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

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.

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

“…The relationships we recovered within Vulpini are identical to those found by Lindblad-Toh et al . [45] after accounting for differences in species sampling. An unexpected result, however, is that Vulpes velox and Vulpes macrotis are not sister species, given the long-standing question as to whether or not they are indeed separate species (for example, compare the two taxonomies [13] and [14] from Wozencraft).…”

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

“…This possibility is also supported by recent progress of genomic studies on domesticated mammals and birds (for example, dog, cat, cow, chicken, and pigeon) (Lindblad‐Toh et al, 2005; Wayne and Ostrander, 2007; Akey et al, 2010; Vonholdt et al, 2010; Shapiro et al, 2013). These studies explain the processes underlying fixation of genetic mutations through selective pressure on favorable morphological and/or physiological features, providing a more specific and promising framework for combined genomic and developmental biological approaches to investigate how fixed mutations altered ontogenetic processes to form the favorable morphological features in domestic animals in the context of evolutionary developmental biology (Cresko et al, 2007).…”

LUPA: A European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

“…The latter is greatly aided by the fact that dogs and humans share roughly the same gene repertoire (Lindblad-Toh et al, 2005;Derrien et al, 2009).…”

“…Concomitantly, a large number of single nucleotide polymorphism (SNPs; >2 million) were discovered and the architecture of the dog genome was largely deciphered (Lindblad-Toh et al, 2005). Linkage disequilibrium (LD) was shown to extend over much longer distances within breeds (as a result of the founder effects accompanying breed formation), hence drastically reducing the number of markers needed for genome-wide association studies (GWAS) compared to humans.…”