Data from: Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar)

Understanding the genomic basis of host-parasite adaptation is important for predicting the long-term viability of species and developing successful management practices. However, in wild populations, identifying specific signatures of parasite-driven selection often presents a challenge, as it is difficult to unravel the molecular signatures of selection driven by different, but correlated, environmental factors. Furthermore, separating parasite-mediated selection from similar signatures due to genetic drift and population history can also be difficult. Populations of Atlantic salmon (Salmo salar L.) from northern Europe have pronounced differences in their reactions to the parasitic flatworm Gyrodactylus salaris Malmberg 1957 and are therefore a good model to search for specific genomic regions underlying inter-population differences in pathogen response. We used a dense Atlantic salmon SNP array, along with extensive sampling of 43 salmon populations representing the two G. salaris response extremes (extreme susceptibility vs resistant), to screen the salmon genome for signatures of directional selection while attempting to separate the parasite effect from other factors. After combining the results from two independent genome scan analyses, 57 candidate genes potentially under positive selection were identified, out of which 50 were functionally annotated. This candidate gene set was shown to be functionally enriched for lymph node development, focal adhesion genes and anti-viral response, which suggests that the regulation of both innate and acquired immunity might be an important mechanism for salmon response to G. salaris. Overall, our results offer insights into the apparently complex genetic basis of pathogen susceptibility in salmon and highlight methodological challenges for separating the effects of various environmental factors

解析宿主-寄生虫适应性的基因组基础，对于预测物种的长期生存能力以及制定高效的物种管理实践方案具有重要价值。然而，在野生种群中，精准识别寄生虫驱动选择的特异性分子特征往往颇具挑战，一方面难以厘清由多种相互关联的环境因素所诱导的选择分子特征，另一方面将寄生虫介导的选择信号与遗传漂变、种群历史所产生的类似特征区分开来，同样存在难度。北欧大西洋鲑（Salmo salar L.）种群对寄生扁形虫Gyrodactylus salaris Malmberg 1957的抗性反应存在显著差异，因此成为探寻病原体响应种群间差异背后特定基因组区域的理想模型。本研究采用高密度大西洋鲑单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片，结合对代表两种极端Gyrodactylus salaris响应类型（极敏感型与抗性型）的43个鲑鱼种群的大规模采样，在尝试剥离寄生虫效应与其他混杂因素的前提下，对鲑鱼基因组开展定向选择特征筛选。在整合两项独立基因组扫描分析的结果后，本研究共鉴定出57个潜在受正向选择的候选基因，其中50个获得了功能注释。功能富集分析显示，该候选基因集显著富集于淋巴结发育、黏着斑基因家族以及抗病毒应答通路，这表明先天免疫与适应性免疫的协同调控，可能是鲑鱼应对Gyrodactylus salaris感染的核心机制之一。总体而言，本研究结果为解析鲑鱼病原体易感性背后看似复杂的遗传基础提供了全新视角，同时也凸显了区分多种环境因素效应所面临的方法学挑战。