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Genome sequence, comparative analysis and haplotype structure of the domestic dog
Open accessAbstract
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.
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“The isolation of strains and breeds in these species results in much longer block lengths than are found in humans.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [24]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Dogs were domesticated from grey wolves at least 15 000–50 000 years ago, through both natural and artificial selection [16,17].”
From Are dark-eyed dogs favoured by humans? Domestication as a potential driver of iris colour difference between dogs and wolves (2023) · cites this paper as [16]
Experimental — accuracy not yet measuredIn the citing paper
“The median value of K S is 1.02.”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [10]
In the citing paper
“The most surprising discovery to emerge from comparative analyses of eutherian genomes is the finding that the majority of evolutionarily conserved sequence does not represent protein-coding genes, but rather are conserved non-coding elements (CNEs) 7,10 .”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [10]
In the citing paper
“Strikingly, the proportion of eutherian-specific CNEs recognizable as transposable-element-derived (16%) is very similar to the proportion of the total aligned sequence between the human, mouse and dog genomes recognizable as ancestral transposable elements (,17% of ,812 Mb; the vast majority of which is inactive) 10 .”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [10]
In the citing paper
“The Felis catus genome is predicted to contain 19,493 protein-coding genes and 1,855 noncoding RNAs, similar to dog (14).”
From Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication (2014) · cites this paper as [14]
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The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Self-citationThe Structure of Haplotype Blocks in the Human Genome
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Metadata
- Authors
- members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., Zody, M. C., Mauceli, E., Xie, X., Breen, M., Wayne, R. K., Ostrander, E. A., Ponting, C. P., Galibert, F., Smith, D. R., deJong, P. J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.-W., Cook, A., Cuff, J., Daly, M. J., DeCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.-P., Parker, H. G., Pollinger, J. P., Searle, S. M. J., Sutter, N. B., Thomas, R., Webber, C., & Lander, E. S.
- Affiliations
- Broad Institute (US)
- North Carolina State University (US)
- National Institutes of Health (US)
- Centre National de la Recherche Scientifique (FR)
- University of California, Los Angeles (US)
- University of Oxford (GB)
- Corresponding author
- Lander, Eric S.
- ORCID
- Wade, Claire M
- Mikkelsen, Tarjei S.
- Karlsson, Elinor K.
- Jaffe, David B.
- Zody, Michael C.
- Xie, Xiaohui
- Breen, Matthew
- Wayne, Robert K.
- Ostrander, Elaine A.
- Ponting, Chris P.
- Galibert, Francis
- Alvarez, Pablo
- Cuff, James
- Daly, Mark J.
- DeCaprio, David
- Grabherr, Manfred
- Kellis, Manolis
- Heger, Andreas
- Hitte, Christophe
- Kim, Lisa
- Koepfli, Klaus-Peter
- Parker, Heidi G.
- Pollinger, John P.
- Sutter, Nathan B.
- Thomas, Rachael
- Webber, Caleb
- Lander, Eric S.
- Venue
- Nature
- Published
- 2005-12
- Volume
- 438
- Issue
- 7069
- Pages
- 803-819
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2114611642
- Semantic Scholar
- b01f00857b9abec4f245c665c5042824f5430711
- Cited by
- 2,568
- References
- 115
- Citations by year
- 2026: 40 · 2025: 66 · 2024: 94 · 2023: 106 · 2022: 95 · 2021: 122 · 2020: 141 · 2019: 122 · 2018: 114 · 2017: 88 · 2016: 116 · 2015: 138 · 2014: 140 · 2013: 131 · 2012: 144
- FWCI
- 84.07
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute
- Topics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Human-Animal Interaction Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- dogs, single nucleotide polymorphisms, breed genetic diversity, haplotype structure, genome evolution, comparative genomics, conserved non-coding elements, genome-wide association study, dog breeds
- MeSH terms
- Animals, Dog Diseases, Dogs, Female, Haplotypes, Humans, Hybridization, Genetic, Male, Mutagenesis, Genome, Conserved Sequence, Evolution, Molecular, Short Interspersed Nucleotide Elements, Polymorphism, Single Nucleotide, Genomics, Synteny, Mice, Rats
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