Environmental changes during the sea lice infestation drive transcriptome and gene regulation plasticity

The sea louse, Caligus rogercresseyi, is one of the main concerns in the Chilean salmon industry. The freeliving copepodid stage can recognize the host and initiate the parasitic phase, where environmental factors can shape the host recognition process. This study aimed to explore the ecological influence on the transcriptome of copepodids infesting Atlantic salmon experimentally exposed to different salinity and temperature (S_T) conditions. Herein, two hundred salmon were infested with 35 copepodids per fish previously acclimatized to four S/T treatments: 32 and 26 PSU; 8 and 16C. After 48 hours of infestation, the attached copepodids from each experimental group were counted and digitalized for geometric morphometric analysis. Copepodids were then collected for RNA sequencing to analyze transcriptome modulation and gene regulation. Morphological changes in copepodids were mainly associated with temperature rather than salinity conditions. The transcriptome survey revealed molecular signatures related to salinity and temperature changes, where salinity drives the gene expression of copepodids. Notably, specific genes, such as those encoding cuticle proteins and trypsin-like kinases, were regulated by all three post-transcriptional mechanisms assessed: alternative splicing, miRNA, and gene fusion. Transcriptome analysis revealed that trypsin-like kinase genes exhibited up and downregulation across the various S_T conditions. In contrast, cuticle protein genes were consistently downregulated in the 32PSU_8C, 26PSU_8C, and 26PSU_16C groups compared to the 32PSU_16C control. This suggests that the three post-transcriptional mechanisms may exert a combined influence on the expression of specific genes, potentially driven by salinity and temperature environmental conditions in sea lice biology.