb	%GCb	N50 (kb)b	Genesd	CDSd
LB-P5	SRR32778091	JBMFZR000000000	5,517,150/ 2,694,444	2,752,994	80.35	100×	4.52%	56	31.06	190.7	2,403	2,352
P3-BQB	SRR32778090	JBMFZS000000000	10,437,554/ 2,749,628	2,800,552	79.98	100×	2.36%	55	31.01	190.5	2,473	2,416

Full text

ANNOUNCEMENT

Tenacibaculum finnmarkense was first isolated in 2016 from diseased Atlantic salmon (Salmo salar) in Finnmark, Norway (1). Taxonomic validation did not occur until 2020, when a subdivision into genomovars finnmarkense and ulcerans was proposed (2). This gram-negative, obligate aerobe forms yellow-pigmented colonies, exhibits gliding motility, and grows at 2°C–20°C in marine salts (2). The AYD7486TD isolate is the only analyzed genome in Chile (3). We present the draft genomes of isolates LB-P5 and P3-BQB, recovered from the skin lesions and gills of diseased Atlantic salmon during tenacibaculosis outbreaks in July 2017 (42°54′59″S, 72°42′30″W) and June 2018 (45°01′47″S, 73°37′29″W), respectively, at separate farming sites. These isolates were obtained as dominant colonies after streaking fish samples onto Marine Agar 2216 (BD Difco) plates and incubating them at 18°C for 1 week.

For genomic sequencing, both isolates were cultured on Marine Agar 2216 at 18°C for 48 h. Genomic DNA was purified (NucleoSpin Soil Kit; Macherey-Nagel), quantified (NanoDrop Lite Spectrophotometer; Thermo Fisher Scientific Inc.), and, afterward, sequenced by SeqCenter (PA, USA). Library preparation was performed using the Illumina DNA Prep Kit with IDT 10 bp UDI indices and sequenced on Illumina NextSeq 2000, generating 2 × 151 bp paired-end reads. Prior to de novo genome assembly, raw Illumina sequencing data underwent quality control (FastQC version 0.12.1; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next-generation sequencing reads were pre-processed (Geneious Prime version 2024.0.5) (4): (i) pairing reads using the “set paired reads” function (insert size = 350 bp); (ii) trimming poor-quality bases from read ends (BBDuk Trimmer plugin version 38.84; reads <50 bp and with a quality score <30 were removed), with paired-read overlaps trimmed to ensure complete adapter removal; (iii) normalizing coverage by down-sampling reads in high-depth genome areas with the “error correct” and “normalize reads” functions (BBNorm version 38.84) (5); and (iv) removing duplicate reads (Dedupe plugin). Assemblies (Spades version 4.0.0) (6) were evaluated for quality (QUAST version 5.2.0) and completeness (CheckM version 1.2.2) (7, 8). Genomes were annotated using RAST server version 2.0 (9) (https://figshare.com/s/5f65c20fb8995e0eff83) and Prokaryotic Genome Annotation Pipeline version 6.9 (19 March 2025). All software used the default settings.

Genome assemblies (Table 1) contained 56 (LB-P5) and 55 (P3-BQB) contigs; 2,752,994 and 2,800,552 bp; and a G + C content of ∼31.0%. Filtered reads were mapped using SOAP (10) to the bacterial plasmid database (11). No plasmids were found in the two isolates analyzed. Both strains were T. finnmarkense (JSpeciesWS-Taxonomic Thresholds [12] and GTDB-Tk version 2.4.0 [13]); the closest reference strain was the ulcerans genomovar (accession number NZ_OENE01000000), with an average nucleotide identity of 98.64% for LB-P5 and 98.75% for P3-BQB.

This study provides initial insights into the genomic characteristics of T. finnmarkense genomovar ulcerans strains isolated from Chilean tenacibaculosis outbreaks in farmed Atlantic salmon, offering genomic details on potential virulence that require further biochemical and physiological studies.