Single-cell analysis of a salmonid immune system (brown trout Salmo trutta) reveals evolutionary divergence and hatchery-induced transcriptional reprogramming

Abstract 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. Competing Interest Statement The authors have declared no competing interest. Footnotes - Readability and flow of the text, namely the abstract and aspects of the introduction and discussion have been streamlined. - Correction to analysis of ohnologue pairs to account for three previously missing pairs. - Added statement in the acknowledgements regarding use of AI. - Additional citations.