Chris Faulk helps to build the first genome for Pallas’s cat

May 25, 2023

Pallas's cat looks straight ahead

University of Minnesota researchers recently led successful efforts to build the first genome for Pallas’s cat (Otocolobus manul), a small wild cat native to central Asia known for its grumpy facial expression. The cat, which faces growing challenges from climate change, habitat fragmentation, and poaching, had no available genetic resources to help with conservation prior to this study. 

The study, published in NAR Genomics and Bioinformatics, was led by Nicole Flack, a doctoral candidate in the College of Veterinary Medicine, along with Christopher Faulk, a professor in the College of Food, Agricultural, and Natural Resource Sciences. 

The researchers used blood samples from Tater, a 6-year-old Pallas’s cat who lives at the Utica Zoo in New York, to construct a high-quality diploid nuclear genome assembly, a representative map of genes for the species.

The study results include confirmation that the Pallas’s cat is more closely related to certain wild cat species and less related to house cat species than some previous studies have suggested. 

An allele-specific methylation analysis — the first of its kind in cats — also sheds light on how gene expression is regulated in mammals through a process called genomic imprinting. Mammals inherit two copies of each gene from their parents; usually these copies are equally active, but imprinted genes have chemical tags that turn off one copy. These findings pave the way to a deeper understanding of growth, development and hybridization among cat species, which could have important implications for genetic diversity and conservation.

The genomic resources the study produced provide a comprehensive genetic reference for conservation efforts working to track the health of wild populations and optimize breeding programs for cats in captivity.

“I’m hopeful our work will help with Pallas’s cat conservation. Genetic diversity is a key factor in the health and trajectory of animal populations, but it’s difficult to study without anything to compare to,” said Flack. “Our reference genome will be useful for monitoring the health of the Pallas’s cat population, both in captive breeding programs and in the wild.”

These resources will enable future research not only on Pallas’s cat, but on the health, disease and physiology of house cats and other species — even translational work to humans. This is particularly true of the assessment of allele-specific methylation, because imprinting is a unique feature of genes shared across mammals, and has significant implications for our understanding of human growth and development. But it has been chronically understudied because of the limitations of existing technology — limitations that nanopore sequencing overcomes. 

“Our small team was able to provide Tater’s high-quality diploid cat genome including epigenetic information while using minimal financial and lab resources,” said Faulk. “We hope to serve as a model for conservation and sequencing projects from pathogens to people, especially by low-resource groups on limited budgets.”

Project funding was provided by the United States Department of Agriculture National Institute of Food and Agriculture, the Norn Group, the National Institutes of Health, and the National Science Foundation.