Genome sequence, comparative analysis and haplotype structure of the domestic dog

Kerstin Lindblad-Toh (), Claire M Wade, Tarjei S. Mikkelsen, Elinor K. Karlsson, David B. Jaffe, Michael Kamal, Michele Clamp, Jean L. Chang, Edward J. Kulbokas, Michael C. Zody, Evan Mauceli, Xiaohui Xie, Matthew Breen, Robert K. Wayne, Elaine A. Ostrander, Chris P. Ponting, Francis Galibert, Douglas R. Smith, Pieter J. deJong, Ewen Kirkness, Pablo Alvarez, Tara Biagi, William Brockman, Jonathan Butler, Chee-Wye Chin, April Cook, James Cuff, Mark J. Daly, David DeCaprio, Sante Gnerre, Manfred Grabherr, Manolis Kellis, Michael Kleber, Carolyne Bardeleben, Leo Goodstadt, Andreas Heger, Christophe Hitte, Lisa Kim, Klaus-Peter Koepfli, Heidi G. Parker, John P. Pollinger, Stephen M. J. Searle, Nathan B. Sutter, Rachael Thomas, Caleb Webber and Eric S. Lander ()
Additional contact information
Kerstin Lindblad-Toh: Broad Institute of Harvard and MIT
Claire M Wade: Broad Institute of Harvard and MIT
Tarjei S. Mikkelsen: Broad Institute of Harvard and MIT
Elinor K. Karlsson: Broad Institute of Harvard and MIT
David B. Jaffe: Broad Institute of Harvard and MIT
Michael Kamal: Broad Institute of Harvard and MIT
Michele Clamp: Broad Institute of Harvard and MIT
Jean L. Chang: Broad Institute of Harvard and MIT
Edward J. Kulbokas: Broad Institute of Harvard and MIT
Michael C. Zody: Broad Institute of Harvard and MIT
Evan Mauceli: Broad Institute of Harvard and MIT
Xiaohui Xie: Broad Institute of Harvard and MIT
Matthew Breen: North Carolina State University
Robert K. Wayne: University of California
Elaine A. Ostrander: National Institutes of Health
Chris P. Ponting: MRC Functional Genetics, University of Oxford
Francis Galibert: CNRS—Université de Rennes 1, Faculté de Médecine
Douglas R. Smith: 500 Cummings Center
Pieter J. deJong: Children's Hospital Oakland Research Institute
Ewen Kirkness: The Institute for Genomic Research
Pablo Alvarez: Broad Institute of Harvard and MIT
Tara Biagi: Broad Institute of Harvard and MIT
William Brockman: Broad Institute of Harvard and MIT
Jonathan Butler: Broad Institute of Harvard and MIT
Chee-Wye Chin: Broad Institute of Harvard and MIT
April Cook: Broad Institute of Harvard and MIT
James Cuff: Broad Institute of Harvard and MIT
Mark J. Daly: Broad Institute of Harvard and MIT
David DeCaprio: Broad Institute of Harvard and MIT
Sante Gnerre: Broad Institute of Harvard and MIT
Manfred Grabherr: Broad Institute of Harvard and MIT
Manolis Kellis: Broad Institute of Harvard and MIT
Michael Kleber: Broad Institute of Harvard and MIT
Carolyne Bardeleben: University of California
Leo Goodstadt: MRC Functional Genetics, University of Oxford
Andreas Heger: MRC Functional Genetics, University of Oxford
Christophe Hitte: CNRS—Université de Rennes 1, Faculté de Médecine
Lisa Kim: National Institutes of Health
Klaus-Peter Koepfli: University of California
Heidi G. Parker: National Institutes of Health
John P. Pollinger: University of California
Stephen M. J. Searle: The Wellcome Trust Genome Campus
Nathan B. Sutter: National Institutes of Health
Rachael Thomas: North Carolina State University
Caleb Webber: MRC Functional Genetics, University of Oxford
Eric S. Lander: Broad Institute of Harvard and MIT

Nature, 2005, vol. 438, issue 7069, 803-819

Abstract: Abstract Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Date: 2005
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DOI: 10.1038/nature04338

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