Aquaculture Europe 2023

September 18 - 21, 2023


Add To Calendar 20/09/2023 10:30:0020/09/2023 10:45:00Europe/ViennaAquaculture Europe 2023SINGLE NUCLEI RNA SEQUENCING UNCOVERS THE CELL TYPE-SPECIFIC RESPONSES TO SEA LICE WITHIN THE SKIN OF RESISTANT AND SUCEPTIBLE SALMONID SPECIESStolz 0The European Aquaculture Societywebmaster@aquaeas.orgfalseDD/MM/YYYYaaVZHLXMfzTRLzDrHmAi181982


S.J. Salisbury1 , R. Ruiz Daniels1 , O. Gervais1 , P.R. Villamayor2 , S.J. Monaghan3 , J.E. Bron3 , L. Sveen4 , M.D. Fast5 , R. Houston6 , N. Robinson4,7 , and D. Robledo1


 1. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.

 2. University of Santiago de Compostela , Santiago de Compostela, Spain.

3. The University of Stirling, Stirling, UK.

 4. Nofima AS, Ås, Norway.

5. Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada.

 6. Benchmark Genetics, 1 Pioneer Building, Edinburgh Technopole, Milton Bridge, Penicuik, UK.

7. The University of Melbourne, Parkville, Australia.




Sea lice parasitism is one of the greatest economic, environmental, a nd animal welfare issues facing the Atlantic salmon ( Salmo salar) aquaculture industry (Torrissen et al. 2013) .  A potential solution may exist in coho salmon (Oncorhynchus kisutch), a species that mounts a massive inflammatory response to sea lice, resulting in their swift detachment from the skin (Fast et al. 2002) . However,  it is not known which of the many cell types pre sent in fish skin underlie this remarkable resistance.  We therefore employed single-nuclei RNA sequencing, a technique facilitating transcriptomic profiling of thousands of individual cells, to investigate the  cell types and gene expression  patterns ch aracterizing  the response of coho  and Atlantic salmon to sea lice.

Materials and Methods

A tlantic and coho salmon were reared in a RAS at the Centre for Aquaculture Technologies (PEI, Canada) . Juvenile f ish  were exposed to copepodid stage sea lice (Lepeophtheirus salmonis) and pelvic fin and skin where lice had attached were sampled at 12h, 24h, 36h, 48h, and 60h after exposure . F in and skin were also taken from  unexposed control fish reared in identical conditions. Nuclei were isolated from one skin and one fin sample from  the control and  each of the five treatment time points for each species (N = 24 samples total) using a custom protocol (Ruiz Daniels et al. 2023). Samples  were processed with Chromium (10X Genomics) and sequenced with Illumina technologies. L ibrary mapping was performed with STAR (Kaminow et al. 2021). Resulting outputs were analysed with Seurat (Stuart et al. 2019). Samples were analysed by species and also integrated into a single dataset using 1:1 orthologs identified with OrthoFinder (Emms & Kelly 2019).


 The variety of cell types we detected (Fig.1 )  were largely consistent in identity  and  marker genes  across species. Integration of both species data using 649 4 1:1 orthologous genes detected most of the cell types observed in each of the species-specific analyses . These results suggest the same cell types are present in the skin and fin of both species.

We identified 4567 and 1799  unique  genes in Atlantic and coho salmon , respectively, which were differentially expressed between control and any of the treatment time points (Fig.2) . Both species upregulated immune genes in response to lice, intriguingly in  both  immune  and  non-immune cell types. However, coho salmon uniquely demonstrated a down-regulation of iron-sequestration related genes in red blood cells, potentially to starve lice. Coho salmon keratinocytes  also dramatically upregulated genes associated with  inflammation and immunity. Our results confirm the importance of previously identified  candidate genes associated with lice-resistance  but also identify new candidates that may have been missed by previous bulk RNAseq studies due to their expression in multiple cell types.


Clearly, multiple cell types, common to both species, are involved in  sea  lice response in Atlantic and coho s almon. Our results also suggest that coho salmon use multiple strategies (with different cell types and genes) to repel lice. This may explain why a single locus for lice resistance has proven elusive. Yet , the candidate genes we found to underlie coho salmon’s  multiple  resistance strategies  to lice  could be targeted in isolation or in combination via gene editing to confer  this innate immunity to Atlantic salmon.


Emms & Kelly. (2019). OrthoFinder : phylogenetic orthology inference for comparative genomics. Genome biology, 20, 1-14.

 Fast et al.  (2002). Susceptibility of rainbow trout Oncorhynchus mykiss , Atlantic salmon  Salmo salar and coho salmon Oncorhynchus kisutch to experimental infection with sea lice Lepeophtheirus salmonis. Diseases of aquatic organisms, 52(1), 57-68.

Kaminow et al.  (2021). STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. Biorxiv, 2021-05.

Ruiz Daniels et al. (2022). A versatile nuclei extraction protocol for single nucleus sequencing in fish species–optimization in various Atlantic salmon tissues.

 Stuart et al. (2019). Comprehensive integration of single-cell data. Cell, 177(7), 1888-1902.

Torrissen et al. (2013). Salmon liceimpact on wild salmonids and salmon aquaculture. Journal of fish diseases, 36(3), 171-194.