Wound atlas of Atlantic salmon skin

The process of wound healing offers a window into how cells coordinate to maintain tissue integrity, repair damage, and restore tissue function. Wound healing in Atlantic salmon, a species of considerable ecological and economic importance, is a tightly coordinated process involving multiple cellular programmes that eventually lead to scarless repair. Here, we present the first single-nucleus atlas of healing salmon skin wounds, providing a comprehensive view of its cellular organisation over multiple timepoints. We have profiled 29,706 nuclei from uninjured skin, 2 days post-wounding (dpw; inflammatory phase), and 14 dpw (proliferative phase), identifying 44 transcriptionally distinct cell clusters. Integration with previously published spatial transcriptomics dataset further enabled the localisation of these populations within the wound microenvironment. We have identified distinct spatial-temporal association for erythrocytes, thrombocytes, macrophages, differentiating muscle cells, fibroblasts, and tenocytes, highlighting their potential contributions to tissue repair. Furthermore, transcriptomic and histological analyses support a previously under-appreciated role for the myosepta in coordinating wound and muscle repair. By linking cellular transcriptional state to the tissue architecture, this spatially resolved wound atlas provides a framework for understanding the repair of cutaneous wounds in Atlantic salmon and establishes a valuable resource for studies of fish health. By exploring wound healing for insights on tissue function, this atlas also offers broader insights into the scarless wound healing biology in non-model organism vertebrates. Data visualisation of the single-nuclei RNA-sequencing and spatial transcriptomics analysis is available on our web portal at https://bshihlab-salmonwoundatlas.share.connect.posit.cloud/.