Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes

Although an increasing number of long-read genome assemblies have been created from a diverse collection of dogs and wolves, most published assemblies represent the diploid genome as a single primary sequence. Here, we generate and analyze phase-resolved diploid dual assemblies from five canines. The most contiguous assemblies represent over half of the canine chromosomes as single contigs, permitting an assessment of the sequence and structure of canine chromosomes. Consistent with a telocentric classification, we find that the centromeres of canine autosomes begin an average of 59 kb from the start of the chromosome and are flanked by a 35 kb subtelomeric segment that is repeat-rich and shared across autosomes. Analysis of a pangenome graph constructed from the 10 haplotype-resolved assemblies shows that short tandem repeat loci are three times more common than variable number tandem repeat loci and that the landscape of canine structural variation features extensive allelic heterogeneity. The pangenome graph includes examples of complex, nested allelic variation involving SINEC (a carnivore-specific SINE) and LINE-1 mobile elements. Analysis of 3′ transductions implicate an uncharacterized source element with high activity and demonstrates the presence of full-length LINE-1s capable of retrotransposition that are segregating among canines.