The sea louse Caligus rogercresseyi is a marine ectoparasite copepod species that impacts the salmon production in Chile, causing losses of more than 400 million dollars per year. This pathogen is mainly controlled by immersion baths with delousing drugs, which are directly applied in salmon cages covered by skirts or tarpaulins. The emergence of resistance has been suggested as the main cause of low efficacy of delousing drugs treatments against sea lice infection. In other arthropods , pharmacological resistance has been associated with duplicated genes at the genome of resistant individuals causing an amplification of the expression levels of critical genes related to the response to drugs, such as those involved in drug detoxification and excretion outside the cells. Pharmacogenomics approaches are now possible to conduct in C. rogercresseyi , having the draft of the full genome as a reference to infer these duplications as copy number variants (CNVs) in different resistant or susceptible strains. T his study aimed to evaluate the presence of gene duplications, or gene-clusters duplications, related to genes with functions in delousing drug response, and its association with resistant phenotypes to azamethiphos in C. rogercresseyi.
The full genome of C. rogercresseyi w as used as a reference to conduct whole-genome resequencing for known sea louse strains with divergent resistance to azamethiphos drug. Then, gene-clusters duplications in the novel specific whole-genome sequences for resistant and susceptible strains were identified and associated with resistant sea lice. Copy number variants (CNVs) in detoxication genes, such as trypsins were identified with differential p-value among resistant and susceptible strains (Table 1). Duplicated regions also implied expression changes in these strains (Fig. 1). T he potential impact of this study for salmon aquaculture is the definition of novel resistant traits in families or populations of sea lice, and the identification of novel molecular markers based on CNVs, supporting the creation of monitoring programs for C. rogercresseyi resistance to delousing drugs. Funding: ANID-Chile through the grant FONDECYT (#11200813 and # 1210852), and FONDAP (#15110027).