Dataset Information

The evolutionary origin and domestication history of goldfish (Carassius auratus).

ABSTRACT: 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.

SUBMITTER: Chen D

PROVIDER: S-EPMC7703540 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Publications

The evolutionary origin and domestication history of goldfish (<i>Carassius auratus</i>).

Chen Duo D Zhang Qing Q Tang Weiqi W Huang Zhen Z Wang Gang G Wang Yongjun Y Shi Jiaxian J Xu Huimin H Lin Lianyu L Li Zhen Z Chi Wenchao W Huang Likun L Xia Jing J Zhang Xingtan X Guo Lin L Wang Yuanyuan Y Ma Panpan P Tang Juan J Zhou Gang G Liu Min M Liu Fuyan F Hua Xiuting X Wang Baiyu B Shen Qiaochu Q Jiang Qing Q Lin Jingxian J Chen Xuequn X Wang Hongbo H Dou Meijie M Liu Lei L Pan Haoran H Qi Yiying Y Wu Bin B Fang Jingping J Zhou Yitao Y Cen Wan W He Wenjin W Zhang Qiujin Q Xue Ting T Lin Gang G Zhang Wenchun W Liu Zhongjian Z Qu Liming L Wang Aiming A Ye Qichang Q Chen Jianming J Zhang Yanding Y Ming Ray R Van Montagu Marc M Tang Haibao H Van de Peer Yves Y Chen Youqiang Y Zhang Jisen J

Proceedings of the National Academy of Sciences of the United States of America 20201102 47

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 b ...[more]

PMID: 33139555

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Project description:BackgroundGoldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. Here we used sequencing approaches to better characterize sex determination and sex-chromosomes in an experimental strain of goldfish.ResultsOur results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18 °C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (~ 11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the coding DNA sequence of the goldfish amh gene.ConclusionsThese results show that our goldfish strain has a relatively large sex locus on LG22, which is likely the Y chromosome of this experimental population. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers, which will be important tools for future research on sex determination in our experimental goldfish population. However, additional work would be needed to explore whether this sex locus is conserved in other populations of goldfish.

Dataset Information

The evolutionary origin and domestication history of goldfish (Carassius auratus).

Publications

The evolutionary origin and domestication history of goldfish (<i>Carassius auratus</i>).

Similar Datasets

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