Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Abstract

Background The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. Results We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. Conclusions We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

Duplications and retrogenes are numerous and widespread in modern canine genomic assemblies

“…The UU_Cfam_GSD_1.0 assembly (accession GCA_011100685.1), derived from a female German Shepherd Dog named Mischka, has extensive annotation, and serves as the reference genome used by the Dog10K consortium [14, 30, 53]. This genome assembly was constructed using PacBio Sequel sequencing and consists of sequence assigned to 39 assembled chromosomes (chr1-38 and chrX), the mitochondria (chrM), and 2,158 unplaced contigs not localized to a chromosome.…”

“…We searched for candidate retrocopies in the Mischka assembly based on the annotation of 19,972 protein coding genes used by the Dog10K consortium [14]. A single transcript was selected for each gene, with priority given to the longest isoforms and fewest number of exons.…”

“…Gene conversion and changes in pseudogene sequence can also give rise to actual and novel function, altering the name from pseudogenes into functional retrogenes. Retrocopies commonly occur in dogs [13,14] and confound the interpretation of genetic variation [15]. Novel developments in sequencing technology have allowed for the rapid and thorough analysis of thousands of samples.…”

Review of Molecular Technologies for Investigating Canine Cancer

“…The National Human Genome Research Institute (NHGRI) Dog Genome Project, which focuses on the genetics of health and body structure in the domestic dog, performed WGS analysis on normal tissue from 722 canines (including 526 purebred dogs, 142 random-bred dogs and 54 wild canids) and identified over 91 million nucleotide variants, creating an extensive catalogue of canine genomic variation [ 115 ]. More recently, the international Dog10K project, which aims to sequence and analyse several thousand canine genomes, performed WGS analysis on normal tissue from 1987 canines (including 1611 dogs from 321 breeds, 309 village dogs, 63 wolves and 4 coyotes) and identified 34 million single-nucleotide variants (SNVs) and 144,000 structural variants (deletions, insertions, duplications and inversions ≥ 50 bp in size), making the Dog10K reference panel the largest canine dataset assembled to date [ 116 ]. This will be an invaluable resource for the field of canine oncogenomics.…”

NDUFS7 variant in dogs with Leigh syndrome and its functional validation in a Drosophila melanogaster model

“…Variant calling was performed using the GATK HaplotypeCaller 10 in gVCF mode as described 9 . To filter for private variants in the affected dogs, we used publicly available genome sequences from 1479 control dogs of diverse breeds 9 , 11 (Table S1 ). Sequences derived from Chihuahuas or Jack Russell Terriers were excluded as controls for variant filtering.…”