By Blake Jackson
Researchers have developed highly complete reference genomes for horses and donkeys by using DNA from a female mule, opening new opportunities to study regions of animal chromosomes that have remained difficult to analyze.
The international research project, led by scientists at the University of Kentucky Martin-Gatton College of Agriculture, Food and Environment, was published in Cell Genomics.
The new genome assemblies provide significantly more detail about complex chromosome regions, including centromeres and telomeres. These areas are important for understanding chromosome function, evolution, genetic variation and traits linked to animal health.
“For a long time, some of the most complex regions of the horse genome were essentially invisible to us,” Kai Li a researcher in the UK Department of Veterinary Science said. “With this new reference genome, we can finally begin to explore those regions and ask how they contribute to chromosome biology, genetic diversity and traits that matter in horses.”
A mule was particularly valuable because it carries chromosomes from both a horse and a donkey. Researchers were able to distinguish the two sets of DNA and use a process called phasing to reconstruct separate horse and donkey genomes from the same animal.
The team combined several advanced sequencing technologies, including methods capable of producing both highly accurate and extremely long DNA reads. These techniques helped researchers assemble repetitive regions that older genome references could not accurately represent. The resulting assemblies are known as telomere-to-telomere, or T2T, genomes.
The new horse genome contains about 11.4% more sequence than the previous reference, while the donkey genome includes approximately 11.5% more. The National Center for Biotechnology Information has adopted and annotated both assemblies as reference genomes.
The study also revealed important differences in centromeres, chromosome regions involved in separating genetic material during cell division. Satellite DNA accounts for about 9% of the horse genome and 8.3% of the donkey genome, while donkey centromeres show greater structural diversity.
“We can now inexpensively build very accurate, very complete phased genomes. These assemblies were derived from a Thoroughbred dam, and a donkey sire,” Ted Kalbfleisch, Ph.D, a researcher in the UK Department of Veterinary Science said.
“We and others are now working to assemble the genomes of horses from different breeds, and different health conditions. This assembly will serve as a backbone to our Horse Pangenome effort, where we will compare all these horses against one another and learn how Clydesdales, Arabians and all other breeds differ from one another both at the nucleotide level and now structurally," Kalbfleisch added.
The findings could strengthen research into equine genetics, breeding, disease and health while supporting broader efforts to understand genetic differences across horse breeds.
Photo Credit: gettyimages-patrick-jennings
Categories: Kentucky, Education, Livestock