ABSTRACT
Draft genome sequences of 23 Tenacibaculum sp. strains that were isolated from Cyclopterus lumpus (lumpfish) were investigated to elucidate possible routes of transmission between Salmo salar (Atlantic salmon) and lumpfish.
ANNOUNCEMENT
The salmon louse (Lepeophtheirus salmonis) is the most common parasite in Norwegian salmon farming at sea and constitutes a serious welfare threat to the Atlantic salmon itself and to wild salmonid populations (1). Cleaner fish is one option to combat salmon lice in fish farms. However, both cleaner fish, like lumpfish, and salmon are susceptible to infections by Tenacibaculum spp. (2), and it can be speculated that infected lumpfish can spread the infection to salmon and vice versa. Bacterial swab samples from skin ulcers, kidney, and/or spleen from lumpfish that were used as cleaner fish in salmon farming were plated on marine agar (Difco) and incubated at 15°C for up to 7 days. Round-to-ovoid, yellow-pigmented colonies morphologically consistent with Tenacibaculum spp. and consisting of filamentous, Gram-negative (determined with the crystal violet/iodine technique), nonmotile rods (by phase-contrast microscopy) were subcultured and cryopreserved at −80°C. DNA from revived cultures on marine agar was extracted on a QIAcube (Qiagen) utilizing a QIAamp DNA QIAcube minikit, following the manufacturer’s recommendations. Twenty-three sequencing libraries were generated with a Nextera DNA Flex library preparation kit (Illumina), following the manufacturer’s standard protocol. Each library was sequenced on a MiSeq system (Illumina) with a v3 flow cell and 300-bp paired-end chemistry.
The resulting numbers of reads per sample are listed in Table 1. Default parameters were used for all software unless otherwise stated. BBduk (from BBmap package v38.18) was used to remove Nextera DNA Flex adapter sequences and to perform quality trimming (using trimq=24 and minlen=150). Reads were assembled with SPAdes v3.15.3 (3) using the careful option. The reads were mapped back on the assemblies with BBmap (using maxindel=80, minid=0.95, ambiguous=toss, and killbadpairs=true), and error correction was subsequently performed with Pilon v1.24 (4). The assemblies were annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (5), and the species and genomovar of each isolate were determined by average nucleotide identity (ANI) analysis using fastANI v1.32 (6). A threshold of 96% ANI was used at the species level and 97.5% at the genomovar level (7). Assemblies with GenBank accession numbers GCA_001483385.1 and GCA_900239185.1 were used as references for Tenacibaculum finnmarkense genomovar finnmarkense, GenBank accession numbers GCA_900239485.1 and GCA_900239495.1 for Tenacibaculum finnmarkense genomovar ulcerans, and GenBank accession numbers GCA_900239455.1 and GCA_900239305.1 for Tenacibaculum dicentrarchi (Table 1).
TABLE 1.
Assembly information for the draft genomes of 23 Tenacibaculum species isolates from lumpfish (Cyclopterus lupus)
| Isolate | Species and genomovara | Genome length (bp) | No. of readsb | Sequencing depth (×)c | GC content (%) | No. of contigs | N50 (bp) | GenBank accession no. | SRA accession no. |
|---|---|---|---|---|---|---|---|---|---|
| NVIO-11151 | T. finnmarkense gv. ulcerans | 2,912,685 | 634,728 | 54.2 | 30.9 | 63 | 341,205 | GCA_021206215.1 | SRR16845319 |
| NVIO-11836 | T. dicentrarchi | 2,665,418 | 1,274,204 | 121.9 | 30.2 | 43 | 290,045 | GCA_021206235.1 | SRR16845318 |
| NVIO-11837 | T. dicentrarchi | 2,718,782 | 1,016,758 | 93.3 | 30.2 | 47 | 299,843 | GCA_021206175.1 | SRR16845307 |
| NVIB-0099 | T. finnmarkense gv. ulcerans | 2,769,811 | 581,146 | 49.3 | 31.1 | 306 | 15,852 | GCA_021206185.1 | SRR16845303 |
| NVIB-0249 | T. finnmarkense gv. finnmarkense | 2,755,194 | 595,486 | 53.6 | 31.1 | 45 | 336,252 | GCA_021206115.1 | SRR16845302 |
| NVIB-0461 | T. dicentrarchi | 2,645,329 | 656,214 | 62.7 | 30.2 | 41 | 267,012 | GCA_021206125.1 | SRR16845301 |
| NVIB-0562 | T. dicentrarchi | 2,715,212 | 834,776 | 76.9 | 30.2 | 60 | 301,712 | GCA_021206145.1 | SRR16845300 |
| NVIB-0714 | T. finnmarkense gv. ulcerans | 2,948,091 | 899,454 | 73.1 | 31.0 | 101 | 113,984 | GCA_021206095.1 | SRR16845299 |
| NVIB-1038 | T. dicentrarchi | 2,729,260 | 890,344 | 78.2 | 30.1 | 60 | 268,855 | GCA_021206065.1 | SRR16845298 |
| NVIB-1058 | T. finnmarkense gv. ulcerans | 2,978,337 | 869,586 | 67.4 | 30.8 | 107 | 264,193 | GCA_021206045.1 | SRR16845297 |
| NVIB-1306 | T. finnmarkense gv. ulcerans | 3,011,088 | 737,008 | 58.3 | 30.9 | 74 | 261,018 | GCA_021206035.1 | SRR16845317 |
| NVIB-1785 | T. finnmarkense gv. finnmarkense | 2,907,856 | 1,011,694 | 87.0 | 30.9 | 75 | 126,450 | GCA_021206015.1 | SRR16845316 |
| NVIB-2771 | T. dicentrarchi | 2,708,961 | 783,294 | 71.9 | 30.2 | 39 | 439,048 | GCA_021205995.1 | SRR16845315 |
| NVIB-2925 | T. finnmarkense gv. ulcerans | 2,847,587 | 892,166 | 77.2 | 30.9 | 76 | 239,559 | GCA_021205955.1 | SRR16845314 |
| NVIB-3068 | T. dicentrarchi | 2,760,614 | 1,026,834 | 91.7 | 30.1 | 66 | 274,565 | GCA_021205975.1 | SRR16845313 |
| NVIB-3688 | T. dicentrarchi | 2,762,784 | 1,118,844 | 100.4 | 30.1 | 67 | 268,943 | GCA_021205915.1 | SRR16845312 |
| NVIB-3865 | T. finnmarkense gv. ulcerans | 2,925,085 | 719,972 | 59.6 | 30.9 | 62 | 365,686 | GCA_021205935.1 | SRR16845311 |
| NVIB-4078 | T. finnmarkense gv. finnmarkense | 3,093,483 | 1,094,616 | 85.2 | 30.9 | 135 | 130,306 | GCA_021205895.1 | SRR16845310 |
| NVIB-4084 | T. finnmarkense gv. ulcerans | 2,973,195 | 892,392 | 73.8 | 30.9 | 135 | 58,884 | GCA_021205875.1 | SRR16845309 |
| NVIB-4330 | T. dicentrarchi | 2,706,007 | 1,061,242 | 96.8 | 30.2 | 65 | 410,240 | GCA_021205835.1 | SRR16845308 |
| NVIB-4331 | T. finnmarkense gv. ulcerans | 2,881,546 | 559,816 | 46.0 | 30.8 | 111 | 256,579 | GCA_021205845.1 | SRR16845306 |
| NVIB-4332 | T. finnmarkense gv. finnmarkense | 2,888,640 | 716,276 | 61.3 | 31.0 | 61 | 338,514 | GCA_021205815.1 | SRR16845305 |
| NVIB-4333 | T. dicentrarchi | 2,733,905 | 1,023,684 | 93.9 | 30.1 | 47 | 231,759 | GCA_021205795.1 | SRR16845304 |
The species and genomovar of each isolate were determined by ANI analysis using fastANI, with similarity thresholds of 95% for species and 97.5% for genomovar.
Read count after quality control.
Sequencing depths were calculated on reads mapped back on the assemblies.
Data availability.
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank as BioProject PRJNA777885, with accession numbers for each assembly as shown in Table 1. The raw sequencing reads have been deposited in the Sequence Read Archive (SRA) as shown in Table 1.
ACKNOWLEDGMENT
This study was financed by the Norwegian Seafood Research Fund under project FHF 901434 (Elucidation of the role of Tenacibaculum spp. in atypical winter-ulcer in sea-farmed Atlantic salmon in Norway).
Contributor Information
Bjørn Spilsberg, Email: bjorn.spilsberg@vetinst.no.
Frank J. Stewart, Montana State University
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Associated Data
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Data Availability Statement
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank as BioProject PRJNA777885, with accession numbers for each assembly as shown in Table 1. The raw sequencing reads have been deposited in the Sequence Read Archive (SRA) as shown in Table 1.