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Pubmed ID :23594743
Publication Date : //

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


Zebrafish have become a popular organism for the study of vertebrate gene function. 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. 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, 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.

Authors : Howe Kerstin , Clark Matthew D , Torroja Carlos F , Torrance James , Berthelot Camille , Muffato Matthieu , Collins John E , Humphray Sean , McLaren Karen , Matthews Lucy , McLaren Stuart , Sealy Ian , Caccamo Mario , Churcher Carol , Scott Carol , Barrett Jeffrey C , Koch Romke , Rauch Gerd-Jörg , White Simon , Chow William , Kilian Britt , Quintais Leonor T , Guerra-Assunção José A , Zhou Yi , Gu Yong , Yen Jennifer , Vogel Jan-Hinnerk , Eyre Tina , Redmond Seth , Banerjee Ruby , Chi Jianxiang , Fu Beiyuan , Langley Elizabeth , Maguire Sean F , Laird Gavin K , Lloyd David , Kenyon Emma , Donaldson Sarah , Sehra Harminder , Almeida-King Jeff , Loveland Jane , Trevanion Stephen , Jones Matt , Quail Mike , Willey Dave , Hunt Adrienne , Burton John , Sims Sarah , McLay Kirsten , Plumb Bob , Davis Joy , Clee Chris , Oliver Karen , Clark Richard , Riddle Clare , Elliot David , Eliott David , Threadgold Glen , Harden Glenn , Ware Darren , Begum Sharmin , Mortimore Beverley , Mortimer Beverly , Kerry Giselle , Heath Paul , Phillimore Benjamin , Tracey Alan , Corby Nicole , Dunn Matthew , Johnson Christopher , Wood Jonathan , Clark Susan , Pelan Sarah , Griffiths Guy , Smith Michelle , Glithero Rebecca , Howden Philip , Barker Nicholas , Lloyd Christine , Stevens Christopher , Harley Joanna , Holt Karen , Panagiotidis Georgios , Lovell Jamieson , Beasley Helen , Henderson Carl , Gordon Daria , Auger Katherine , Wright Deborah , Collins Joanna , Raisen Claire , Dyer Lauren , Leung Kenric , Robertson Lauren , Ambridge Kirsty , Leongamornlert Daniel , McGuire Sarah , Gilderthorp Ruth , Griffiths Coline , Manthravadi Deepa , Nichol Sarah , Barker Gary , Whitehead Siobhan , Kay Michael , Brown Jacqueline , Murnane Clare , Gray Emma , Humphries Matthew , Sycamore Neil , Barker Darren , Saunders David , Wallis Justene , Babbage Anne , Hammond Sian , Mashreghi-Mohammadi Maryam , Barr Lucy , Martin Sancha , Wray Paul , Ellington Andrew , Matthews Nicholas , Ellwood Matthew , Woodmansey Rebecca , Clark Graham , Cooper James D , Cooper James , Tromans Anthony , Grafham Darren , Skuce Carl , Pandian Richard , Andrews Robert , Harrison Elliot , Kimberley Andrew , Garnett Jane , Fosker Nigel , Hall Rebekah , Garner Patrick , Kelly Daniel , Bird Christine , Palmer Sophie , Gehring Ines , Berger Andrea , Dooley Christopher M , Ersan-Ürün Zübeyde , Eser Cigdem , Geiger Horst , Geisler Maria , Karotki Lena , Kirn Anette , Konantz Judith , Konantz Martina , Oberländer Martina , Rudolph-Geiger Silke , Teucke Mathias , Lanz Christa , Raddatz Günter , Osoegawa Kazutoyo , Zhu Baoli , Rapp Amanda , Widaa Sara , Langford Cordelia , Yang Fengtang , Schuster Stephan C , Carter Nigel P , Harrow Jennifer , Ning Zemin , Herrero Javier , Searle Steve M J , Enright Anton , Geisler Robert , Plasterk Ronald H A , Lee Charles , Westerfield Monte , de Jong Pieter J , Zon Leonard I , Postlethwait John H , Nüsslein-Volhard Christiane , Hubbard Tim J P , Roest Crollius Hugues , Rogers Jane , Stemple Derek L ,

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