Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin

Author:

Sveen Lene R1,Robinson Nicholas12,Krasnov Aleksei1,Daniels Rose Ruiz3,Vaadal Marianne1,Karlsen Christian1,Ytteborg Elisabeth1,Robledo Diego3,Salisbury Sarah3,Dagnachew Binyam1,Lazado Carlo C1,Tengs Torstein1

Affiliation:

1. Nofima , Fish Health, Tromsø NO-9291 , Norway

2. School of BioSciences, The University of Melbourne , Melbourne 3010 , Australia

3. The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh , Edinburgh EH25 9RG , UK

Abstract

Abstract In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from 4 distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the lateral line, obtained from 2 Atlantic salmon (150 g). High-quality frozen tissue sections were obtained by embedding tissue in optimal cutting temperature media prior to freezing and sectioning. Further, we generated libraries and spatial transcriptomic maps, achieving a minimum of 80 million reads per sample with mapping efficiencies ranging from 79.3 to 89.4%. Our analysis revealed the detection of over 80,000 transcripts and nearly 30,000 genes in each sample. Among the tissue types observed in the skin, the epithelial tissues exhibited the highest number of transcripts (unique molecular identifier counts), followed by muscle tissue, loose and fibrous connective tissue, and bone. Notably, the widest nodes in the transcriptome network were shared among the epithelial clusters, while dermal tissues showed less consistency, which is likely attributable to the presence of multiple cell types at different body locations. Additionally, we identified collagen type 1 as the most prominent gene family in the skin, while keratins were found to be abundant in the epithelial tissue. Furthermore, we successfully identified gene markers specific to epithelial tissue, bone, and mesenchyme. To validate their expression patterns, we conducted a meta-analysis of the microarray database, which confirmed high expression levels of these markers in mucosal organs, skin, gills, and the olfactory rosette.

Funder

Norwegian Seafood Research Fund

Genomics4Robust

Norwegian Research Council

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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