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

Author

Listed:
  • Kerstin Lindblad-Toh

    (Broad Institute of Harvard and MIT)

  • Claire M Wade

    (Broad Institute of Harvard and MIT
    Massachusetts General Hospital)

  • Tarjei S. Mikkelsen

    (Broad Institute of Harvard and MIT
    Massachusetts Institute of Technology)

  • Elinor K. Karlsson

    (Broad Institute of Harvard and MIT
    Boston University)

  • 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
    Massachusetts General Hospital)

  • 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
    Computer Science and Artificial Intelligence Laboratory)

  • 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
    9 Cambridge Center)

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.

Suggested Citation

  • 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 &, 2005. "Genome sequence, comparative analysis and haplotype structure of the domestic dog," Nature, Nature, vol. 438(7069), pages 803-819, December.
    • Handle: RePEc:nat:nature:v:438:y:2005:i:7069:d:10.1038_nature04338
    DOI: 10.1038/nature04338
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    Cited by:

    1. Matthias Hörtenhuber & Marjo K. Hytönen & Abdul Kadir Mukarram & Meharji Arumilli & César L. Araujo & Ileana Quintero & Pernilla Syrjä & Niina Airas & Maria Kaukonen & Kaisa Kyöstilä & Julia Niskanen , 2024. "The DoGA consortium expression atlas of promoters and genes in 100 canine tissues," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Paul A.M. Overgaauw & Claudia M. Vinke & Marjan A.E. van Hagen & Len J.A. Lipman, 2020. "A One Health Perspective on the Human–Companion Animal Relationship with Emphasis on Zoonotic Aspects," IJERPH, MDPI, vol. 17(11), pages 1-29, May.

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