Lumpfish (Cyclopterus lumpus) genome assembly
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ABSTRACT:
PROVIDER: PRJEB29001 | ENA |
REPOSITORIES: ENA
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Project description:Cyclopterus lumpus (Lumpfish) genoem, fCycLum1, primary haplotype
| PRJNA562003 | ENA
Project description:Cyclopterus lumpus (Lumpfish) genoem, fCycLum1, alternate haplotype
| PRJNA562004 | ENA
Project description:Cyclopterus lumpus isolate:Atl_lumpfish Genome sequencing and assembly
| PRJNA781657 | ENA
Project description:Both bacterial and viral diseases are a major threat to farmed fish, as well as wild fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of virus dsRNA, and RNA sequencing was performed. Immune genes were identified, and transcriptome-wide analyses of early immune responses in lumpfish leukocytes showed that 310 and 1872 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of differentially expressed genes (DEGs) showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, MDA5, TRIM25, STING, as well as IRF3, IL-8 and TNFα. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Our analyses unravel the innate immune pathways playing a major role in antiviral defence in lumpfish. The information gathered can be used to compare research findings and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar).
2023-06-01 | E-MTAB-12884 | biostudies-arrayexpress
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:Fish skin mucus serves as a first line of defense against pathogens and external stressors. In this study the proteomic profile of lumpsucker skin mucus was characterized using 2D gels coupled with tandem mass spectrometry. Mucosal proteins were identified by homology searches across the databases SwissProt, NCBInr and vertebrate EST. The identified proteins were clustered into ten groups based on their gene ontology biological process in PANTHER (www.patherdb.org). Calmodulin, cystatin-B, histone H2B, peroxiredoxin1, apolipoprotein A1, natterin-2, 14-3-3 protein, alfa enolase, pentraxin, warm temperature acclimation 65 kDa (WAP65kDa) and heat shock proteins were identified. Several of the proteins are known to be involved in immune and/or stress responses. Proteomic profile established in this study could be a benchmark for differential proteomics studies.
| S-EPMC5614610 | 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