Mule's DNA Helps Scientists Build the Most Complete Horse and Donkey Genomes Yet

Researchers have built the most complete reference genomes yet for horses and donkeys, using DNA from a female mule to capture genome regions earlier versions could not fully assemble. The international study, led by researchers at the University of Kentucky's Martin-Gatton College of Agriculture, Food and Environment, was published in the journal Cell Genomics.

A mule inherits one set of chromosomes from its horse mother and another from its donkey father. Because the two sets differ enough in their DNA, researchers could tell which pieces came from which parent, a process called phasing, letting them reconstruct a horse genome and a donkey genome from a single animal. Combining accurate short DNA reads with very long reads of hundreds of thousands of bases and chromosome-folding data, the team assembled telomere-to-telomere, or T2T, genomes with few gaps. The new horse assembly has about 11.4% more sequence than the genome it replaces, and the donkey assembly about 11.5% more; both are now adopted by the National Center for Biotechnology Information as reference genomes.

The biggest improvement involves centromeres, the regions that pull chromosome copies apart when a cell divides, often surrounded by repetitive satellite DNA once nearly impossible to assemble with older technology. Satellite DNA makes up about 9% of the horse genome and 8.3% of the donkey genome. Most horse centromeres sit within large blocks of satellite DNA, but donkeys differ: 16 of their centromeres contain no satellite DNA at all, while the remaining 15 use several different satellite sequence types. Centromeres can also shift position within a chromosome without changing the underlying DNA sequence; the study found donkey centromere variation spanning an area as large as 2.8 million DNA letters, compared with about 600,000 letters found in earlier research on satellite-free centromeres.

The new genomes will underpin the Horse Pangenome and Equine Pangenome projects, comparing breeds such as Clydesdales and Arabians to study genetic diversity, immune-response genes and disease risk.