DataSheet_1_Transcriptome Analysis of Atlantic Salmon (Salmo salar) Skin in Response to Sea Lice and Infectious Salmon Anemia Virus Co-Infection Under Different Experimental Functional Diets.zip

Sea lice (Lepeophtheirus salmonis) are ectoparasitic copepods that cause significant economic loss in marine salmoniculture. In commercial salmon farms, infestation with sea lice can enhance susceptibility to other significant pathogens, such as the highly contagious infectious salmon anemia virus (ISAv). In this study, transcriptomic analysis was used to evaluate the impact of four experimental functional feeds (i.e. 0.3% EPA/DHA+high-ω6, 0.3% EPA/DHA+high-ω6+immunostimulant (IS), 1% EPA/DHA+high-ω6, and 1% EPA/DHA+high-ω3) on Atlantic salmon (Salmo salar) during a single infection with sea lice (L. salmonis) and a co-infection with sea lice and ISAv. The overall objectives were to compare the transcriptomic profiles of skin between lice infection alone with co-infection groups and assess differences in gene expression response among animals with different experimental diets. Atlantic salmon smolts were challenged with L. salmonis following a 28-day feeding trial. Fish were then challenged with ISAv at 18 days post-sea lice infection (dpi), and maintained on individual diets, to establish a co-infection model. Skin tissues sampled at 33 dpi were subjected to RNA-seq analysis. The co-infection’s overall survival rates were between 37%-50%, while no mortality was observed in the single infection with lice. With regard to the infection status, 756 and 1303 consensus differentially expressed genes (DEGs) among the four diets were identified in “lice infection vs. pre-infection” and “co-infection vs. pre-infection” groups, respectively, that were shared between the four experimental diets. The co-infection groups (co-infection vs. pre-infection) included up-regulated genes associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix. Pathway enrichment analysis conducted between infected groups (lice infection vs. co-infection) resulted in several immune-related significant GO terms and pathways unique to this group, such as “autophagosome”, “cytosolic DNA-sensing pathway” and “response to type I interferons”. Understanding how experimental functional feeds can impact the host response and the trajectory of co-infections will be an essential step in identifying efficacious intervention strategies that account for the complexities of disease in open cage culture.

鲑疮痂鱼虱（Lepeophtheirus salmonis）是一类桡足类外寄生生物，给海水鲑鱼养殖业造成了显著经济损失。在商业化鲑鱼养殖场中，鲑疮痂鱼虱感染会提升宿主对其他重要病原体的易感性，例如高传染性的鲑传染性贫血病毒（infectious salmon anemia virus, ISAv）。本研究采用转录组学分析手段，评估四种实验功能性饲料——即0.3% EPA/DHA+高ω6、0.3% EPA/DHA+高ω6+免疫刺激剂（immunostimulant, IS）、1% EPA/DHA+高ω6以及1% EPA/DHA+高ω3——对大西洋鲑（Salmo salar）在单纯鲑疮痂鱼虱（L. salmonis）感染以及鲑疮痂鱼虱与ISAv混合感染状态下的影响。本研究的总体目标为：对比单纯鱼虱感染组与混合感染组的皮肤转录组特征，并评估不同实验饲料组间宿主的基因表达响应差异。研究人员先对大西洋鲑幼鱼开展为期28天的饲喂试验，随后用L. salmonis进行感染攻毒。在鲑疮痂鱼虱感染后第18天（days post-infection, dpi），再用ISAv对受试鱼进行攻毒，并全程维持各自的饲喂方案，以此构建混合感染模型。在感染后第33天采集皮肤组织样本，进行RNA测序（RNA-seq）分析。混合感染组的总体存活率介于37%至50%之间，而单纯鱼虱感染组未出现死亡个体。针对感染状态分析，在"单纯鱼虱感染vs感染前"与"混合感染vs感染前"两组中，分别鉴定出756个和1303个在四种实验饲料组中均共享的差异表达基因（differentially expressed genes, DEGs）。混合感染组（混合感染vs感染前）中，上调基因主要与糖酵解、干扰素通路、补体级联反应以及热休克蛋白家族相关；而下调基因则涉及抗原呈递与加工、T细胞活化、胶原形成以及细胞外基质。对单纯鱼虱感染组与混合感染组进行通路富集分析后，得到了该组特有的多个免疫相关显著GO（Gene Ontology）条目与通路，例如"自噬体"、"胞质DNA感知通路"以及"I型干扰素应答"。阐明实验功能性饲料如何影响宿主响应与混合感染的病程进展，将是针对开放式网箱养殖中疾病复杂性制定有效干预策略的关键一环。