Simultaneous Differential Expression Analysis in Host and Parasite Using RNA-Seq: The Interaction Between Sea-Lice and Coho Salmon

Sea-lice is a major problem in salmonid aquaculture in the Atlantic Ocean and leads to substantial losses in profit. The louse (Lepeophtheirus salmonis) challenge is aggravated by the emergence of the strains resistant to therapeutics such as emamectin benzoate. Coho salmon (Oncorhynchus kisutch), unlike Atlantic salmon (Salmo salar) presents a natural resistance to sea-lice and has the ability to reject the parasite. Therefore, understanding the interaction between a resistant host (coho salmon) and the sea-louse may provide insight on targets for selection in Atlantic salmon and targets for novel therapeutics. Herein, we present the use of deep sequencing to evaluate changes in mRNA expression on both the parasite and host simultaneously. We leveraged the available draft of the lice genome to extract reads mapping to it exclusively and separated content originating from lice or salmonid RNA. Our results indicate that coho salmon can mount an early and aggressive inflammatory response coupled with the up-regulation of genes relevant to the complement cascade, infiltration of cellular effectors, tissue remodelling, acute-phase responses, and wound healing. This response is likely to contribute to the process of rejecting the parasite. On the other hand, the lice express transcripts relevant to a stress response while attempting to maintain its molting development. The interface between these and other biological processes from host and parasite most likely determine the outcome of the infection and will give valuable insight on mechanisms of resistance and virulence simultaneously.