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

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

Nature, Volume: 496, Issue: 7446, Pages: 498 - 503

Swansea University Author: Emma Kenyon Orcid Logo

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DOI (Published version): 10.1038/nature12111

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 verte...

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Published in: Nature
ISSN: 0028-0836 1476-4687
Published: Springer Science and Business Media LLC 2013
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URI: https://cronfa.swan.ac.uk/Record/cronfa64045
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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. 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spelling v2 64045 2023-08-08 The zebrafish reference genome sequence and its relationship to the human genome 8f07d20c6cb93623521101c62c4e4eb3 0000-0002-3898-1866 Emma Kenyon Emma Kenyon true false 2023-08-08 BMS 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. Journal Article Nature 496 7446 498 503 Springer Science and Business Media LLC 0028-0836 1476-4687 25 4 2013 2013-04-25 10.1038/nature12111 http://dx.doi.org/10.1038/nature12111 COLLEGE NANME Biomedical Sciences COLLEGE CODE BMS Swansea University 2023-09-12T14:36:24.5188904 2023-08-08T11:18:23.3009628 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Biomedical Science Kerstin Howe 1 Matthew D. Clark 2 Carlos F. Torroja 3 James Torrance 4 Camille Berthelot 5 Matthieu Muffato 6 John E. Collins 7 Sean Humphray 8 Karen McLaren 9 Lucy Matthews 10 Stuart McLaren 11 Ian Sealy 12 Mario Caccamo 13 Carol Churcher 14 Carol Scott 15 Jeffrey C. Barrett 16 Romke Koch 17 Gerd-Jörg Rauch 18 Simon White 19 William Chow 20 Britt Kilian 21 Leonor T. Quintais 22 José A. Guerra-Assunção 23 Yi Zhou 24 Yong Gu 25 Jennifer Yen 26 Jan-Hinnerk Vogel 27 Tina Eyre 28 Seth Redmond 29 Ruby Banerjee 30 Jianxiang Chi 31 Beiyuan Fu 32 Elizabeth Langley 33 Sean F. Maguire 34 Gavin K. Laird 35 David Lloyd 36 Emma Kenyon 0000-0002-3898-1866 37 Sarah Donaldson 38 Harminder Sehra 39 Jeff Almeida-King 40 Jane Loveland 41 Stephen Trevanion 42 Matt Jones 43 Mike Quail 44 Dave Willey 45 Adrienne Hunt 46 John Burton 47 Sarah Sims 48 Kirsten McLay 49 Bob Plumb 50 Joy Davis 51 Chris Clee 52 Karen Oliver 53 Richard Clark 54 Clare Riddle 55 David Elliott 56 Glen Threadgold 57 Glenn Harden 58 Darren Ware 59 Sharmin Begum 60 Beverley Mortimore 61 Giselle Kerry 62 Paul Heath 63 Benjamin Phillimore 64 Alan Tracey 65 Nicole Corby 66 Matthew Dunn 67 Christopher Johnson 68 Jonathan Wood 69 Susan Clark 70 Sarah Pelan 71 Guy Griffiths 72 Michelle Smith 73 Rebecca Glithero 74 Philip Howden 75 Nicholas Barker 76 Christine Lloyd 77 Christopher Stevens 78 Joanna Harley 79 Karen Holt 80 Georgios Panagiotidis 81 Jamieson Lovell 82 Helen Beasley 83 Carl Henderson 84 Daria Gordon 85 Katherine Auger 86 Deborah Wright 87 Joanna Collins 88 Claire Raisen 89 Lauren Dyer 90 Kenric Leung 91 Lauren Robertson 92 Kirsty Ambridge 93 Daniel Leongamornlert 94 Sarah McGuire 95 Ruth Gilderthorp 96 Coline Griffiths 97 Deepa Manthravadi 98 Sarah Nichol 99 Gary Barker 100 Siobhan Whitehead 101 Michael Kay 102 Jacqueline Brown 103 Clare Murnane 104 Emma Gray 105 Matthew Humphries 106 Neil Sycamore 107 Darren Barker 108 David Saunders 109 Justene Wallis 110 Anne Babbage 111 Sian Hammond 112 Maryam Mashreghi-Mohammadi 113 Lucy Barr 114 Sancha Martin 115 Paul Wray 116 Andrew Ellington 117 Nicholas Matthews 118 Matthew Ellwood 119 Rebecca Woodmansey 120 Graham Clark 121 James D. Cooper 122 Anthony Tromans 123 Darren Grafham 124 Carl Skuce 125 Richard Pandian 126 Robert Andrews 127 Elliot Harrison 128 Andrew Kimberley 129 Jane Garnett 130 Nigel Fosker 131 Rebekah Hall 132 Patrick Garner 133 Daniel Kelly 134 Christine Bird 135 Sophie Palmer 136 Ines Gehring 137 Andrea Berger 138 Christopher M. Dooley 139 Zübeyde Ersan-Ürün 140 Cigdem Eser 141 Horst Geiger 142 Maria Geisler 143 Lena Karotki 144 Anette Kirn 145 Judith Konantz 146 Martina Konantz 147 Martina Oberländer 148 Silke Rudolph-Geiger 149 Mathias Teucke 150 Christa Lanz 151 Günter Raddatz 152 Kazutoyo Osoegawa 153 Baoli Zhu 154 Amanda Rapp 155 Sara Widaa 156 Cordelia Langford 157 Fengtang Yang 158 Stephan C. Schuster 159 Nigel P. Carter 160 Jennifer Harrow 161 Zemin Ning 162 Javier Herrero 163 Steve M. J. Searle 164 Anton Enright 165 Robert Geisler 166 Ronald H. A. Plasterk 167 Charles Lee 168 Monte Westerfield 169 Pieter J. de Jong 170 Leonard I. Zon 171 John H. Postlethwait 172 Christiane Nüsslein-Volhard 173 Tim J. P. Hubbard 174 Hugues Roest Crollius 175 Jane Rogers 176 Derek L. Stemple 177 64045__28508__5a4bdc509bb94816a1729fc9fe998117.pdf 64045.VOR.pdf 2023-09-12T14:31:33.9225529 Output 803209 application/pdf Version of Record true Distributed under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (CC BY-NC-SA 3.0). true eng https://creativecommons.org/licenses/by-nc-sa/3.0/
title The zebrafish reference genome sequence and its relationship to the human genome
spellingShingle The zebrafish reference genome sequence and its relationship to the human genome
Emma Kenyon
title_short The zebrafish reference genome sequence and its relationship to the human genome
title_full The zebrafish reference genome sequence and its relationship to the human genome
title_fullStr The zebrafish reference genome sequence and its relationship to the human genome
title_full_unstemmed The zebrafish reference genome sequence and its relationship to the human genome
title_sort The zebrafish reference genome sequence and its relationship to the human genome
author_id_str_mv 8f07d20c6cb93623521101c62c4e4eb3
author_id_fullname_str_mv 8f07d20c6cb93623521101c62c4e4eb3_***_Emma Kenyon
author Emma Kenyon
author2 Kerstin Howe
Matthew D. Clark
Carlos F. Torroja
James Torrance
Camille Berthelot
Matthieu Muffato
John E. Collins
Sean Humphray
Karen McLaren
Lucy Matthews
Stuart McLaren
Ian Sealy
Mario Caccamo
Carol Churcher
Carol Scott
Jeffrey C. Barrett
Romke Koch
Gerd-Jörg Rauch
Simon White
William Chow
Britt Kilian
Leonor T. Quintais
José A. Guerra-Assunção
Yi Zhou
Yong Gu
Jennifer Yen
Jan-Hinnerk Vogel
Tina Eyre
Seth Redmond
Ruby Banerjee
Jianxiang Chi
Beiyuan Fu
Elizabeth Langley
Sean F. Maguire
Gavin K. Laird
David Lloyd
Emma Kenyon
Sarah Donaldson
Harminder Sehra
Jeff Almeida-King
Jane Loveland
Stephen Trevanion
Matt Jones
Mike Quail
Dave Willey
Adrienne Hunt
John Burton
Sarah Sims
Kirsten McLay
Bob Plumb
Joy Davis
Chris Clee
Karen Oliver
Richard Clark
Clare Riddle
David Elliott
Glen Threadgold
Glenn Harden
Darren Ware
Sharmin Begum
Beverley Mortimore
Giselle Kerry
Paul Heath
Benjamin Phillimore
Alan Tracey
Nicole Corby
Matthew Dunn
Christopher Johnson
Jonathan Wood
Susan Clark
Sarah Pelan
Guy Griffiths
Michelle Smith
Rebecca Glithero
Philip Howden
Nicholas Barker
Christine Lloyd
Christopher Stevens
Joanna Harley
Karen Holt
Georgios Panagiotidis
Jamieson Lovell
Helen Beasley
Carl Henderson
Daria Gordon
Katherine Auger
Deborah Wright
Joanna Collins
Claire Raisen
Lauren Dyer
Kenric Leung
Lauren Robertson
Kirsty Ambridge
Daniel Leongamornlert
Sarah McGuire
Ruth Gilderthorp
Coline Griffiths
Deepa Manthravadi
Sarah Nichol
Gary Barker
Siobhan Whitehead
Michael Kay
Jacqueline Brown
Clare Murnane
Emma Gray
Matthew Humphries
Neil Sycamore
Darren Barker
David Saunders
Justene Wallis
Anne Babbage
Sian Hammond
Maryam Mashreghi-Mohammadi
Lucy Barr
Sancha Martin
Paul Wray
Andrew Ellington
Nicholas Matthews
Matthew Ellwood
Rebecca Woodmansey
Graham Clark
James D. Cooper
Anthony Tromans
Darren Grafham
Carl Skuce
Richard Pandian
Robert Andrews
Elliot Harrison
Andrew Kimberley
Jane Garnett
Nigel Fosker
Rebekah Hall
Patrick Garner
Daniel Kelly
Christine Bird
Sophie Palmer
Ines Gehring
Andrea Berger
Christopher M. Dooley
Zübeyde Ersan-Ürün
Cigdem Eser
Horst Geiger
Maria Geisler
Lena Karotki
Anette Kirn
Judith Konantz
Martina Konantz
Martina Oberländer
Silke Rudolph-Geiger
Mathias Teucke
Christa Lanz
Günter Raddatz
Kazutoyo Osoegawa
Baoli Zhu
Amanda Rapp
Sara Widaa
Cordelia Langford
Fengtang Yang
Stephan C. Schuster
Nigel P. Carter
Jennifer Harrow
Zemin Ning
Javier Herrero
Steve M. J. Searle
Anton Enright
Robert Geisler
Ronald H. A. Plasterk
Charles Lee
Monte Westerfield
Pieter J. de Jong
Leonard I. Zon
John H. Postlethwait
Christiane Nüsslein-Volhard
Tim J. P. Hubbard
Hugues Roest Crollius
Jane Rogers
Derek L. Stemple
format Journal article
container_title Nature
container_volume 496
container_issue 7446
container_start_page 498
publishDate 2013
institution Swansea University
issn 0028-0836
1476-4687
doi_str_mv 10.1038/nature12111
publisher Springer Science and Business Media LLC
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Biomedical Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Biomedical Science
url http://dx.doi.org/10.1038/nature12111
document_store_str 1
active_str 0
description 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.
published_date 2013-04-25T14:36:27Z
_version_ 1776839072401063936
score 11.03559

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