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).
Project description:The process of producing the GRC zebrafish assembly included the high-quality sequencing and finishing of clones representing alternate haplotypes to corresponding regions in the current primary assembly. This project reports the variation between those alternate haplotype clones and the primary assembly.
