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

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, Eliott, David, Threadgold, Glen, Harden, Glenn, Ware, Darren, 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, 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, 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, Osoegawa, Kazutoyo, Zhu, Baoli, Rapp, Amanda, Widaa, Sara, Langford, Cordelia, Yang, Fengtang, 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, Crollius, Hugues Roest, Rogers, Jane and Stemple, Derek L (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature, 496 (7446). pp. 498-503. ISSN 0028-0836

Full text not available from this repository.

Abstract

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.

Item Type: Article
Keywords: Comparative genomics
Schools and Departments: School of Life Sciences > Neuroscience
Subjects: Q Science
Depositing User: Emma Kenyon
Date Deposited: 11 Jul 2016 10:52
Last Modified: 05 Apr 2017 10:34
URI: http://sro.sussex.ac.uk/id/eprint/60354
📧 Request an update