The zebrafish reference genome sequence and its relationship to the human genome

被引：3560

作者：

Howe, Kerstin ^{[1
]}

Clark, Matthew D. ^{[1
,2
]}

Torroja, Carlos F. ^{[1
,3
]}

Torrance, James ^{[1
]}

Berthelot, Camille ^{[4
,5
,6
]}

Muffato, Matthieu ^{[7
]}

Collins, John E. ^{[1
]}

Humphray, Sean ^{[1
,8
]}

McLaren, Karen ^{[1
]}

Matthews, Lucy ^{[1
]}

McLaren, Stuart ^{[1
]}

Sealy, Ian ^{[1
]}

Caccamo, Mario ^{[2
]}

Churcher, Carol ^{[1
]}

Scott, Carol ^{[1
]}

Barrett, Jeffrey C. ^{[1
]}

Koch, Romke ^{[9
]}

Rauch, Gerd-Joerg ^{[10
]}

White, Simon ^{[1
]}

Chow, William ^{[1
]}

Kilian, Britt ^{[1
]}

Quintais, Leonor T. ^{[7
]}

Guerra-Assuncao, Jose A. ^{[7
]}

Zhou, Yi ^{[11
,12
,13
]}

Gu, Yong ^{[1
]}

Yen, Jennifer ^{[1
]}

Vogel, Jan-Hinnerk ^{[1
]}

Eyre, Tina ^{[1
]}

Redmond, Seth ^{[1
]}

Banerjee, Ruby ^{[1
]}

Chi, Jianxiang ^{[1
]}

Fu, Beiyuan ^{[1
]}

Langley, Elizabeth ^{[1
]}

Maguire, Sean F. ^{[1
]}

Laird, Gavin K. ^{[1
]}

Lloyd, David ^{[1
]}

Kenyon, Emma ^{[1
]}

Donaldson, Sarah ^{[1
]}

Sehra, Harminder ^{[1
]}

Almeida-King, Jeff ^{[1
]}

Loveland, Jane ^{[1
]}

Trevanion, Stephen ^{[1
]}

Jones, Matt ^{[1
]}

Quail, Mike ^{[1
]}

Willey, Dave ^{[1
]}

Hunt, Adrienne ^{[1
]}

Burton, John ^{[1
]}

Sims, Sarah ^{[1
]}

McLay, Kirsten ^{[1
]}

Plumb, Bob ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Genome Anal Ctr, Norwich NR4 7UH, Norfolk, England

[3] Ctr Nacl Invest Cardiovasc, Bioinformat Unit, Madrid 28029, Spain

[4] ENS, Inst Biol, IBENS, F-75005 Paris, France

[5] INSERM, U1024, F-75005 Paris, France

[6] CNRS, UMR 8197, F-75005 Paris, France

[7] EMBL European Bioinformat Inst, Cambridge CB10 1SD, England

[8] Illumina Cambridge, Saffron Walden CB10 1XL, Essex, England

[9] Hubrecht Lab, NL-3584 CT Utrecht, Netherlands

[10] Max Planck Inst Dev Biol, D-72076 Tubingen, Germany

[11] Childrens Hosp, Stem Cell Program, Boston, MA 02115 USA

[12] Childrens Hosp, Div Hematol & Oncol, Boston, MA 02115 USA

[13] Dana Farber Canc Inst, Boston, MA 02115 USA

[14] Childrens Hosp Oakland, Oakland, CA 94609 USA

[15] Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA

[16] KIT, ITG, D-76344 Eggenstein Leopoldshafen, Germany

[17] Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

[18] Harvard Univ, Sch Med, Boston, MA 02115 USA

来源：

NATURE | 2013年 / 496卷 / 7446期

基金：

英国生物技术与生命科学研究理事会; 美国国家卫生研究院; 英国惠康基金;

关键词：

GENE; DUPLICATION; MUTATIONS; EVOLUTION; REVEALS;

D O I：

10.1038/nature12111

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Zebrafish have become a popular organism for the study of vertebrate gene function(1,2). The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease(3-5). However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes(6), the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

引用

页码：498 / 503

页数：6

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