Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

by: RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, G Okwuonu, S Hines, L Lewis, C Deramo, O Delgado, Dugan S Rocha, G Miner, M Morgan, A Hawes, R Gill, Celera, RA Holt, MD Adams, PG Amanatides, Baden H Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, HM Lee, E Gustafson, P Cahill, A Kana, Doucette L Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ De Jong, K Osoegawa, B Zhu, M Marra, J Schein, I Bosdet, C Fjell, S Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, J Mcpherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, PH Havlak, R Chen, KJ Durbin, A Egan, Y Ren, XZ Song, B Li, Y Liu, X Qin, S Cawley, KC Worley, AJ Cooney, LM D'Souza, K Martin, JQ Wu, Gonzalez ML Garay, AR Jackson, KJ Kalafus, MP Mcleod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, Ureta A Vidal, C Woodwark, E Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, H Huang, H Wang, H Xing, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, Mar M Albà, JF Abril, R Guigo, A Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, YA Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, Gullings J Handley, Jensen MI Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, K Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SM Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, JC Venter, BA Payseur, G Bourque, López C Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, M Brent, M Arumugam, D Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, And F Collins

Nature, Vol. 428, No. 6982. (1 April 2004), pp. 493-521.

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DOI, Nature, Pubmed, Hubmed, DOI, http://dx.doi.org/10.1038/nature02426

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Abstract

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

@article{gibbs04, abstract = {The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90\% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.}, address = {Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu>.}, author = {Gibbs, R. A. and Weinstock, G. M. and Metzker, M. L. and Muzny, D. M. and Sodergren, E. J. and Scherer, S. and Scott, G. and Steffen, D. and Worley, K. C. and Burch, P. E. and Okwuonu, G. and Hines, S. and Lewis, L. and Deramo, C. and Delgado, O. and Rocha, Dugan S. and Miner, G. and Morgan, M. and Hawes, A. and Gill, R. and Celera and Holt, R. A. and Adams, M. D. and Amanatides, P. G. and Tillson, Baden H. and Barnstead, M. and Chin, S. and Evans, C. A. and Ferriera, S. and Fosler, C. and Glodek, A. and Gu, Z. and Jennings, D. and Kraft, C. L. and Nguyen, T. and Pfannkoch, C. M. and Sitter, C. and Sutton, G. G. and Venter, J. C. and Woodage, T. and Smith, D. and Lee, H. M. and Gustafson, E. and Cahill, P. and Kana, A. and Stamm, Doucette L. and Weinstock, K. and Fechtel, K. and Weiss, R. B. and Dunn, D. M. and Green, E. D. and Blakesley, R. W. and Bouffard, G. G. and De Jong, P. J. and Osoegawa, K. and Zhu, B. and Marra, M. and Schein, J. and Bosdet, I. and Fjell, C. and Jones, S. and Krzywinski, M. and Mathewson, C. and Siddiqui, A. and Wye, N. and Mcpherson, J. and Zhao, S. and Fraser, C. M. and Shetty, J. and Shatsman, S. and Geer, K. and Chen, Y. and Abramzon, S. and Nierman, W. C. and Havlak, P. H. and Chen, R. and Durbin, K. J. and Egan, A. and Ren, Y. and Song, X. Z. and Li, B. and Liu, Y. and Qin, X. and Cawley, S. and Worley, K. C. and Cooney, A. J. and D'Souza, L. M. and Martin, K. and Wu, J. Q. and Garay, Gonzalez M. L. and Jackson, A. R. and Kalafus, K. J. and Mcleod, M. P. and Milosavljevic, A. and Virk, D. and Volkov, A. and Wheeler, D. A. and Zhang, Z. and Bailey, J. A. and Eichler, E. E. and Tuzun, E. and Birney, E. and Mongin, E. and Vidal, Ureta A. and Woodwark, C. and Zdobnov, E. and Bork, P. and Suyama, M. and Torrents, D. and Alexandersson, M. and Trask, B. J. and Young, J. M. and Huang, H. and Wang, H. and Xing, H. and Daniels, S. and Gietzen, D. and Schmidt, J. and Stevens, K. and Vitt, U. and Wingrove, J. and Camara, F. and Alb\`{a}, Mar M. and Abril, J. F. and Guigo, R. and Smit, A. and Dubchak, I. and Rubin, E. M. and Couronne, O. and Poliakov, A. and H\"{u}bner, N. and Ganten, D. and Goesele, C. and Hummel, O. and Kreitler, T. and Lee, Y. A. and Monti, J. and Schulz, H. and Zimdahl, H. and Himmelbauer, H. and Lehrach, H. and Jacob, H. J. and Bromberg, S. and Handley, Gullings J. and Seaman, Jensen M. I. and Kwitek, A. E. and Lazar, J. and Pasko, D. and Tonellato, P. J. and Twigger, S. and Ponting, C. P. and Duarte, J. M. and Rice, S. and Goodstadt, L. and Beatson, S. A. and Emes, R. D. and Winter, E. E. and Webber, C. and Brandt, P. and Nyakatura, G. and Adetobi, M. and Chiaromonte, F. and Elnitski, L. and Eswara, P. and Hardison, R. C. and Hou, M. and Kolbe, D. and Makova, K. and Miller, W. and Nekrutenko, A. and Riemer, C. and Schwartz, S. and Taylor, J. and Yang, S. and Zhang, Y. and Lindpaintner, K. and Andrews, T. D. and Caccamo, M. and Clamp, M. and Clarke, L. and Curwen, V. and Durbin, R. and Eyras, E. and Searle, S. M. and Cooper, G. M. and Batzoglou, S. and Brudno, M. and Sidow, A. and Stone, E. A. and Venter, J. C. and Payseur, B. A. and Bourque, G. and Ot\'{i}n, L\'{o}pez C. and Puente, X. S. and Chakrabarti, K. and Chatterji, S. and Dewey, C. and Pachter, L. and Bray, N. and Yap, V. B. and Caspi, A. and Tesler, G. and Pevzner, P. A. and Haussler, D. and Roskin, K. M. and Baertsch, R. and Clawson, H. and Furey, T. S. and Hinrichs, A. S. and Karolchik, D. and Kent, W. J. and Rosenbloom, K. R. and Trumbower, H. and Weirauch, M. and Cooper, D. N. and Stenson, P. D. and Ma, B. and Brent, M. and Arumugam, M. and Shteynberg, D. and Copley, R. R. and Taylor, M. S. and Riethman, H. and Mudunuri, U. and Peterson, J. and Guyer, M. and Felsenfeld, A. and Old, S. and Mockrin, S. and Collins, And F. }, citeulike-article-id = {444860}, doi = {http://dx.doi.org/10.1038/nature02426}, issn = {1476-4687}, journal = {Nature}, keywords = {comparative\_genomics, genome, rat, sequence, whole\_genome}, month = {April}, number = {6982}, pages = {493--521}, posted-at = {2005-12-19 22:27:51}, priority = {4}, title = {Genome sequence of the Brown Norway rat yields insights into mammalian evolution.}, url = {http://dx.doi.org/10.1038/nature02426}, volume = {428}, year = {2004} }

RIS record

TY - JOUR ID - gibbs04 L3 - citeulike-article-id:444860 N2 - The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution. IS - 6982 JF - Nature SN - 1476-4687 AD - Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu>. EP - 521 TI - Genome sequence of the Brown Norway rat yields insights into mammalian evolution. VL - 428 SP - 493 KW - comparative_genomics KW - genome KW - rat KW - sequence KW - whole_genome AU - Gibbs, RA AU - Weinstock, GM AU - Metzker, ML AU - Muzny, DM AU - Sodergren, EJ AU - Scherer, S AU - Scott, G AU - Steffen, D AU - Worley, KC AU - Burch, PE AU - Okwuonu, G AU - Hines, S AU - Lewis, L AU - Deramo, C AU - Delgado, O AU - Rocha, Dugan AU - Miner, G AU - Morgan, M AU - Hawes, A AU - Gill, R AU - Celera AU - Holt, RA AU - Adams, MD AU - Amanatides, PG AU - Tillson, Baden AU - Barnstead, M AU - Chin, S AU - Evans, CA AU - Ferriera, S AU - Fosler, C AU - Glodek, A AU - Gu, Z AU - Jennings, D AU - Kraft, CL AU - Nguyen, T AU - Pfannkoch, CM AU - Sitter, C AU - Sutton, GG AU - Venter, JC AU - Woodage, T AU - Smith, D AU - Lee, HM AU - Gustafson, E AU - Cahill, P AU - Kana, A AU - Stamm, Doucette AU - Weinstock, K AU - Fechtel, K AU - Weiss, RB AU - Dunn, DM AU - Green, ED AU - Blakesley, RW AU - Bouffard, GG AU - De Jong, PJ AU - Osoegawa, K AU - Zhu, B AU - Marra, M AU - Schein, J AU - Bosdet, I AU - Fjell, C AU - Jones, S AU - Krzywinski, M AU - Mathewson, C AU - Siddiqui, A AU - Wye, N AU - Mcpherson, J AU - Zhao, S AU - Fraser, CM AU - Shetty, J AU - Shatsman, S AU - Geer, K AU - Chen, Y AU - Abramzon, S AU - Nierman, WC AU - Havlak, PH AU - Chen, R AU - Durbin, KJ AU - Egan, A AU - Ren, Y AU - Song, XZ AU - Li, B AU - Liu, Y AU - Qin, X AU - Cawley, S AU - Worley, KC AU - Cooney, AJ AU - D'Souza, LM AU - Martin, K AU - Wu, JQ AU - Garay, Gonzalez AU - Jackson, AR AU - Kalafus, KJ AU - Mcleod, MP AU - Milosavljevic, A AU - Virk, D AU - Volkov, A AU - Wheeler, DA AU - Zhang, Z AU - Bailey, JA AU - Eichler, EE AU - Tuzun, E AU - Birney, E AU - Mongin, E AU - Vidal, Ureta AU - Woodwark, C AU - Zdobnov, E AU - Bork, P AU - Suyama, M AU - Torrents, D AU - Alexandersson, M AU - Trask, BJ AU - Young, JM AU - Huang, H AU - Wang, H AU - Xing, H AU - Daniels, S AU - Gietzen, D AU - Schmidt, J AU - Stevens, K AU - Vitt, U AU - Wingrove, J AU - Camara, F AU - Albà, Mar AU - Abril, JF AU - Guigo, R AU - Smit, A AU - Dubchak, I AU - Rubin, EM AU - Couronne, O AU - Poliakov, A AU - Hübner, N AU - Ganten, D AU - Goesele, C AU - Hummel, O AU - Kreitler, T AU - Lee, YA AU - Monti, J AU - Schulz, H AU - Zimdahl, H AU - Himmelbauer, H AU - Lehrach, H AU - Jacob, HJ AU - Bromberg, S AU - Handley, Gullings AU - Seaman, Jensen AU - Kwitek, AE AU - Lazar, J AU - Pasko, D AU - Tonellato, PJ AU - Twigger, S AU - Ponting, CP AU - Duarte, JM AU - Rice, S AU - Goodstadt, L AU - Beatson, SA AU - Emes, RD AU - Winter, EE AU - Webber, C AU - Brandt, P AU - Nyakatura, G AU - Adetobi, M AU - Chiaromonte, F AU - Elnitski, L AU - Eswara, P AU - Hardison, RC AU - Hou, M AU - Kolbe, D AU - Makova, K AU - Miller, W AU - Nekrutenko, A AU - Riemer, C AU - Schwartz, S AU - Taylor, J AU - Yang, S AU - Zhang, Y AU - Lindpaintner, K AU - Andrews, TD AU - Caccamo, M AU - Clamp, M AU - Clarke, L AU - Curwen, V AU - Durbin, R AU - Eyras, E AU - Searle, SM AU - Cooper, GM AU - Batzoglou, S AU - Brudno, M AU - Sidow, A AU - Stone, EA AU - Venter, JC AU - Payseur, BA AU - Bourque, G AU - Otín, López AU - Puente, XS AU - Chakrabarti, K AU - Chatterji, S AU - Dewey, C AU - Pachter, L AU - Bray, N AU - Yap, VB AU - Caspi, A AU - Tesler, G AU - Pevzner, PA AU - Haussler, D AU - Roskin, KM AU - Baertsch, R AU - Clawson, H AU - Furey, TS AU - Hinrichs, AS AU - Karolchik, D AU - Kent, WJ AU - Rosenbloom, KR AU - Trumbower, H AU - Weirauch, M AU - Cooper, DN AU - Stenson, PD AU - Ma, B AU - Brent, M AU - Arumugam, M AU - Shteynberg, D AU - Copley, RR AU - Taylor, MS AU - Riethman, H AU - Mudunuri, U AU - Peterson, J AU - Guyer, M AU - Felsenfeld, A AU - Old, S AU - Mockrin, S AU - Collins, And PY - 2004/April/01/ UR - http://dx.doi.org/10.1038/nature02426 ER -

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