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Amur Leopard Genome Sequenced for Comparative Genomics Study of Carnivory

NEW YORK (GenomeWeb) – Korean researchers have sequenced and have begun analyzing the genome of the Far Eastern Amur leopard, Panthera pardus orientalis, an endangered sub-species of leopard found in southern Russia and northern China.

As it reported online recently in Genome Biology, the team developed a de novo genome assembly for a captive Amur leopard before re-sequencing wild Amur leopards from Russia and Korea. It also used comparative genomics to search for signs of selection related to obligatory carnivory in the Amur leopard and other animals such as the domestic cat, lion, and cheetah — a feature found in a subset of mammalian species.

"Carnivory related genetic adaptations such as extreme agility, muscle power and specialized diet make leopards such successful predators, but these lifestyle traits also make them genetically vulnerable," co-first author Yun Sung Cho, a researcher affiliated with the Ulsan National Institute of Science and Technology in Korea and the Personal Genomics Institute, said in a statement.

The Amur leopard is the second leopard sub-species to be sequenced. The snow leopard genome was described in a big cat comparative genomics study in Nature Communications in 2013, though that genome was not assembled de novo. Tiger, lion, cheetah, and domestic cat genomes have also been described in the past.

Given the similarities between some feline conditions and those found in humans, investigators from several teams have thought to sequence domestic and wild cats in an effort to better understand human traits and diseases.

For this new study, the researchers used Illumina HiSeq instruments to sequence genomic DNA isolated from a captive female Amur leopard's muscle. They then put the resulting sequence, along with synthetic long reads for two wild Amur leopards, together into a de novo assembly that spanned almost 2.6 billion base pairs and contained 19,043 predicted protein-coding genes.

After re-sequencing two more wild Amur leopards, the team then analyzed the Amur leopard genomes alongside sequences from 18 other mammals: eight carnivores, including lions, tigers, and polar bears; five omnivores such as mice and humans; and five herbivores ranging from rabbits to elephants and giant pandas.

In one finding, the researchers identified 52 gene family expansions and 567 gene family contractions in the cat family compared with other carnivores, including expansions to gene families involved in muscle functions and movement. On the other hand, gene families involved in metabolizing starches and sugars were among those condensed in cats and other carnivores.

Meanwhile, the team saw an over-representation of motor axon and bone development genes across the 184 genes that appeared to be under positive selection in three or more carnivore genomes. Genes related to immune function appeared more likely to be under positive selection in the omnivorous or herbivorous animals.

The analyses also uncovered apparent adaptations to a meat-heavy diet in cat species, along with cat-specific conservation involving genes involved in light response, nerve impulse transmission, and other features. The study's authors suggested that such findings may offer a refined look at dietary adaptations in cats and other animals, providing a framework for untangling animals' broader biological responses to different food types and diet-related diseases. 

"Cats are also a good model for studying health issues, such as human diabetes," senior author Soonok Kim, a researcher at Korea's National Institute of Biological Resources, said in a statement. "This new leopard genome reference is an environmental treasure that could help us understand these conditions further."