16.05.2023: Reference genomes are high-quality genome datasets that provide important information of value for the protection of endangered species. An international research team led by the University of Veterinary Medicine Vienna has now succeeded in sequencing an even higher quality genome for cheetahs. The newly acquired dataset represents a milestone that will significantly improve the knowledge and understanding of this threatened feline.
The cheetah is a vulnerable species at risk of extinction. To help make the right conservation decisions, genomic analyses are becoming an increasingly important tool. Several genomic analyses of the cheetah, based on so-called short-read sequences, have already been published. In-depth genomic analyses, however, such as analyses of mutational load and genetic health, require highly continuous reference genomes. These reference genomes can provide information about the fitness and inbreeding status of a threatened species and play a crucial role in the development of management measures in conservation.
Reference genomes answer key biological questions
As a reference genome was currently unavailable for the cheetah, the researchers sequenced and assembled a chromosome-level genome for this threatened species. “The new reference genome VMU_Ajub_asm_v1.0 reflects a major improvement compared to the previously available cheetah genomes. It is the first assembly based on so-called long reads of long sequences of DNA molecules, which enabled us to assign even difficult areas of the genome, especially repetitive regions, and to fill previously existing gaps. The improved continuity of the genome will enable a variety of genome analyses that were not previously possible,” explains the study’s first author, Sven Winter of the Research Institute of Wildlife Ecology (FIWI) at Vetmeduni.
According to the researchers, the new genome resource provides a solid foundation for answering key biological questions for understanding the process of natural selection and adaptation. The study’s final author, Pamela Burger from the Research Institute of Wildlife Ecology at Vetmeduni, explains: “Highly continuous annotated chromosome-scale genome assemblies are valuable references for evolutionary or conservation genome analyses and allow in-depth studies on structural variation or the diversity and function of certain genes such as immune response genes. Genome assemblies of non-model organisms of this quality are currently rare, however.”
Fastest land animal in the world threatened with extinction
The cheetah (Acinonyx jubatus) is a large cat known as the fastest land animal, capable of speeds of up to 105 km/h. Historically, the cheetah could be found in open grasslands across Africa, the Arabian Peninsula and southwestern Asia. At present, it inhabits only a fraction of its former range, resulting in small and fragmented populations. The cheetah as a species is currently considered “vulnerable” on the International Union for Conservation of Nature (IUCN) Red List of threatened species, with two subspecies, A. j. venaticus (Iran) and A. j. hecki (northwest Africa), listed as “critically endangered”.
The article “A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus)” by Sven Winter, René Meißner, Carola Greve, Alexander Ben Hamadou, Petr Horin, Stefan Prost and Pamela A. Burger was published in Journal of Heredity.