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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #428987
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

Author
item KIDD, JEFFREY - University Of Michigan
item SOUILMI, YASSINE - University Of Adelaide
item Rosen, Benjamin
item KHAN, RUQAYYA - Baylor College Of Medicine
item WEISZ, DAVID - Baylor College Of Medicine
item DUDCHENKO, OLGA - Baylor College Of Medicine
item AIDEN, EREZ - Baylor College Of Medicine
item ZAMMIT, ROBERT - Collaborator
item BALLARD, J. WILLIAM - Collaborator

Submitted to: NAR Genomics and Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2026
Publication Date: 4/23/2026
Citation: Kidd, J.M., Souilmi, Y., Rosen, B.D., Khan, R., Weisz, D., Dudchenko, O., Aiden, E.L., Zammit, R., Ballard, J.O. 2026. Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes. NAR Genomics and Bioinformatics. 8(2). Article lqag035. https://doi.org/10.1093/nargab/lqag035.
DOI: https://doi.org/10.1093/nargab/lqag035

Interpretive Summary: Companion animals share many genetic similarities with livestock species. Better understanding of genetic selection in pets can provide valuable models for understanding livestock selection. Representations of an organism's entire genetic code, called a genome, are traditionally constructed by artificially merging the genetic information inherited from both parents into a single reference sequence. However, in this study, we took a different approach. For five different canines (dogs and wolves), we created two distinct and complete genome sequences: one representing the genetic material inherited from the mother, and the other from the father. This method allowed us to achieve highly continuous genome assemblies. In fact, for over half of the canine chromosomes, we were able to create single, unbroken sequences. This level of completeness is crucial because it allowed us to analyze the entire structure and sequence of these chromosomes in detail. Our analysis confirmed that canine autosomes (non-sex chromosomes) are structured in a specific way, often referred to as "telocentric," meaning the centromere is located very close to one end. We found that these centromeres typically begin about 59,000 base pairs from the chromosome's start. They are also bordered by a 35,000 base pair segment that is rich in repetitive DNA sequences and is consistently found across different autosomes. To understand the full range of genetic variation in canines, we combined these 10 individual, phase-resolved genome assemblies into a "pangenome graph." This comprehensive graph allowed us to investigate structural variations – large-scale differences in DNA sequence or arrangement. We found a wide variety of these structural variations present among different individual canines. The pangenome graph also revealed complex, nested variations involving mobile genetic elements. These are segments of DNA that can move around the genome. Furthermore, our analysis suggests that canine population contain full-length mobile elements that are actively moving around the genome.

Technical Abstract: 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 STR loci are three times more common than VNTR 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 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.