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

Vertebrate immune systems exhibit striking evolutionary diversity, yet our understanding remains biased toward mammalian models. Here, we generate a single-cell atlas of immune cells from the ecologically and economically important salmonid Salmo trutta (brown trout), a lineage characterized by an ancestral whole-genome duplication (WGD). Profiling over 83,000 kidney-derived immune cells, we resolved 34 transcriptionally distinct populations, identified core immune lineages, and uncovered novel markers in neutrophils, macrophages, T- and B-cells. We detected pervasive transcriptional divergence between WGD-derived ohnologue pairs, indicating putative sub- and neofunctionalization in immune gene regulation. We further show that the transcriptional identity of immune cells is shaped by rearing history: fish raised in hatcheries--whether for one or multiple generations--showed shifts in immune gene expression across cell types. These included genes involved in G protein-coupled receptor signalling, a process which has previously been implicated in domestication. Our findings provide insight into the evolution of vertebrate immunity and raise concerns about the immunological fitness of hatchery-reared fish released into the wild.