基于基因富集数据的中国金鱼品种谱系研究

金鱼（Carassius auratus）起源于中国，是由野生鲫鱼驯化而来的一种观赏性鱼类。金鱼不同品种间存在巨大外形差异，长期的杂交与人工选择产生了众多的品种，但也导致其谱系关系混乱复杂，划分品种的难度加大。人们尝试了许多方法明确金鱼各品种间的谱系历史与杂交关系，但是至今未取得进展。本研究收集了11个中国金鱼品种，共计59个个体，利用跨物种靶基因富集和高通量测序获取了各品种目标基因序列。以斑马鱼4 434个单拷贝基因位点为参考序列，将金鱼对应的基因按照异源四倍体亚基因组分组，富集的序列分别按照两个亚基因组进行比对分型，产生35 298个单核苷酸多态性（SNPs）位点数据，用于金鱼品种谱系历史和杂交关系的研究。通过主成分分析，品种遗传结构以及系统发育网状图的构建，揭示了中国部分金鱼品种的遗传关系，解释了它们的遗传演化过程：（1）龙睛、琉金两种文种金鱼与和金（文种金鱼）关系较近；珍珠鳞、狮头不是来自于和金，而是独立演化而来。（2）以兰寿为代表的蛋种金鱼虽然早于水泡眼出现，但水泡眼是文种金鱼先出现水泡眼特征，然后文种水泡背鳍消失，演化出现代金鱼中的主流水泡眼。这也解释了蛋种金鱼中，水泡眼出...

Phylogenetic History of Chinese Goldfish Based on Gene Enrichment Data

Goldfish, is an ornamental fish originated in China, which was domesticated from wild crucian carp. There are large differences between different types of goldfish, such as presence or absence of dorsal fin, telescope or bubble eyes, oranda and other characters. Long-term hybridization and artificial selection have produced a large number of goldfish strains, but it also leads to the confusion and complexity in determining pedigree relationship of goldfish, which makes it more difficult to distinguish goldfish strains. People tried many ways to clarify the pedigree history and hybridization relationship between various goldfish strains, but so far no progress has been made. That is why the selection history of most goldfish strains has not been clarified and the hybridization relationships of many goldfish strain have not been confirmed.In this study, tissue samples of 59 individuals from 11 Chinese goldfish strains were collected. Cross-species target gene enrichment and high-throughput sequencing were used to obtain the target gene sequencing data of each goldfish individual. Using 4434 single-copy gene loci of zebrafish as reference sequences, the corresponding goldfish genes were grouped according to its heterotetraploid subgenome, and the enriched sequences were compared to and categorized according to two subgenomes respectively. A total of 35298 single nucleotide polymorphism (SNPs) loci were called, which were used to study the pedigree history and hybridization relationship of the goldfish strains.Principal component analyses, genetic structure analyses and phylogenetic network map of the two subgenomes were reconstructed to reveal genetic relationship of these Chinese goldfish strains and explain their selection and hybridization history: 1. The telescope and Ryukin are directly evolved from the wakin, while pearlscale and lionhead were not directly evolved from the wakin. 2. Ranchu evolved earlier than egg bubble eye, while the bubble eye had secondly lost its dorsal fin. 3. The telescope-oranda is closely related to the lionhead, which first generated the character of oranda, and later obtained the telescope eyes. 4. Pearlscale, pearlscale-oranda and telescope-pearlscale-oranda are genetically similar. Pearlscale-oranda is directly evolved from pearlscale, telescope-pearlscale-oranda is the latest bred form, probably a hybrid of telescope and pearlscale-oranda. The results of this study may help to understand the evolution history of Chinese goldfish and provide some reference for the classification and breeding of goldfish varieties.