This supplementary information follows the structure and layout of the main paper. Here we describe the methodology in detail and include additional analysis not covered in depth in the main text. Generating a draft genome sequence Data generation: We sequenced the genome of a female boxer, using a whole genome shotgun approach. A female dog was selected to obtain equal coverage of the X chromosome and the autosomes. In order to facilitate the assembly process, we sought to identify a highly homozygous individual. Breed Clubs, Veterinary schools, and specific breeders were contacted via web sites, as well as by direct communiqué, to obtain potentially useful DNA samples. We estimated mean heterozygosity for each of 185 candidate dogs by resequencing 19,860 base pairs representing 60 unlinked loci 1. A female boxer was selected based on the presence of only one heterozygous base pair within this sample. However, large scale data now shows that, after accounting for sample variance, this is within the expected rate of heterozygosity for the majority of dogs. DNA was isolated from the chosen dog via peripheral blood samples. A BAC library was made by Children's Hospital Oakland Research Institute (CHORI) and 4 kb, 10 kb and Fosmid libraries were made at the Broad Institute of Harvard and MIT. Both BAC an
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