Single-cell RNA sequencing reveals influences of rearing environment on cellular immunity in brown trout (Salmo trutta)

The ability to profile gene expression at the single cell level can offer unprecedented insight into the vertebrate immune system. While such profiling of non-model organisms can present unique challenges (e.g. evolutionary idiosyncrasies), high resolution data on immune function could yield valuable insights into ecologically and economically important species. Here, we used single-cell RNA sequencing (scRNAseq) to profile the immune system transcriptional repertoire of brown trout (Salmo trutta), a threatened index species and commonly using for stocking endangered wild populations, using multiple individuals derived from three distinct rearing backgrounds (wild-caught, farm reared for one generation or farm-reared for at least three generations). We subsequently present a collection of markers that are representative of the species accounting for disparate rearing histories. This revealed a repertoire which is broadly evolutionarily conserved, although many of the genes characterising neutrophil, macrophage, T-cell, B-cell and other lineages likely reflect the specific facets of salmonid immune evolution. The fates of duplicate gene pairs putatively arising from the salmonid-specific whole genome duplication event were also investigated, revealing that approximately half of duplicate genes examined show some degree of functional divergence within the immune system in terms of loss or gain of expression in certain clusters. Finally, comparing cluster-level gene expression profiles between different rearing backgrounds revealed that single or multigenerational exposure to a farm environment induces transcriptional alterations in neutrophils, macrophages, B-cells and T-cells.