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

For over a thousand years, the common goldfish ( ) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp ( ), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of...

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Bibliographic Details
Published in:	Science advances Vol. 5; no. 6; p. eaav0547
Main Authors:	Chen, Zelin, Omori, Yoshihiro, Koren, Sergey, Shirokiya, Takuya, Kuroda, Takuo, Miyamoto, Atsushi, Wada, Hironori, Fujiyama, Asao, Toyoda, Atsushi, Zhang, Suiyuan, Wolfsberg, Tyra G, Kawakami, Koichi, Phillippy, Adam M, Mullikin, James C, Burgess, Shawn M
Format:	Journal Article
Language:	English
Published:	United States American Association for the Advancement of Science 01-06-2019
Subjects:	Animals Asia Carps - genetics Evolution, Molecular Exons - genetics Gene Duplication - genetics Genetics Genome - genetics Genomics - methods Genotype Goldfish - genetics Phenotype SciAdv r-articles Zebrafish - genetics Asia
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Summary:	For over a thousand years, the common goldfish ( ) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp ( ), 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work. Present address: Laboratory of Functional Genomics, Department of Bioscience, Nagahama Institute of Bio-science and Technology, Nagahama, Shiga, Japan. The list of members of the NISC Comparative Sequencing Program can be found in the Supplementary Materials. Present address: College of Liberal Arts and Sciences, Kitasato University, Sagamihara, Kanagawa, Japan.
ISSN:	2375-2548 2375-2548
DOI:	10.1126/sciadv.aav0547