Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish—the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.

金鱼已经进行了超过1,000年的密集驯化和选择性繁殖。在本报告中，我们描述了一个高质量的金鱼基因组（2n = 100），将95.75％的重叠群锚定到50个假染色体中。比较基因组学使我们能够区分古代杂交事件产生的两个亚基因组。对185个代表性金鱼变种和16个野生cru进行重新测序，揭示了金鱼的起源，并鉴定了通过与其驯化相关的选择性扫描而形成的基因组区域。我们对金鱼品种的全面收集使我们能够将遗传变异与许多众所周知的解剖特征相关联，其中包括区分传统金鱼进化枝的特征。另外，我们将酪氨酸蛋白激酶受体鉴定为金鱼孟德尔遗传的第一个众所周知的案例的候选病因基因-透明突变体。金鱼的基因组和多样性数据提供了独特的资源，使金鱼成为功能基因组学和驯化的有前途的模型。