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

K. Howe; M.D. Clark; C.F. Torroja; J. Torrance; C. Berthelot; M. Muffato; J.E. Collins; S. Humphray; K. McLaren; L. Matthews; S. McLaren; I. Sealy; M. Caccamo; C. Churcher; C. Scott; J.C. Barrett; R. Koch; G.J. Rauch; S. White; W. Chow; B. Kilian; L.T. Quintais; J.A. Guerra-Assuncao; Y. Zhou; Y. Gu; J. Yen; J.H. Vogel; T. Eyre; S. Redmond; R. Banerjee; J. Chi; B. Fu; E. Langley; S.F. Maguire; G.K. Laird; D. Lloyd; E. Kenyon; S. Donaldson; H. Sehra; J. Almeida-King; J. Loveland; S. Trevanion; M. Jones; M. Quail; D. Willey; A. Hunt; J. Burton; S. Sims; K. McLay; B. Plumb; J. Davis; C. Clee; K. Oliver; R. Clark; C. Riddle; D. Elliot; G. Threadgold; G. Harden; D. Ware; B. Mortimore; G. Kerry; P. Heath; B. Phillimore; A. Tracey; N. Corby; M. Dunn; C. Johnson; J. Wood; S. Clark; S. Pelan; G. Griffiths; M. Smith; R. Glithero; P. Howden; N. Barker; C. Stevens; J. Harley; K. Holt; G. Panagiotidis; J. Lovell; H. Beasley; C. Henderson; D. Gordon; K. Auger; D. Wright; J. Collins; C. Raisen; L. Dyer; K. Leung; L. Robertson; K. Ambridge; D. Leongamornlert; S. McGuire; R. Gilderthorp; C. Griffiths; D. Manthravadi; S. Nichol; G. Barker; S. Whitehead; M. Kay; J. Brown; C. Murnane; E. Gray; M. Humphries; N. Sycamore; D. Barker; D. Saunders; J. Wallis; A. Babbage; S. Hammond; M. Mashreghi-Mohammadi; L. Barr; S. Martin; P. Wray; A. Ellington; N. Matthews; M. Ellwood; R. Woodmansey; G. Clark; J. Cooper; A. Tromans; D. Grafham; C. Skuce; R. Pandian; R. Andrews; E. Harrison; A. Kimberley; J. Garnett; N. Fosker; R. Hall; P. Garner; D. Kelly; C. Bird; S. Palmer; I. Gehring; A. Berger; C.M. Dooley; Z. Ersan-Urun; C. Eser; H. Geiger; M. Geisler; L. Karotki; A. Kirn; J. Konantz; M. Konantz; M. Oberlander; S. Rudolph-Geiger; M. Teucke; K. Osoegawa; B. Zhu; A. rapp; S. Widaa; C. Langford; F. Yang; N.P. Carter; J. Harrow; Z. Ning; J. Herrero; S.M. Searle; A. Enright; R. Geisler; R.H.A. Plasterk; C. Lee; M. Westerfield; P.J. de Jong; L.I. Zon; J.H. Postlethwait; C. Nusslein-Volhard; T.J. Hubbard; H. Roest Crollius; J. Rogers; D.L. Stemple; S. Begum; C. Lloyd; C. Lanz; G. Raddatz; S.C. Schuster

doi:10.1038/nature12111

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

K. Howe, M.D. Clark, C.F. Torroja, J. Torrance, C. Berthelot, M. Muffato, J.E. Collins, S. Humphray, K. McLaren, L. Matthews, S. McLaren, I. Sealy, M. Caccamo, C. Churcher, C. Scott, J.C. Barrett, R. Koch, G.J. Rauch, S. White, W. ChowB. Kilian, L.T. Quintais, J.A. Guerra-Assuncao, Y. Zhou, Y. Gu, J. Yen, J.H. Vogel, T. Eyre, S. Redmond, R. Banerjee, J. Chi, B. Fu, E. Langley, S.F. Maguire, G.K. Laird, D. Lloyd, E. Kenyon, S. Donaldson, H. Sehra, J. Almeida-King, J. Loveland, S. Trevanion, M. Jones, M. Quail, D. Willey, A. Hunt, J. Burton, S. Sims, K. McLay, B. Plumb, J. Davis, C. Clee, K. Oliver, R. Clark, C. Riddle, D. Elliot, G. Threadgold, G. Harden, D. Ware, B. Mortimore, G. Kerry, P. Heath, B. Phillimore, A. Tracey, N. Corby, M. Dunn, C. Johnson, J. Wood, S. Clark, S. Pelan, G. Griffiths, M. Smith, R. Glithero, P. Howden, N. Barker, C. Stevens, J. Harley, K. Holt, G. Panagiotidis, J. Lovell, H. Beasley, C. Henderson, D. Gordon, K. Auger, D. Wright, J. Collins, C. Raisen, L. Dyer, K. Leung, L. Robertson, K. Ambridge, D. Leongamornlert, S. McGuire, R. Gilderthorp, C. Griffiths, D. Manthravadi, S. Nichol, G. Barker, S. Whitehead, M. Kay, J. Brown, C. Murnane, E. Gray, M. Humphries, N. Sycamore, D. Barker, D. Saunders, J. Wallis, A. Babbage, S. Hammond, M. Mashreghi-Mohammadi, L. Barr, S. Martin, P. Wray, A. Ellington, N. Matthews, M. Ellwood, R. Woodmansey, G. Clark, J. Cooper, A. Tromans, D. Grafham, C. Skuce, R. Pandian, R. Andrews, E. Harrison, A. Kimberley, J. Garnett, N. Fosker, R. Hall, P. Garner, D. Kelly, C. Bird, S. Palmer, I. Gehring, A. Berger, C.M. Dooley, Z. Ersan-Urun, C. Eser, H. Geiger, M. Geisler, L. Karotki, A. Kirn, J. Konantz, M. Konantz, M. Oberlander, S. Rudolph-Geiger, M. Teucke, K. Osoegawa, B. Zhu, A. rapp, S. Widaa, C. Langford, F. Yang, N.P. Carter, J. Harrow, Z. Ning, J. Herrero, S.M. Searle, A. Enright, R. Geisler, R.H.A. Plasterk, C. Lee, M. Westerfield, P.J. de Jong, L.I. Zon, J.H. Postlethwait, C. Nusslein-Volhard, T.J. Hubbard, H. Roest Crollius, J. Rogers, D.L. Stemple, S. Begum, C. Lloyd, C. Lanz, G. Raddatz, S.C. Schuster

Hubrecht Institute

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

3605 Citaten (Scopus)

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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.

Originele taal-2	Engels
Pagina's (van-tot)	498-503
Tijdschrift	Nature
Volume	496
Nummer van het tijdschrift	7446
DOI's	https://doi.org/10.1038/nature12111
Status	Gepubliceerd - 2013

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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., ... Schuster, S. C. (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{5a12fd0c065a4a53b77016c9ada3ff36,

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 = "K. Howe and M.D. Clark and C.F. Torroja and J. Torrance and C. Berthelot and M. Muffato and J.E. Collins and S. Humphray and K. McLaren and L. Matthews and S. McLaren and I. Sealy and M. Caccamo and C. Churcher and C. Scott and J.C. Barrett and R. Koch and G.J. Rauch and S. White and W. Chow and B. Kilian and L.T. Quintais and J.A. Guerra-Assuncao and Y. Zhou and Y. Gu and J. Yen and J.H. Vogel and T. Eyre and S. Redmond and R. Banerjee and J. Chi and B. Fu and E. Langley and S.F. Maguire and G.K. Laird and D. Lloyd and E. Kenyon and S. Donaldson and H. Sehra and J. Almeida-King and J. Loveland and S. Trevanion and M. Jones and M. Quail and D. Willey and A. Hunt and J. Burton and S. Sims and K. McLay and B. Plumb and J. Davis and C. Clee and K. Oliver and R. Clark and C. Riddle and D. Elliot and G. Threadgold and G. Harden and D. Ware and B. Mortimore and G. Kerry and P. Heath and B. Phillimore and A. Tracey and N. Corby and M. Dunn and C. Johnson and J. Wood and S. Clark and S. Pelan and G. Griffiths and M. Smith and R. Glithero and P. Howden and N. Barker and C. Stevens and J. Harley and K. Holt and G. Panagiotidis and J. Lovell and H. Beasley and C. Henderson and D. Gordon and K. Auger and D. Wright and J. Collins and C. Raisen and L. Dyer and K. Leung and L. Robertson and K. Ambridge and D. Leongamornlert and S. McGuire and R. Gilderthorp and C. Griffiths and D. Manthravadi and S. Nichol and G. Barker and S. Whitehead and M. Kay and J. Brown and C. Murnane and E. Gray and M. Humphries and N. Sycamore and D. Barker and D. Saunders and J. Wallis and A. Babbage and S. Hammond and M. Mashreghi-Mohammadi and L. Barr and S. Martin and P. Wray and A. Ellington and N. Matthews and M. Ellwood and R. Woodmansey and G. Clark and J. Cooper and A. Tromans and D. Grafham and C. Skuce and R. Pandian and R. Andrews and E. Harrison and A. Kimberley and J. Garnett and N. Fosker and R. Hall and P. Garner and D. Kelly and C. Bird and S. Palmer and I. Gehring and A. Berger and C.M. Dooley and Z. Ersan-Urun and C. Eser and H. Geiger and M. Geisler and L. Karotki and A. Kirn and J. Konantz and M. Konantz and M. Oberlander and S. Rudolph-Geiger and M. Teucke and K. Osoegawa and B. Zhu and A. rapp and S. Widaa and C. Langford and F. Yang and N.P. Carter and J. Harrow and Z. Ning and J. Herrero and S.M. Searle and A. Enright and R. Geisler and R.H.A. Plasterk and C. Lee and M. Westerfield and {de Jong}, P.J. and L.I. Zon and J.H. Postlethwait and C. Nusslein-Volhard and T.J. Hubbard and {Roest Crollius}, H. and J. Rogers and D.L. Stemple and S. Begum and C. Lloyd and C. Lanz and G. Raddatz and S.C. Schuster",

note = "Reporting year: 2013",

year = "2013",

doi = "10.1038/nature12111",

language = "English",

volume = "496",

pages = "498--503",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

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-Assuncao, 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, Elliot, D, Threadgold, G, Harden, G, Ware, D, Mortimore, 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-Urun, Z, Eser, C, Geiger, H, Geisler, M, Karotki, L, Kirn, A, Konantz, J, Konantz, M, Oberlander, 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, SM, Enright, A, Geisler, R, Plasterk, RHA, Lee, C, Westerfield, M, de Jong, PJ, Zon, LI, Postlethwait, JH, Nusslein-Volhard, C, Hubbard, TJ, Roest Crollius, H, Rogers, J, Stemple, DL, Begum, S, Lloyd, C, Lanz, C, Raddatz, G & Schuster, SC 2013, 'The zebrafish reference genome sequence and its relationship to the human genome.', Nature, vol. 496, nr. 7446, blz. 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, K.

AU - Clark, M.D.

AU - Torroja, C.F.

AU - Torrance, J.

AU - Berthelot, C.

AU - Muffato, M.

AU - Collins, J.E.

AU - Humphray, S.

AU - McLaren, K.

AU - Matthews, L.

AU - McLaren, S.

AU - Sealy, I.

AU - Caccamo, M.

AU - Churcher, C.

AU - Scott, C.

AU - Barrett, J.C.

AU - Koch, R.

AU - Rauch, G.J.

AU - White, S.

AU - Chow, W.

AU - Kilian, B.

AU - Quintais, L.T.

AU - Guerra-Assuncao, J.A.

AU - Zhou, Y.

AU - Gu, Y.

AU - Yen, J.

AU - Vogel, J.H.

AU - Eyre, T.

AU - Redmond, S.

AU - Banerjee, R.

AU - Chi, J.

AU - Fu, B.

AU - Langley, E.

AU - Maguire, S.F.

AU - Laird, G.K.

AU - Lloyd, D.

AU - Kenyon, E.

AU - Donaldson, S.

AU - Sehra, H.

AU - Almeida-King, J.

AU - Loveland, J.

AU - Trevanion, S.

AU - Jones, M.

AU - Quail, M.

AU - Willey, D.

AU - Hunt, A.

AU - Burton, J.

AU - Sims, S.

AU - McLay, K.

AU - Plumb, B.

AU - Davis, J.

AU - Clee, C.

AU - Oliver, K.

AU - Clark, R.

AU - Riddle, C.

AU - Elliot, D.

AU - Threadgold, G.

AU - Harden, G.

AU - Ware, D.

AU - Mortimore, B.

AU - Kerry, G.

AU - Heath, P.

AU - Phillimore, B.

AU - Tracey, A.

AU - Corby, N.

AU - Dunn, M.

AU - Johnson, C.

AU - Wood, J.

AU - Clark, S.

AU - Pelan, S.

AU - Griffiths, G.

AU - Smith, M.

AU - Glithero, R.

AU - Howden, P.

AU - Barker, N.

AU - Stevens, C.

AU - Harley, J.

AU - Holt, K.

AU - Panagiotidis, G.

AU - Lovell, J.

AU - Beasley, H.

AU - Henderson, C.

AU - Gordon, D.

AU - Auger, K.

AU - Wright, D.

AU - Collins, J.

AU - Raisen, C.

AU - Dyer, L.

AU - Leung, K.

AU - Robertson, L.

AU - Ambridge, K.

AU - Leongamornlert, D.

AU - McGuire, S.

AU - Gilderthorp, R.

AU - Griffiths, C.

AU - Manthravadi, D.

AU - Nichol, S.

AU - Barker, G.

AU - Whitehead, S.

AU - Kay, M.

AU - Brown, J.

AU - Murnane, C.

AU - Gray, E.

AU - Humphries, M.

AU - Sycamore, N.

AU - Barker, D.

AU - Saunders, D.

AU - Wallis, J.

AU - Babbage, A.

AU - Hammond, S.

AU - Mashreghi-Mohammadi, M.

AU - Barr, L.

AU - Martin, S.

AU - Wray, P.

AU - Ellington, A.

AU - Matthews, N.

AU - Ellwood, M.

AU - Woodmansey, R.

AU - Clark, G.

AU - Cooper, J.

AU - Tromans, A.

AU - Grafham, D.

AU - Skuce, C.

AU - Pandian, R.

AU - Andrews, R.

AU - Harrison, E.

AU - Kimberley, A.

AU - Garnett, J.

AU - Fosker, N.

AU - Hall, R.

AU - Garner, P.

AU - Kelly, D.

AU - Bird, C.

AU - Palmer, S.

AU - Gehring, I.

AU - Berger, A.

AU - Dooley, C.M.

AU - Ersan-Urun, Z.

AU - Eser, C.

AU - Geiger, H.

AU - Geisler, M.

AU - Karotki, L.

AU - Kirn, A.

AU - Konantz, J.

AU - Konantz, M.

AU - Oberlander, M.

AU - Rudolph-Geiger, S.

AU - Teucke, M.

AU - Osoegawa, K.

AU - Zhu, B.

AU - rapp, A.

AU - Widaa, S.

AU - Langford, C.

AU - Yang, F.

AU - Carter, N.P.

AU - Harrow, J.

AU - Ning, Z.

AU - Herrero, J.

AU - Searle, S.M.

AU - Enright, A.

AU - Geisler, R.

AU - Plasterk, R.H.A.

AU - Lee, C.

AU - Westerfield, M.

AU - de Jong, P.J.

AU - Zon, L.I.

AU - Postlethwait, J.H.

AU - Nusslein-Volhard, C.

AU - Hubbard, T.J.

AU - Roest Crollius, H.

AU - Rogers, J.

AU - Stemple, D.L.

AU - Begum, S.

AU - Lloyd, C.

AU - Lanz, C.

AU - Raddatz, G.

AU - Schuster, S.C.

N1 - Reporting year: 2013

PY - 2013

Y1 - 2013

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.

U2 - 10.1038/nature12111

DO - 10.1038/nature12111

M3 - Article

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.

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