ABSTRACT: Chile is the second largest producer of Atlantic salmon (Salmo salar), making it the second most important national industry. This industry is not exempt from challenges, such as sea lice infestation. Caligus rogercresseyi is the only sea louse that affects the Chilean salmon industry and the etiological agent of caligidosis. This pathology alters the state of health of the fish and causes significant economic losses. Despite its relevance, there are currently no studies that consider the environmental variables present in marine culture centers in each of the different seasons of the year and their effect on the response capacity of Atlantic salmon due to its poikilothermic characteristic, which limits its applicability in the development of new approaches and strategies for the control of caligidosis. For this reason, this study evaluated the skin transcriptome of Atlantic salmon infested with C. rogercresseyi in culture centers located in the fjords of the Aysén Region due to its leadership in the productivity of Atlantic salmon in Chile. The study focused on two critical periods of the year: autumn, marked by a gradual thermal decrease (from summer to winter); and spring, characterized by a gradual temperature increase (from winter to summer). For this purpose, RNA sequencing techniques (RNA-seq) and functional network analysis were used to identify differences in transcriptomic profiles between autumn and spring. In autumn, 253 differentially expressed genes (DEGs) were obtained, where 185 were upregulated and 67 DEGs were downregulated. In spring, 103 DEGs were obtained; 70 upregulated and 33 downregulated. The results reveal that, in autumn, the analysis presents an activation of processes in response to stress and negative regulation of T-cell proliferation, suggesting an increased susceptibility to Caligus infestation during this season. In spring, an overexpression of genes involved in protein synthesis was observed, accompanied by various biological processes involved in the immune response, including activation of the complement pathway, granulocyte chemotaxis, and antigen processing and presentation of peptide antigen, suggesting activation of immunity at different levels in the presence of Caligus. Validation of the RNA-seq results by qPCR confirmed the modulation and magnitude of expression of the differentially expressed genes, confirming the robustness of the data obtained. To the best of our knowledge, this is the first study to analyze the transcriptomic response of healthy skin of Caligus-infested salmon under productive conditions, and underscores the importance of considering seasonal variations for the development of more effective management strategies in the aquaculture industry.
