GSD_1.0 (canFam4): A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

We present GSD_1.0, a novel high-quality domestic dog reference genome with chromosome length scaffolds and gap number reduced 41-fold, from 23,836 to 585. Annotation with novel and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of closed gaps harboured previously hidden functional elements, including promoters, genes and miRNAs. 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 Leukocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. The sequencing of 27 dogs from 19 breeds with linked read technology uncovered 22.1 million SNPs, indels and larger structural variants. Intersection with protein coding genes showed that 1.4% could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.