De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication
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DOI：
10.1126/sciadv.aav0547
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发表时间：
2019-06-01
期刊：
影响因子：
13.6
通讯作者：
Burgess, Shawn M.
中科院分区：
文献类型：
--
作者：
Chen, Zelin;Omori, Yoshihiro;Burgess, Shawn M.
一千多年来，常见的金鱼(Carassius Auratus)在整个亚洲被作为食物和观赏宠物饲养。作为鲤鱼(鲤鱼)的近亲，金鱼拥有大约1400万年前共同祖先的基因组复制。几个世纪的繁育和各种有趣的身体形态相结合，提供了一个令人兴奋的机会，将基因型与表型联系起来，并了解基因组进化和物种形成的动态。我们使用71X PacBio Long Read生成了一条“Wakin”金鱼的高质量草稿序列和基因注释。金鱼的这两个亚基因组在金鱼和斑马鱼之间保持了广泛的共性和共线性。然而，鲤鱼全基因组复制后，基因迅速丢失，30%的保留复制基因在七个样本组织中的表达存在显著差异。序列同一性和/或外显子的丢失决定了所有组织表达水平的差异，而保守非编码元件的丢失决定了不同组织之间的表达差异。这一组装为比较基因组学和理解金鱼变异的原因提供了重要的资源。
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.