Impact of sea lice (Caligus rogercresseyi) infection levels on skin transcriptome in Atlantic salmon (Salmo salar)

Abstract

Abstract Skin is a complex mucosal tissue, which is exposed to the outer environment, interacts with a plethora of environmental insults and represents the first line of defence against many pathogens. Sea lice Lepeophtheirus salmonis and Caligus rogercresseyi constitute a major threat to farmed salmonids, in both Northern and Southern hemispheres, respectively. We examined the response of skin transcriptome to different levels of infection with C. rogercresseyi in Atlantic salmon (Salmo salar). The infections were carried out on post- smolts using copepods, with a non- infected, control group. On day 14 post- infection, fish were examined for the total number of lice and grouped into low- and high-infected individuals, with 25 ± 5.3 and 59 ± 9.2 lice per fish, respectively. Skin samples (∼100 mg) were collected from the area anterior to the dorsal fin and midway to the lateral line. In total, 36 samples samples –with 12 fish allocated to control, low-infected and high- infected group, accordingly- were subjected to total RNA extraction, followed by library preparation and RNA- seq (Illumina NextSeq 500 platform, single reads 150bp long, sequencing depth 20M reads per sample). Raw reads were aligned to the Atlantic salmon reference genome (GCA_000233375.4 ICSASG_v2) and assessed for differential gene expression using EdgeR. Differentially expressed genes were identified following statistical analysis many of which could be defined as immune response genes. Of interest, genes from encoding mucins were detected as being highly enriched in the infected fish compared to control, suggesting an increase in transcription of this gene family. Other genes of interest included lectins and antimicrobial peptides such as hepcidin and cathelicidin. Many cytokines were also found modulated suggesting a complex immunological response. Full gene set enrichment is being performed to define more comprehensively the immune pathways responding to the lice infection. Keywords: Atlantic salmon, transcriptomics, Caligus rogercresseyi, RNA-Seq, differential gene expression