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We present GSD₁. 0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3. 1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32. 1% of lifted over CanFam3. 1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD₁. 0. A catalogue of canine "dark" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22. 1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1. 4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.
Wang et al. (Wed,) studied this question.