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1. The DNA sequence of human chromosome 7

Author

Robert Baertsch, Karen A. Phelps, Lisa Cook, Joelle Kalicki, Michelle O'Laughlin, Kerry L. Bubb, David Torrents, Kristine M. Wylie, Andrew Vanbrunt, Mark E. Schaller, Dan Layman, Kelsi Scott, LaDeana W. Hillier, Marco A. Marra, Caryn Wagner-McPherson, Cindy Strong, Phil Latreille, Hui Sun, Maynard V. Olson, Holland Bradshaw-Cordum, Amanda Abbott, Robert S. Fulton, Nicolas Berkowicz, Richard Harkins, Asif T. Chinwalla, Rajinder Kaul, William E. Nash, Chad Tomlinson, Susan M. Rock, Patricia Wohldmann, Paul Flicek, Elaine R. Mardis, Catrina Strowmatt, James M. Eldred, Betty Lamar, Christopher K. Raymond, Michael C. Wendl, Lauren Bielicki, Shawn Leonard, John Douglas Mcpherson, Christine Nguyen, Jennifer Murray, Michael C. Becker, Lucinda Fulton, Amber Isak, Will Gillett, Matt Cordes, James B. Clendenning, Kymberlie H. Pepin, Mandeep Sekhon, Eric Haugen, Feiyu Du, Theresa Rohlfing, Kimberly D. Delehaunty, Nancy Miller, Amy Kozlowicz-Reilly, Eric D. Green, W. James Kent, Tamberlyn Bieri, Peer Bork, Richard K. Wilson, Patrick Minx, John Spieth, Evan E. Eichler, Shawn Iadanoto, Terrence S. Furey, Matthew E. Portnoy, Shunfang Hou, R. James, Warren Gish, Brian Schultz, Doug Johnson, Philip Ozersky, Jennifer Edwards, Stephanie L. Chissoe, Jeffrey A. Bailey, Tracie L. Miner, Jason Maas, Andrea Holmes, Sandra W. Clifton, Sara Jaeger, Tina Graves, Ruth Levy, Joseph A. Bedell, Ginger A. Fewell, Mikita Suyama, Shiaw-Pyng Yang, Sean R. Eddy, Rebecca S. Walker, Aye-Mon Tin-Wollam, Hui Du, Evan Keibler, Matthew T. Hickenbotham, Sara Dauphin-Kohlberg, Robert H. Waterston, Yang Zhou, Stephanie Andrews, Johar Ali, John W. Wallis, Michael R. Brent, Rachel Maupin, Donald Williams, Elizabeth Simms, Laura Courtney, Anthony R. Harris, Jeffrey Woessner, and Joanne O. Nelson

Subjects
Williams Syndrome, Chromosome 7 (human), Genetics, RNA, Untranslated, Multidisciplinary, Base Sequence, Sequence analysis, Pseudogene, Molecular Sequence Data, Proteins, Sequence Analysis, DNA, Genome project, Biology, Physical Chromosome Mapping, Conserved sequence, Sequence-tagged site, Mice, Sequence logo, Species Specificity, Gene Duplication, Consensus sequence, Animals, Humans, Chromosomes, Human, Pair 7, Pseudogenes
Abstract

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

Published
2003
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2. Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Author

Rui Chen, George M. Weinstock, Cynthia Pfannkoch, Chris P. Ponting, Mark S. Guyer, Manuel L. Gonzalez-Garay, James Taylor, Yixin Chen, Eric D. Green, Simon Cawley, Jo Gullings-Handley, Granger G. Sutton, Jose M. Duarte, Stephen M. J. Searle, Laura Elnitski, Aleksandar Milosavljevic, Alicia Hawes, Stephen C. Mockrin, Oliver Delgado, Shannon Dugan-Rocha, Christine Deramo, Dean Pasko, Marina Alexandersson, Eitan E. Winter, Robert W. Blakesley, Donna Karolchik, Huajun Wang, David Shteynberg, Diane M. Dunn, Carlos López-Otín, Abel Ureta-Vidal, Jia Qian Wu, A. Glodek, Shan Yang, Natasja Wye, Sue Daniels, Keita Geer, Arian F.A. Smit, Jozef Lazar, Pallavi Eswara, Carl Fosler, Douglas Smith, Martin Krzywinski, Uma Mudunuri, George Miner, Herbert Schulz, Angie S. Hinrichs, Manimozhiyan Arumugam, Josep F. Abril, Ursula Vitt, Andrei Volkov, Peter J. Tonellato, Von Bing Yap, Bingshan Li, Jyoti Shetty, Ian Bosdet, Evgeny M. Zdobnov, San Diego Glenn Tesler, Chris Fjell, Yi Zhang, Francis S. Collins, Serafim Batzoglou, Robert Baertsch, Laura Clarke, David Neil Cooper, Carrie Mathewson, Diana L. Kolbe, Kate R. Rosenbloom, Valerie Curwen, Bret A. Payseur, Gerard G. Bouffard, Michael R. Brent, Barbara J. Trask, Scott A. Beatson, Sourav Chatterji, Francisco Camara, Detlev Ganten, Andrew R. Jackson, Claire M. Fraser, Klaus Lindpaintner, Yue Liu, Mark Raymond Adams, Robert A. Holt, Erik Gustafson, Hiram Clawson, Michael L. Metzker, John Douglas Mcpherson, Gregory M. Cooper, Martin S. Taylor, Scott Schwartz, Hui Huang, Darryl Gietzen, Patrick Cahill, Geoffrey Okwuonu, Sandra Hines, J. Craig Venter, Jan Monti, David Steffen, Marco A. Marra, Arnold Kana, Richard D. Emes, Asim Sarosh Siddiqui, Erica Sodergren, Mario Caccamo, Jim Wingrove, Richard R. Copley, Leo Goodstadt, Francesca Chiaromonte, Davinder Virk, Kirt Martin, Colin N. Dewey, Xiang Qin, T. Dan Andrews, K. James Durbin, Michael P. McLeod, Susan Bromberg, Pavel A. Pevzner, Petra Brandt, Austin J. Cooney, Don Jennings, Baoli Zhu, Lynn Doucette-Stamm, Heather Trumbower, Eray Tüzün, Kristian Stevens, Norbert Hubner, Young-Ae Lee, Zhiping Gu, Harold Riethman, Xose S. Puente, Cynthia Sitter, Michael Brudno, Gerald Nyakatura, Oliver Hummel, Caleb Webber, Olivier Couronne, Kim Fechtel, W. J. Kent, Zhengdong D. Zhang, Xing Zhi Song, Matt Weirauch, Ewan Birney, Richard A. Gibbs, William C. Nierman, Anne E. Kwitek, Alexander Poliakov, Mary Barnstead, Jeanette Schmidt, Yanru Ren, Howard J. Jacob, Kateryna D. Makova, Edward M. Rubin, Susan Old, Trixie Nguyen, Arend Sidow, Nicolas Bray, Hong Mei Lee, Lisa M. D'Souza, Heinz Himmelbauer, Cara Woodwark, Peter G. Amanatides, Paul Havlak, Janet M. Young, Eduardo Eyras, Thomas Kreitler, Heming Xing, Sofiya Shatsman, Kushal Chakrabarti, Stephen Rice, Cheryl A. Evans, Kim C. Worley, Peter D. Stenson, Rachel Gill, Pieter J. de Jong, Jacqueline E. Schein, Lior Pachter, Steve Ferriera, Santa Cruz David Haussler, Ross C. Hardison, Holly Baden-Tillson, Margaret Adetobi, Krishna M. Roskin, Guillaume Bourque, Eric A. Stone, Emmanuel Mongin, Michele Clamp, Margaret Morgan, Richard Durbin, Cathy Riemer, Anton Nekrutenko, Mikita Suyama, Soo H. Chin, Kenneth J. Kalafus, Anat Caspi, Donna M. Muzny, Inna Dubchak, Shaying Zhao, Sofyia Abramzon, Michael I. Jensen-Seaman, Steven E. Scherer, Lora Lewis, M. Mar Albà, Terrence S. Furey, Peer Bork, Trevor Woodage, David A. Wheeler, Hans Lehrach, Graham R. Scott, Bin Ma, Paula E. Burch, Robert B. Weiss, Kazutoyo Osoegawa, Evan E. Eichler, Amy Egan, Webb Miller, Cheryl L. Kraft, Steven J.M. Jones, Jeffrey A. Bailey, Roderic Guigó, David Torrents, Heike Zimdahl, Adam Felsenfeld, Jane Peterson, Simon N. Twigger, Claudia Goesele, Keith Weinstock, Minmei Hou, and Zdobnov, Evgeny

Subjects
Male, Models, Molecular, Mammalian Genetics, RNA, Untranslated, Retroelements, Sequence analysis, Gene prediction, Centromere, Genomics, Biology, Regulatory Sequences, Nucleic Acid, Genome, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Rat Genome Database, Evolution, Molecular, Mice, Gene Duplication, Rats, Inbred BN, Animals, Humans, ddc:576.5, Gene, Whole genome sequencing, Genetics, Base Composition, Multidisciplinary, Sequence Analysis, DNA, Telomere, Chromosomes, Mammalian, Introns, Rats, Evolutionary biology, Mutagenesis, DNA Transposable Elements, CpG Islands, RNA Splice Sites
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.

Published
2003

3. Initial sequencing and comparative analysis of the mouse genome

Author

Laura Elnitski, David B. Jaffe, Jia Li, Marina Alexandersson, Michael J. Morgan, Shiaw Pyng Yang, Robert Baertsch, Claire M. Wade, John Tromp, Michael C. Zody, Terrence S. Furey, Emma Overton-Larty, Stephen D. Brown, Scott Schwartz, Diane M. Dunn, J. P. Leger, Kris A. Wetterstrand, David Torrents, Ratna Shownkeen, Brian Schultz, Kim C. Worley, Richard D. Emes, John Mayer, Tom Landers, Beverley Meredith, Carol Scott, R. J. Weber, Sean R. Eddy, David Kulp, Jun Kawai, J Bailey, Fan Hsu, Diana L. Kolbe, Kirsten McLay, Marc Botcherby, Richard Mott, Tracie L. Miner, Jill P. Mesirov, Cristyn Kells, Michael A. Quail, Melanie M. Wall, Alistair G. Rust, Josep F. Abril, Ian F Korf, Peter An, Roderic Guigó, Abel Ureta-Vidal, Evan Mauceli, L. Steven Johnson, Arian F.A. Smit, Arkadiusz Kasprzyk, Michael C. Wendl, Deanna M. Church, Francis S. Collins, Wayne N. Frankel, Pallavi Eswara, Bin Ma, Robert H. Waterston, Stylianos E. Antonarakis, Edward M. Rubin, John Douglas Mcpherson, Andrew Sheridan, Megan McCarthy, Ming Li, Colin N. Dewey, Justin Deri, Rosie Levine, Matthew Jones, Sheila Dodge, Richard R. Copley, Leo Goodstadt, Shan Yang, Donna Maglott, Jamey Wierzbowski, Nick Goldman, Evgeny M. Zdobnov, Simon G. Gregory, C M Clee, Steven Leonard, Elaine R. Mardis, Simon C. Potter, Sarah Sims, Richard A. Gibbs, Mark S. Guyer, Francesca Chiaromonte, Susan Lucas, Mark Diekhans, Steve Searle, Rachel Ainscough, Jane Peterson, Emmanouil T. Dermitzakis, Robert Nicol, Lucy Matthews, Guy Slater, Adam Felsenfeld, Karen Foley, Lucinda Fulton, Tim Hubbard, Richard K. Wilson, Deana W. LaHillier, W. Richard McCombie, Johanna Thompson, Robert David, John Attwood, Anthony P. West, Jane Rogers, Evan Keibler, Lisa Cook, Raju Kucherlapati, Steven Seaman, William E. Nash, Ian J. Jackson, Jonathan Singer, Axin Hua, Tina Graves, Ted Sharpe, Dudley Wyman, Bruce W. Birren, Stuart McLaren, David Willey, A Joy, Douglas Smith, Alexandre Reymond, Paul Flicek, Simon Cawley, Richa Agarwala, Diane Gage, Evanne Trevaskis, Ginger A. Fewell, Michael R. Brent, Tracy C. Ponce, W. James Kent, Timothy Holzer, Eduardo Eyras, Michael J. O’Connor, Webb Miller, Donna M. Muzny, Andrew von Niederhausern, Inna Dubchak, Eitan E. Winter, Catherine Ucla, Arne Stabenau, Michael N. Nhan, Piero Carninci, Michele Clamp, Pavel A. Pevzner, James Meldrim, Tim Cutts, R. D. Campbell, Joy Davies, Wratko Hlavina, Elinor K. Karlsson, David Haussler, John Burton, Peer Bork, Nicole Stange-Thomann, Mikita Suyama, Mark J. Daly, Ewan Birney, Edward J. Kulbokas, Craig Pohl, James C. Mullikin, Chad Nusbaum, Genís Parra, Jade P. Vinson, Yoshihide Hayashizaki, Sante Gnerre, Eric Berry, Daniel G. Brown, Asif T. Chinwalla, Emmanuel Mongin, Robert B. Weiss, Raymond Wheeler, Andrew Kirby, Yasushi Okazaki, Lior Pachter, Ross C. Hardison, Brian Spencer, Carol J. Bult, Joanne O. Nelson, Pankaj K. Agarwal, Darren Grafham, Gustavo Glusman, Thomas A. Jones, Glenn Tesler, Simon Whelan, James Cuff, Robert S. Fulton, K F Barlow, Jörg Schultz, Matthias S. Schwartz, Alex Poliakov, Jonathan Butler, Bruce A. Roe, Angela S. Hinrichs, Alan Coulson, Kate Montgomery, Eric D. Green, Stephan Beck, Val Curwen, Krishna M. Roskin, Robert W. Plumb, Chris P. Ponting, Ralph Santos, Victor Sapojnikov, Nicolas Bray, Kymberlie H. Pepin, Charles W. Sugnet, Olivier Couronne, Ivica Letunic, Sophie Williams, Kimberly D. Delehaunty, Kerstin Lindblad-Toh, Zemin Ning, Karen Oliver, Toby Bloom, Michael Kamal, Nicholas J. Dickens, Eric S. Lander, Christine Lloyd, Donna Karolchik, Adrienne Hunt, Antonarakis, Stylianos, Couronne, Olivier, Dermitzakis, Emmanouil, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, Proteome, Untranslated/genetics, Genome, Transgenic, Repetitive Sequences, Mice, Models, Neoplasms, Conserved Sequence, ddc:616, Genetics, Mice, Knockout, Base Composition, Multidisciplinary, Sex Chromosomes, Pseudogenes/genetics, Genomics, Multigene Family/genetics, Physical Chromosome Mapping, Neoplasms/genetics, CpG Islands/genetics, Proteome/genetics, Genetic Variation/genetics, Multigene Family, Mice/classification/ genetics, Models, Animal, Conserved Sequence/genetics, Sequence Analysis, Pseudogenes, Human, Genome evolution, Evolution, Sequence analysis, Knockout, Quantitative Trait Loci, Mice, Transgenic, Sex Chromosomes/genetics, Computational biology, Biology, Synteny, Chromosomes, Evolution, Molecular, Nucleic Acid/genetics, Genetic, Species Specificity, Mammalian/ genetics, Animals, Humans, Genes/genetics, Selection, Genetic, Selection, Repetitive Sequences, Nucleic Acid, Comparative genomics, Animal, Genome, Human, Molecular, Genetic Variation, DNA, Sequence Analysis, DNA, Chromosomes, Mammalian, Gene Expression Regulation, Genes, Mutagenesis, RNA, Human genome, CpG Islands, Quantitative Trait Loci/genetics, Reference genome
Abstract

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Published
2002

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