Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

中文翻译：

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全基因组分析揭示了Goldsinny濑鱼种群之间的遗传差异

海水鱼类种群通常以高水平的基因流动和相应的低遗传差异为特征。这给定义管理单位提出了挑战。Goldsinny濑鱼（Ctenolabrus rupestris）由于在商业鲑鱼养殖中作为清洁鱼的重要性而被广泛利用。但是，目前，该物种的种群遗传结构仍未完全解析。在这里，全基因组测序被用于产生该物种的第一个基因组参考，研究四个地理上不同种群之间的种群基因组差异，并鉴定信息丰富的SNP标记物以供将来研究。在构建了一个从头组装后，该基因组被认为是高度多态的，大小约为600Mbp。33，此后选择了235个SNP，以评估从斯堪的纳维亚半岛，苏格兰和西班牙收集的四个种群之间的基因组多样性和分化。这些人群中的全球FST为0.015-0.092。大约4％的调查基因座被确定为推定的全球异常值，而在斯堪的纳维亚半岛则约为1％。选择显示出较大差异（FST> 0.15）的SNP作为人群分配的候选诊断标记。通过对斯堪的纳维亚物种分布范围的每一端的47个个体进行基因分型，验证了两个斯堪的纳维亚种群之间的173个最具诊断性的SNP。这些SNP中有69个有显着差异（p <0.05）（平均FST_173_loci = 0.065，FST_69_loci = 0.140）。使用这些经过验证的SNP，个人被分配到其原籍人口的可能性很高（≥94％）。Goldsinny濑鱼显示出高度多态的基因组和大量的人口基因组结构。选择多样化可能会影响全球和斯堪的纳维亚半岛内部的人口结构。现在鉴定出的诊断基因座提供了一种有前途且具有成本效益的工具，可以进一步调查金鱼母濑鱼种群。