Article
Nature 432, 988-994 (23 December 2004) | doi:10.1038/nature03187; Received 9 September 2004; Accepted 15 November 2004
The sequence and analysis of duplication-rich human chromosome 16
Joel Martin1, Cliff Han2, Laurie A. Gordon1, Astrid Terry1, Shyam Prabhakar4, Xinwei She5, Gary Xie1,2, Uffe Hellsten1, Yee Man Chan6, Michael Altherr1,2, Olivier Couronne4, Andrea Aerts1, Eva Bajorek6, Stacey Black6, Heather Blumer2, Elbert Branscomb1,3, Nancy C. Brown2, William J. Bruno2, Judith M. Buckingham2, David F. Callen2, Connie S. Campbell2, Mary L. Campbell2, Evelyn W. Campbell2, Chenier Caoile6, Jean F. Challacombe2, Leslie A. Chasteen2, Olga Chertkov2, Han C. Chi2, Mari Christensen3, Lynn M. Clark2, Judith D. Cohn2, Mirian Denys6, John C. Detter1, Mark Dickson6, Mira Dimitrijevic-Bussod2, Julio Escobar6, Joseph J. Fawcett2, Dave Flowers6, Dea Fotopulos6, Tijana Glavina1, Maria Gomez6, Eidelyn Gonzales6, David Goodstein1, Lynne A. Goodwin2, Deborah L. Grady2, Igor Grigoriev1, Matthew Groza3, Nancy Hammon1, Trevor Hawkins1, Lauren Haydu6, Carl E. Hildebrand2, Wayne Huang1, Sanjay Israni1, Jamie Jett1, Phillip B. Jewett2, Kristen Kadner1, Heather Kimball1, Arthur Kobayashi1,3, Marie-Claude Krawczyk2, Tina Leyba2, Jonathan L. Longmire2, Frederick Lopez6, Yunian Lou1, Steve Lowry1, Thom Ludeman2, Chitra F. Manohar3, Graham A. Mark2, Kimberly L. McMurray2, Linda J. Meincke2, Jenna Morgan1, Robert K. Moyzis2, Mark O. Mundt2, A. Christine Munk2, Richard D. Nandkeshwar3, Sam Pitluck1, Martin Pollard1, Paul Predki1, Beverly Parson-Quintana2, Lucia Ramirez6, Sam Rash1, James Retterer6, Darryl O. Ricke2, Donna L. Robinson2, Alex Rodriguez6, Asaf Salamov1, Elizabeth H. Saunders2, Duncan Scott1, Timothy Shough2, Raymond L. Stallings2, Malinda Stalvey2, Robert D. Sutherland2, Roxanne Tapia2, Judith G. Tesmer2, Nina Thayer1,2, Linda S. Thompson2, Hope Tice1, David C. Torney2, Mary Tran-Gyamfi1, Ming Tsai6, Levy E. Ulanovsky2, Anna Ustaszewska1, Nu Vo6, P. Scott White2, Albert L. Williams2, Patricia L. Wills2, Jung-Rung Wu2, Kevin Wu6, Joan Yang6, Pieter DeJong7, David Bruce2, Norman A. Doggett2, Larry Deaven2, Jeremy Schmutz6, Jane Grimwood6, Paul Richardson1, Daniel S. Rokhsar1, Evan E. Eichler5, Paul Gilna2, Susan M. Lucas1, Richard M. Myers6, Edward M. Rubin1,4 & Len A. Pennacchio1,4
- DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA
- Children's Hospital Oakland, Oakland, California 94609, USA
Correspondence to: Edward M. Rubin1,4Len A. Pennacchio1,4
Email: emrubin@lbl.gov
Email: LAPennacchio@lbl.gov
The sequence described here has been deposited in public databases with accession number NC_000016.
Abstract
Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.
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