Draft Genome Sequences of 23 Tenacibaculum Isolates from Farmed Norwegian Lumpfish, Cyclopterus lumpus.
Ontology highlight
ABSTRACT:
SUBMITTER: Spilsberg B
PROVIDER: S-EPMC9022500 | biostudies-literature | 2022 Apr
REPOSITORIES: biostudies-literature
Publications
Draft Genome Sequences of 23 <i>Tenacibaculum</i> Isolates from Farmed Norwegian Lumpfish, <i>Cyclopterus lumpus</i>.
Spilsberg Bjørn B Nilsen Hanne K HK Gulla Snorre S Lagesen Karin K Olsen Anne Berit AB Colquhoun Duncan J DJ
Microbiology resource announcements 20220315 4
Draft genome sequences of 23 <i>Tenacibaculum</i> sp. strains that were isolated from Cyclopterus lumpus (lumpfish) were investigated to elucidate possible routes of transmission between Salmo salar (Atlantic salmon) and lumpfish. ...[more]
Similar Datasets
Project description:This study has established a successful protocol to cryopreserve lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt. Three cryosolutions were tested based on Mounib's medium; the original medium including reduced l-glutathione (GSH), the basic sucrose and potassium bicarbonate medium without GSH, or with hen's egg yolk (EY). Dimethyl sulphoxide (DMSO) was used as the cryoprotectant along with all three diluents in a 1-2 dilution. Cryopreservation was performed with the mentioned cryosolutions at two freezing rates. Motility percentages of spermatozoa were evaluated using ImageJ with a computer assisted sperm analyzer (CASA) plug-in. Findings revealed that spermatozoa cryopreserved in Mounib's medium without GSH had a post-thaw motility score of 6.4 percentage points (pp) higher than those in the original Mounib's medium, and an addition of EY to the modified Mounib's medium lowered the post-thaw motility score by 19.3 pp. The difference in motility between both freezing rates was 13.0 pp, and samples cryopreserved on a 4.8 cm high tray resulted in a better post-thaw motility score. On average, cryopreserved milt had a 24.1 pp lower post-thaw motility score than fresh milt. There was no significant difference in fertilisation success between cryopreserved and fresh milt. Cryopreservation of lumpfish milt has, to our knowledge, never been successfully carried out before. The established protocol will be a main contributing factor in a stable production of lumpfish juveniles in future.
| S-EPMC4458125 | biostudies-literature
Project description:The bacterium Pseudomonas anguilliseptica has in recent years emerged as a serious threat to production of lumpfish in Norway. Little is known about the population structure of this bacterium despite its association with disease in a wide range of different fish species throughout the world. The phylogenetic relationships between 53 isolates, primarily derived from diseased lumpfish, but including a number of reference strains from diverse geographical origins and fish species, were reconstructed by Multi-Locus Sequence Analysis (MLSA) using nine housekeeping genes (rpoB, atpD, gyrB, rpoD, ileS, aroE, carA, glnS and recA). MLSA revealed a high degree of relatedness between the studied isolates, altough the seven genotypes identified formed three main phylogenetic lineages. While four genotypes were identified amongst Norwegian lumpfish isolates, a single genotype dominated, irrespective of geographic origin. This suggests the existence of a dominant genotype associated with disease in production of lumpfish in Norwegian aquaculture. Elucidation of the population structure of the bacterium has provided valuable information for potential future vaccine development.
| S-EPMC8608339 | biostudies-literature
Project description:In this study, we determined the complete coding sequence of a putative new member of the family Flaviviridae, named "Cyclopterus lumpus virus" (CLuV), which is associated with a serious disease in lumpfish (Cyclopterus lumpus). The virus was present in all tissues tested, but pathology was primarily observed in the liver and kidneys. CLuV shows low but distinct similarity to the unassigned Tamana bat virus (TABV). Unlike other known members of the family Flaviviridae, translation of the entire CLuV polyprotein is dependent on a - 1 ribosomal frameshift in the NS2A region.
| S-EPMC5814470 | biostudies-literature
Project description:The commercial farming of juvenile lumpfish requires monitoring of gonadal development to achieve synchronized production. Conventional methods such as gonadosomatic index (GSI), sex hormone analyses, gonadal histology, endoscopy, and gene expression analyses are costly, invasive, and often involve sacrificing the fish. We assessed the efficiency of ultrasound as a non-invasive method for monitoring gonadal development in lumpfish. Based on ultrasound observations, we categorized the fish into six stages; F0 to F5 for females and M0 to M5 for males, that represented maturity levels from immature to spent. Importantly, the ultrasound gonadal stages aligned with histological gonadal stages. Additionally, ultrasound stages aligned with profiles of GSI, testosterone (T), 11-ketotestosterone, and 17β-estradiol throughout gonadal development including the spawning period. Moreover, these parameters exhibited significant positive correlations with each other reflecting their parallel trends during gonadal development. To minimize the frequency of ultrasound usage and fish handling, we established F3 and M3/M4 as arbitrary thresholds for identifying ripe females and males, respectively. By using these thresholds, the need for regular ultrasound monitoring could be reduced during most of the rearing period. Ultrasound proves to be useful and reliable for monitoring gonadal development in lumpfish, enabling synchronized production of juvenile fish.
| S-EPMC10513926 | biostudies-literature
Project description:Lumpfish (Cyclopterus lumpus) genome assembly
| PRJEB29001 | ENA
Project description:BACKGROUND: Commercial fisheries of lumpfish Cyclopterus lumpus have been carried out in Iceland for centuries. Traditionally the most valuable part is the eggs which are harvested for use as a caviar substitute.Previously reported parasitic infections from lumpfish include an undescribed intranuclear microsporidian associated with abnormal kidneys and mortalities in captive lumpfish in Canada. During Icelandic lumpfish fisheries in spring 2011, extensive enlargements to the kidneys were observed in some fish during processing. The aim of this study was to identify the pathogen responsible for these abnormalities. METHODS: Lumpfish from the Icelandic coast were examined for the causative agent of kidney enlargement. Fish were dissected and used in histological and molecular studies. RESULTS: Lumpfish, with various grades of clinical signs, were observed at 12 of the 43 sites sampled around Iceland. From a total of 77 fish examined, 18 had clear clinical signs, the most prominent of which was an extensive enlargement and pallor of the kidneys. The histopathology of the most severely affected fish consisted of extensive degeneration and necrosis of kidney tubules and vacuolar degeneration of the haematopoietic tissue. Intranuclear microsporidians were detected in all organs examined in fish with prominent clinical signs and most organs of apparently healthy fish using the new PCR and histological examination. One or multiple uniformly oval shaped spores measuring 3.12?±?0.15?×?1.30?±?0.12 ?m were observed in the nucleus of affected lymphocytes and lymphocyte precursor cells. DNA sequencing provided a ribosomal DNA sequence that was strongly supported in phylogenetic analyses in a clade containing other microsporidian parasites from the Enterocytozoonidae, showing highest similarity to the intranuclear microsporidian Nucleospora salmonis. CONCLUSIONS: Intranuclear microsporidian infections are common in wild caught lumpfish from around the Icelandic coast. Infections can cause severe clinical signs and extensive histopathological changes, but are also present, at lower levels, in fish that do not show clinical signs. Some common features exist with the intranuclear microsporidian previously reported from captive Canadian lumpfish, but DNA sequence data is required from Canadian fish to confirm conspecificity.Based on phylogenetic analysis and the intranuclear location of the parasite, the name Nucleospora cyclopteri n. sp. is proposed.
| S-EPMC3606367 | biostudies-literature
Project description:Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms-a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at-risk wild populations. Here, we characterize the spatial population structure and genomic-environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole-genome re-sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome-wide variation in F ST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at-risk species throughout Atlantic Canada.
| S-EPMC10519416 | biostudies-literature
Project description:MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies.
| S-EPMC8773022 | biostudies-literature
Project description:The use of lumpfish (Cyclopterus lumpus L.) as cleaner fish in Atlantic salmon aquaculture has emerged as a promising solution to combat the issue of sea lice infestation, as they have proven effective under the right conditions. The aquaculture industry, however, is facing challenges in ensuring the welfare and survival of lumpfish in salmon cages. Part of the welfare monitoring of lumpfish is the estimation of body condition. Previous research on standard length-weight relationships for lumpfish has primarily relied on the growth patterns of lumpfish in salmon cages, which might not align with the natural growth patterns of the fish. In this study, we argue for another perspective: using the standard weight of wild lumpfish to estimate the body condition of lumpfish in salmon cages. We assert that this approach aligns more closely with the natural growth pattern of the fish and may offer a more accurate representation of their condition. Our findings show significant differences in growth patterns between wild lumpfish, which show positive allometric growth, and those in salmon cages, which show slightly negative allometric growth. The findings underscore the importance of using appropriate length-weight relationships for lumpfish in aquaculture to ensure an accurate assessment of their body condition.
| S-EPMC11556749 | biostudies-literature
Project description:Studies on the effects of environmental changes with increasing depth (e.g. temperature and oxygen level) on fish physiology rarely consider how hydrostatic pressure might influence the observed responses. In this study, lumpfish (Cyclopterus lumpus, 200-400 g), which can exhibit vertical migrations of over 100 m daily and can be found at depths of 500 m or more, were implanted with Star-Oddi micro-HRT loggers. Then, their heart rate (f H) was measured in a pressure chamber when exposed to the following: (i) increasing pressure (up to 80 bar; 800 m in depth) at 10°C or (ii) increasing temperature (12-20°C), decreasing temperature (12 to 4°C) or decreasing oxygen levels (101-55% air saturation at 12°C) in the absence or presence of 80 bar of pressure. Additionally, we determined their f H response to chasing and to increasing temperature (to 22°C) at atmospheric pressure. Pressure-induced increases in f H (e.g. from 48 to 61 bpm at 12°C) were associated with hyperactivity. The magnitude of the rise in f H with temperature was greater in pressure-exposed vs. control fish (i.e. by ~30 bpm vs. 45 bpm between 5°C and 20°C). However, the relative increase (i.e. slope of the relationship) was not different between groups. In contrast, 80 bar of pressure eliminated the small (5 bpm) increase in f H when control fish were exposed to hypoxia. Exhaustive exercise and increasing temperature to 22°C resulted in a maximum f H of 77 and 81 bpm, respectively. Our research shows that pressure influences the f H response to environmental challenges and provides the first evidence that lumpfish have a limited capacity to increase f H.
| S-EPMC8299717 | biostudies-literature