PUBLICATION

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

Authors
Chen, Z., Omori, Y., Koren, S., Shirokiya, T., Kuroda, T., Miyamoto, A., Wada, H., Fujiyama, A., Toyoda, A., Zhang, S., Wolfsberg, T.G., Kawakami, K., Phillippy, A.M., NISC Comparative Sequencing Program, Mullikin, J.C., Burgess, S.M.
ID
ZDB-PUB-190701-10
Date
2019
Source
Science advances   5: eaav0547 (Journal)
Registered Authors
Kawakami, Koichi, Omori, Yoshihiro, Wada, Hironori
Keywords
none
MeSH Terms
  • Animals
  • Asia
  • Carps/genetics
  • Evolution, Molecular
  • Exons/genetics
  • Gene Duplication/genetics*
  • Genome/genetics*
  • Genomics/methods
  • Genotype
  • Goldfish/genetics*
  • Phenotype
  • Zebrafish/genetics
PubMed
31249862 Full text @ Sci Adv
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.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes