Whole-genome resequencing in the sea louse Caligus rogercresseyi uncovers gene duplications and copy number variants associated with pesticide resistance

The sea louse Caligus rogercresseyi is a marine ectoparasite that constitutes one of the major threats to salmon farming industry, where primary control strategy use delousing drugs through immersion treatments. emergence pharmacological resistance in this copepodid species has previously been described using transcriptome data. However, molecular mechanisms underlying chromosome rearrangements have not yet explored. This study aimed identify structural genomic variations and gene expression C. associated with pesticide sensitivity. In study, genome resequencing was conducted Oxford Nanopore Technology on lice strains contrasting sensitivity azamethiphos detect duplications. Transcriptome profiling putative duplications performed by Illumina sequencing. Copy Number Variants (CNVs) were identified comparative coverage, collinear/tandem over all chromosomal regions sequence homology. Duplications or CNVs functional genes primarily transposable elements related drug response, differential values calculated RNA-seq analyses same strains. Notably, differentially duplicated found coding cuticle proteins, suggesting mechanism may be cuticular structure formation proteins involved. Collectively, results revealed intensive pesticides populations increases frequency duplication, expanding involved response. first report an association between populations.