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Sci Adv. 2019 Jun 26;5(6):eaav0547. doi: 10.1126/sciadv.aav0547. eCollection 2019 Jun.

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

Author information

1
Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
2
Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
3
Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
4
Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Aichi, Japan.
5
Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan.
6
Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan.
7
Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
8
NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, MD, USA.
9
Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.

Abstract

For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a "Wakin" goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.

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