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; 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 Eliott; Glen Threadgold; Glenn Harden; Darren Ware; Beverly Mortimer; 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; 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 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; Kazutoyo Osoegawa; Baoli Zhu; Amanda Rapp; Sara Widaa; Cordelia Langford; Fengtang Yang; 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

doi:10.1038/nature12111

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 ChowBritt 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 Eliott, Glen Threadgold, Glenn Harden, Darren Ware, Beverly Mortimer, 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, 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 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, Kazutoyo Osoegawa, Baoli Zhu, Amanda Rapp, Sara Widaa, Cordelia Langford, Fengtang Yang, 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^*

^*Corresponding author for this work

Clinic of Surgery

4235 Citations (Scopus)

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.

Original language	English
Journal	Nature
Volume	496
Issue number	7446
Pages (from-to)	498-503
Number of pages	6
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature12111
Publication status	Published - 25.04.2013

Funding

Acknowledgements We wish to thank R. Durbin, E. Birney, A. Scally, C. P. Ponting, E. Busch-Nentwich and R. Kettleborough for helpful discussions, as well as F. L. Marlow and P.Aanstad for criticalreadingand helpfulcommentsonmanuscripts.Wethankthe zebrafish information network (ZFIN) for funding part of the manual annotation of the zebrafish genome and the ZFIN staff for support with gene nomenclature and other genome issues. We also thank the Genome Reference Consortium for the maintenance and improvement of the zebrafish genome assembly. We are indebted to the Ensembl team for providing a browser and database that greatly facilitated the use and the analyses of the zebrafish genome. We thank A. Pirani at Affymetrix for genotyping advice support, and the Zebrafish International Resource Center (ZIRC) for distributing the SAT strain. J.H.P.was supportedbythe NationalInstitutesofHealth(NIH) grantR01 GM085318 (to J.H.P.), NIH grant P01 HD22486 (to J.H.P.) and R01 OD011116 (later changed to R01 RR020833) (to J.H.P.). We would like to acknowledge the support of the European Commission’s Sixth Framework Programme (contract no. LSHG-CT-2003-503496, ZF-MODELS) and Seventh Framework Programme (grant no. HEALTH-F4-2010-242048, ZF-HEALTH). R.G. was supported by the German Human Genome Project (DHGP Grant 01 KW 9627 and 01 KW 9919). C.N.-V., G.-J.R. and R.G. were supported by the NIH (NIH grant1 R01DK55377-01A1). S.C.S. was supported by the German Research Foundation (DFG Grant NU 22/5). The Zebrafish Genome Project at the Wellcome Trust Sanger Institute was funded by Wellcome Trust grant number 098051. S.M., C.S., J.C., B.F., E.L., S.F.M., M.J., M.Q., D.W., A.H., J.B., S.S., K.M., B.P., J..D., C.C., K.O., B.M., G.K., B.P., A.T., N.C., C.J., S.C., M.S., R.G., P.H., N.B., C.Lanz, C.S., J.H., K.H., G.P., J.L., H.B., C.H., D.G., D.W., C.R., L.D., K.L., L.R., K.A., D.L., S.M., R.G., C.G., D.M., S.N., G.B., S.W., M.K., J.B., C.M., E.G., M.H.,N.S., D.B.,D.S.,J.W.,A.B.,S.H., K.O., M.M.-M.,L.B.,S.M., P.W.,A.E., N.M., M.E., R.W., G.C., J.C., A.T., D.G., C.S., R.P., R.A., E.H., A.K., J.G., N.F., R.H., P.G., D.K., C.B. and S.P. The generation of maps used in the initial assemblies and the production of clone tiling paths were carried out by R.K., S.H., G.-J.R., Y.Z., C.R., R.C., D.E., D.W., S.B., L.M., M.D., I.G., A.B., C.M.D., Z.E.-Ü., C.E., H.G., M.G., L.K., A.K., J.K., M.K., M.O., S.R.-G., M.T., C.Lanz, G.R., S.C.S., R.B., F.Y., N.P.C., R.G., R.H.A.P. and C.Lee. K.O., B.Z. and P.J.d.J. generated and provided clone libraries. The Zebrafish Genome Project was coordinated by L.I.Z., J.H.P., C.N.-V., T.J.P.H., J.R. and D.L.S. In this Letter, five authors were inadvertently omitted: Sharmin Begum and Christine Lloyd from the Wellcome Trust Sanger Institute, and Christa Lanz, Günter Raddatz and Stephan C. Schuster from the Max Planck Institute for Developmental Biology. David Elliot was incorrectly listed as David Eliot, Beverley Mortimore was incorrectly listed as Beverly Mortimer, and James D. Cooper was incorrectly listed as James Cooper. In addition, the acknowledgements section should state that author S.C.S. was supported by the German Research Foundation (DFG Grant NU 22/5). These errors, along with corresponding minor changes to the Author Contributions section, have been corrected in the HTML and PDF versions of the original manuscript.

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10.1038/nature12111

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Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J. C., Koch, R., Rauch, G. J., White, S., ... Stemple, D. L. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature, 496(7446), 498-503. https://doi.org/10.1038/nature12111

@article{9b03a152fcbd48b48b5aa4ecac8bdf59,

title = "The zebrafish reference genome sequence and its relationship to the human genome",

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.",

author = "Kerstin Howe and Clark, \{Matthew D.\} and Torroja, \{Carlos F.\} and James Torrance and Camille Berthelot and Matthieu Muffato and Collins, \{John E.\} and Sean Humphray and Karen McLaren and Lucy Matthews and Stuart McLaren and Ian Sealy and Mario Caccamo and Carol Churcher and Carol Scott and Barrett, \{Jeffrey C.\} and Romke Koch and Rauch, \{Gerd J{\"o}rg\} and Simon White and William Chow and Britt Kilian and Quintais, \{Leonor T.\} and Guerra-Assun{\c c}{\~a}o, \{Jos{\'e} A.\} and Yi Zhou and Yong Gu and Jennifer Yen and Vogel, \{Jan Hinnerk\} and Tina Eyre and Seth Redmond and Ruby Banerjee and Jianxiang Chi and Beiyuan Fu and Elizabeth Langley and Maguire, \{Sean F.\} and Laird, \{Gavin K.\} and David Lloyd and Emma Kenyon and Sarah Donaldson and Harminder Sehra and Jeff Almeida-King and Jane Loveland and Stephen Trevanion and Matt Jones and Mike Quail and Dave Willey and Adrienne Hunt and John Burton and Sarah Sims and Kirsten McLay and Bob Plumb and Joy Davis and Chris Clee and Karen Oliver and Richard Clark and Clare Riddle and David Eliott and Glen Threadgold and Glenn Harden and Darren Ware and Beverly Mortimer and Giselle Kerry and Paul Heath and Benjamin Phillimore and Alan Tracey and Nicole Corby and Matthew Dunn and Christopher Johnson and Jonathan Wood and Susan Clark and Sarah Pelan and Guy Griffiths and Michelle Smith and Rebecca Glithero and Philip Howden and Nicholas Barker and Christopher Stevens and Joanna Harley and Karen Holt and Georgios Panagiotidis and Jamieson Lovell and Helen Beasley and Carl Henderson and Daria Gordon and Katherine Auger and Deborah Wright and Joanna Collins and Claire Raisen and Lauren Dyer and Kenric Leung and Lauren Robertson and Kirsty Ambridge and Daniel Leongamornlert and Sarah McGuire and Ruth Gilderthorp and Coline Griffiths and Deepa Manthravadi and Sarah Nichol and Gary Barker and Siobhan Whitehead and Michael Kay and Jacqueline Brown and Clare Murnane and Emma Gray and Matthew Humphries and Neil Sycamore and Darren Barker and David Saunders and Justene Wallis and Anne Babbage and Sian Hammond and Maryam Mashreghi-Mohammadi and Lucy Barr and Sancha Martin and Paul Wray and Andrew Ellington and Nicholas Matthews and Matthew Ellwood and Rebecca Woodmansey and Graham Clark and James Cooper and Anthony Tromans and Darren Grafham and Carl Skuce and Richard Pandian and Robert Andrews and Elliot Harrison and Andrew Kimberley and Jane Garnett and Nigel Fosker and Rebekah Hall and Patrick Garner and Daniel Kelly and Christine Bird and Sophie Palmer and Ines Gehring and Andrea Berger and Dooley, \{Christopher M.\} and Z{\"u}beyde Ersan-{\"U}r{\"u}n and Cigdem Eser and Horst Geiger and Maria Geisler and Lena Karotki and Anette Kirn and Judith Konantz and Martina Konantz and Martina Oberl{\"a}nder and Silke Rudolph-Geiger and Mathias Teucke and Kazutoyo Osoegawa and Baoli Zhu and Amanda Rapp and Sara Widaa and Cordelia Langford and Fengtang Yang and Carter, \{Nigel P.\} and Jennifer Harrow and Zemin Ning and Javier Herrero and Searle, \{Steve M.J.\} and Anton Enright and Robert Geisler and Plasterk, \{Ronald H.A.\} and Charles Lee and Monte Westerfield and \{De Jong\}, \{Pieter J.\} and Zon, \{Leonard I.\} and Postlethwait, \{John H.\} and Christiane N{\"u}sslein-Volhard and Hubbard, \{Tim J.P.\} and Crollius, \{Hugues Roest\} and Jane Rogers and Stemple, \{Derek L.\}",

year = "2013",

month = apr,

day = "25",

doi = "10.1038/nature12111",

language = "English",

volume = "496",

pages = "498--503",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7446",

}

Howe, K, Clark, MD, Torroja, CF, Torrance, J, Berthelot, C, Muffato, M, Collins, JE, Humphray, S, McLaren, K, Matthews, L, McLaren, S, Sealy, I, Caccamo, M, Churcher, C, Scott, C, Barrett, JC, Koch, R, Rauch, GJ, White, S, Chow, W, Kilian, B, Quintais, LT, Guerra-Assunção, JA, Zhou, Y, Gu, Y, Yen, J, Vogel, JH, Eyre, T, Redmond, S, Banerjee, R, Chi, J, Fu, B, Langley, E, Maguire, SF, Laird, GK, Lloyd, D, Kenyon, E, Donaldson, S, Sehra, H, Almeida-King, J, Loveland, J, Trevanion, S, Jones, M, Quail, M, Willey, D, Hunt, A, Burton, J, Sims, S, McLay, K, Plumb, B, Davis, J, Clee, C, Oliver, K, Clark, R, Riddle, C, Eliott, D, Threadgold, G, Harden, G, Ware, D, Mortimer, B, Kerry, G, Heath, P, Phillimore, B, Tracey, A, Corby, N, Dunn, M, Johnson, C, Wood, J, Clark, S, Pelan, S, Griffiths, G, Smith, M, Glithero, R, Howden, P, Barker, N, Stevens, C, Harley, J, Holt, K, Panagiotidis, G, Lovell, J, Beasley, H, Henderson, C, Gordon, D, Auger, K, Wright, D, Collins, J, Raisen, C, Dyer, L, Leung, K, Robertson, L, Ambridge, K, Leongamornlert, D, McGuire, S, Gilderthorp, R, Griffiths, C, Manthravadi, D, Nichol, S, Barker, G, Whitehead, S, Kay, M, Brown, J, Murnane, C, Gray, E, Humphries, M, Sycamore, N, Barker, D, Saunders, D, Wallis, J, Babbage, A, Hammond, S, Mashreghi-Mohammadi, M, Barr, L, Martin, S, Wray, P, Ellington, A, Matthews, N, Ellwood, M, Woodmansey, R, Clark, G, Cooper, J, Tromans, A, Grafham, D, Skuce, C, Pandian, R, Andrews, R, Harrison, E, Kimberley, A, Garnett, J, Fosker, N, Hall, R, Garner, P, Kelly, D, Bird, C, Palmer, S, Gehring, I, Berger, A, Dooley, CM, Ersan-Ürün, Z, Eser, C, Geiger, H, Geisler, M, Karotki, L, Kirn, A, Konantz, J, Konantz, M, Oberländer, M, Rudolph-Geiger, S, Teucke, M, Osoegawa, K, Zhu, B, Rapp, A, Widaa, S, Langford, C, Yang, F, Carter, NP, Harrow, J, Ning, Z, Herrero, J, Searle, SMJ, Enright, A, Geisler, R, Plasterk, RHA, Lee, C, Westerfield, M, De Jong, PJ, Zon, LI, Postlethwait, JH, Nüsslein-Volhard, C, Hubbard, TJP, Crollius, HR, Rogers, J & Stemple, DL 2013, 'The zebrafish reference genome sequence and its relationship to the human genome', Nature, vol. 496, no. 7446, pp. 498-503. https://doi.org/10.1038/nature12111

TY - JOUR

T1 - The zebrafish reference genome sequence and its relationship to the human genome

AU - Howe, Kerstin

AU - Clark, Matthew D.

AU - Torroja, Carlos F.

AU - Torrance, James

AU - Berthelot, Camille

AU - Muffato, Matthieu

AU - Collins, John E.

AU - Humphray, Sean

AU - McLaren, Karen

AU - Matthews, Lucy

AU - McLaren, Stuart

AU - Sealy, Ian

AU - Caccamo, Mario

AU - Churcher, Carol

AU - Scott, Carol

AU - Barrett, Jeffrey C.

AU - Koch, Romke

AU - Rauch, Gerd Jörg

AU - White, Simon

AU - Chow, William

AU - Kilian, Britt

AU - Quintais, Leonor T.

AU - Guerra-Assunção, José A.

AU - Zhou, Yi

AU - Gu, Yong

AU - Yen, Jennifer

AU - Vogel, Jan Hinnerk

AU - Eyre, Tina

AU - Redmond, Seth

AU - Banerjee, Ruby

AU - Chi, Jianxiang

AU - Fu, Beiyuan

AU - Langley, Elizabeth

AU - Maguire, Sean F.

AU - Laird, Gavin K.

AU - Lloyd, David

AU - Kenyon, Emma

AU - Donaldson, Sarah

AU - Sehra, Harminder

AU - Almeida-King, Jeff

AU - Loveland, Jane

AU - Trevanion, Stephen

AU - Jones, Matt

AU - Quail, Mike

AU - Willey, Dave

AU - Hunt, Adrienne

AU - Burton, John

AU - Sims, Sarah

AU - McLay, Kirsten

AU - Plumb, Bob

AU - Davis, Joy

AU - Clee, Chris

AU - Oliver, Karen

AU - Clark, Richard

AU - Riddle, Clare

AU - Eliott, David

AU - Threadgold, Glen

AU - Harden, Glenn

AU - Ware, Darren

AU - Mortimer, Beverly

AU - Kerry, Giselle

AU - Heath, Paul

AU - Phillimore, Benjamin

AU - Tracey, Alan

AU - Corby, Nicole

AU - Dunn, Matthew

AU - Johnson, Christopher

AU - Wood, Jonathan

AU - Clark, Susan

AU - Pelan, Sarah

AU - Griffiths, Guy

AU - Smith, Michelle

AU - Glithero, Rebecca

AU - Howden, Philip

AU - Barker, Nicholas

AU - Stevens, Christopher

AU - Harley, Joanna

AU - Holt, Karen

AU - Panagiotidis, Georgios

AU - Lovell, Jamieson

AU - Beasley, Helen

AU - Henderson, Carl

AU - Gordon, Daria

AU - Auger, Katherine

AU - Wright, Deborah

AU - Collins, Joanna

AU - Raisen, Claire

AU - Dyer, Lauren

AU - Leung, Kenric

AU - Robertson, Lauren

AU - Ambridge, Kirsty

AU - Leongamornlert, Daniel

AU - McGuire, Sarah

AU - Gilderthorp, Ruth

AU - Griffiths, Coline

AU - Manthravadi, Deepa

AU - Nichol, Sarah

AU - Barker, Gary

AU - Whitehead, Siobhan

AU - Kay, Michael

AU - Brown, Jacqueline

AU - Murnane, Clare

AU - Gray, Emma

AU - Humphries, Matthew

AU - Sycamore, Neil

AU - Barker, Darren

AU - Saunders, David

AU - Wallis, Justene

AU - Babbage, Anne

AU - Hammond, Sian

AU - Mashreghi-Mohammadi, Maryam

AU - Barr, Lucy

AU - Martin, Sancha

AU - Wray, Paul

AU - Ellington, Andrew

AU - Matthews, Nicholas

AU - Ellwood, Matthew

AU - Woodmansey, Rebecca

AU - Clark, Graham

AU - Cooper, James

AU - Tromans, Anthony

AU - Grafham, Darren

AU - Skuce, Carl

AU - Pandian, Richard

AU - Andrews, Robert

AU - Harrison, Elliot

AU - Kimberley, Andrew

AU - Garnett, Jane

AU - Fosker, Nigel

AU - Hall, Rebekah

AU - Garner, Patrick

AU - Kelly, Daniel

AU - Bird, Christine

AU - Palmer, Sophie

AU - Gehring, Ines

AU - Berger, Andrea

AU - Dooley, Christopher M.

AU - Ersan-Ürün, Zübeyde

AU - Eser, Cigdem

AU - Geiger, Horst

AU - Geisler, Maria

AU - Karotki, Lena

AU - Kirn, Anette

AU - Konantz, Judith

AU - Konantz, Martina

AU - Oberländer, Martina

AU - Rudolph-Geiger, Silke

AU - Teucke, Mathias

AU - Osoegawa, Kazutoyo

AU - Zhu, Baoli

AU - Rapp, Amanda

AU - Widaa, Sara

AU - Langford, Cordelia

AU - Yang, Fengtang

AU - Carter, Nigel P.

AU - Harrow, Jennifer

AU - Ning, Zemin

AU - Herrero, Javier

AU - Searle, Steve M.J.

AU - Enright, Anton

AU - Geisler, Robert

AU - Plasterk, Ronald H.A.

AU - Lee, Charles

AU - Westerfield, Monte

AU - De Jong, Pieter J.

AU - Zon, Leonard I.

AU - Postlethwait, John H.

AU - Nüsslein-Volhard, Christiane

AU - Hubbard, Tim J.P.

AU - Crollius, Hugues Roest

AU - Rogers, Jane

AU - Stemple, Derek L.

PY - 2013/4/25

Y1 - 2013/4/25

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/84876798186

U2 - 10.1038/nature12111

DO - 10.1038/nature12111

M3 - Journal articles

C2 - 23594743

AN - SCOPUS:84876798186

SN - 0028-0836

VL - 496

SP - 498

EP - 503

JO - Nature

JF - Nature

IS - 7446

ER -

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

Abstract

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