Cat genomics can help decode variations in the human genome and pave the way toward precision genomic medicine. A new reference haploid phased genome assembly generated through long-read sequencing of 54 domestic cats provides a resource that can be applied in understanding the biological impact of single nucleotide and structural variants in the protein-coding regions of the genome and in the intergenic dark matter that had long been dubbed junk DNA, but is now understood to be pivotal in the regulation of gene expression.