Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 117, Issue 47, Pages 29775-29785Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.2005545117
Keywords
Carassius auratus; goldfish; domestication; GWAS; genome evolution
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Funding
- 13th Five-Year Plan for the Marine Innovation and Economic Development Demonstration Projects [FZHJ14]
- Science and Technology Programof Fuzhou [2018-N-27]
- European Research Council under the European Union's Horizon 2020 research and innovation program [833522]
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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.
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