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1. The sequence and analysis of duplication-rich human chromosome 16

Author

Kimberly L. Mcmurray, James Retterer, Nancy C. Brown, Dea Fotopulos, Michael R. Altherr, Judith G. Tesmer, Jane Grimwood, Joel Martin, Jonathan L. Longmire, Elizabeth Saunders, P. Scott White, Malinda Stalvey, Elbert Branscomb, Norman A. Doggett, Nina Thayer, C.E. Hildebrand, Mary Bao Tran-Gyamfi, Yunian Lou, Trevor Hawkins, Lucía Ramírez, Shyam Prabhakar, Ming Tsai, D. Scott, Hope Tice, Linda Meincke, Jean F. Challacombe, Gary Xie, Maria Gomez, Eidelyn Gonzales, Jeremy Schmutz, Kevin Wu, Marie-Claude Krawczyk, Heather Kimball, Graham A. Mark, David C. Torney, John C. Detter, Laurie Gordon, Albert L. Williams, Susan Lucas, Len A. Pennacchio, Linda S. Thompson, Robert K. Moyzis, Kristen Kadner, Arthur Kobayashi, Larry L. Deaven, Richard D. Nandkeshwar, E.W. Campbell, Patricia L. Wills, Andrea Aerts, Joan Yang, Darryl O. Ricke, Mark Dickson, Astrid Terry, Steve Lowry, Paul Gilna, Paul G. Richardson, Thom Ludeman, Olivier Couronne, Timothy Shough, Chitra Manohar, David Bruce, Jamie Jett, Evan E. Eichler, Pieter J. deJong, Mark Mundt, Judith M. Buckingham, Robert D. Sutherland, Roxanne Tapia, Heather Blumer, Wayne Huang, Leslie Chasteen, A. Christine Munk, Sanjay Israni, Deborah L. Grady, Igor V. Grigoriev, Stacey Black, Judith D. Cohn, David F. Callen, Han C. Chi, William J. Bruno, Cliff Han, Mirian Denys, Mira Dimitrijevic-Bussod, Martin Pollard, Connie S. Campbell, Richard M. Myers, Yee Man Chan, Sam Pitluck, Sam Rash, Joseph J. Fawcett, Mari Christensen, Lauren Haydu, Frederick Lopez, Lynn M. Clark, Julio Escobar, B. Parson-Quintana, Raymond L. Stallings, Tina Leyba, Dave Flowers, Eva Bajorek, Jenna Morgan, Mary L. Campbell, Anna Ustaszewska, Donna L. Robinson, Nu Vo, Edward M. Rubin, Lynne Goodwin, Paul Predki, Uffe Hellsten, Daniel S. Rokhsar, Phillip B. Jewett, Matthew Groza, Tijana Glavina, Chenier Caoile, Alex Rodriguez, Xinwei She, David Goodstein, Jung-Rung Wu, Levy E. Ulanovsky, Asaf Salamov, Nancy Hammon, and Olga Chertkov

Subjects
Genetics, Multidisciplinary, Autosome, Polymorphism, Genetic, Sequence analysis, Pseudogene, Molecular Sequence Data, Genomics, Sequence Analysis, DNA, Biology, Physical Chromosome Mapping, Synteny, Chromosome 16, Genes, Gene Duplication, Heterochromatin, Gene duplication, Gene family, Animals, Humans, Gene, Chromosomes, Human, Pair 16, Segmental duplication
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.

Published
2004

2. The DNA sequence and biology of human chromosome 19

Author

Mary Bao Tran-Gyamfi, Ivan Ovcharenko, Trevor Hawkins, Maria Gomez, Mirian Denys, Victor V. Solovyev, Terrence S. Furey, Jamie Jett, Jeremy Schmutz, Dea Fotopulos, David Gordon, Tom Slezak, Kevin Wu, Heather Kimball, Pieter J. deJong, Catherine Medina, Vladimer Larionov, Paula McCready, Stephanine Rogers, James Retterer, John C. Detter, Diego Martinez, Richard M. Myers, Paul Predki, Stacey Black, Eva Bajorek, Chenier Caoile, Alex Rodriguez, Isaac Ho, Arthur Kobayashi, Jane Lamerdin, Xinwei She, Yunian Lou, Jane Grimwood, Kristen Kadner, Alex Copeland, Wayne Huang, Sanjay Israni, Carmen Rosa Albacete García, Gary Xie, Doug Smith, Anthony V. Carrano, Matthew Groza, Catherine A. Cleland, Matt Nolan, Paul G. Richardson, Eidelyn Gonzales, Nina Thayer, Anna Ustaszewska, Eileen Dalin, Olivier Couronne, Evan E. Eichler, Tijana Glavina, Astrid Terry, Sun-Hee Leem, Steve Lowry, Anne S. Olsen, Lucía Ramírez, Ming Tsai, Stephanie Malfatti, Hope Tice, Uffe Hellsten, David Goodstein, Martin Pollard, Daniel S. Rokhsar, Nancy Hammon, Angelica Salazar, Jenna Morgan, Yee Man Chan, Michael R. Altherr, Paramvir S. Dehal, Nu Vo, Linda K. Ashworth, Elbert Branscomb, Laurie Gordon, Julio Escobar, Anthony P. Popkie, Dave Flowers, Anca M. Georgescu, Len A. Pennacchio, Sam Pitluck, Sam Rash, Edward M. Rubin, Sean Caenepeel, Glenda Quan, Asaf Salamov, Inna Dubchak, Lisa Stubbs, Andrea Aerts, Mark Dickson, Kathryn Nelson, Mari Christensen, Lauren Haydu, Frederick Lopez, Mark C. Wagner, Jeremy Wheeler, Joan Yang, and Susan Lucas

Subjects
Genetics, Medical, Molecular Sequence Data, Biology, Evolution, Molecular, Chromosome 15, Mice, Chromosome 16, Chromosome 19, Gene Duplication, Animals, Humans, Conserved Sequence, Genetics, Base Composition, Multidisciplinary, Sequence Analysis, DNA, Physical Chromosome Mapping, Chromosome 17 (human), Alternative Splicing, Chromosome 4, Chromosome 3, Genes, Multigene Family, CpG Islands, Chromosome 21, Chromosome 22, Chromosomes, Human, Pair 19, Pseudogenes
Abstract

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

Published
2003

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