Perspectives provided by leopard and other cat genomes: how diet determined the evolutionary history of carnivores, omnivores, and herbivores

摘要

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment. Since the Convention on Biological Diversity (CBD) was enforced in 1993, the conservation and sustainable use of biodiversity has become an essential issue for the survival of living entities, including humans, in the rapidly changing current ecosystems. Biodiversity traditionally includes species diversity, genetic diversity, and ecosystem diversity. In addition to these components, genomic diversity has recently been added as one of the fundamental layers of biodiversity. Recent advances in genome sequencing technologies and the resulting decrease in cost assisted by the refinement of bioinformatics tools to interpret genomic codes made genomics readily available to biodiversity researches in non-model, wild species. The genome sequences of wild animal species are rapidly being accumulated, providing rich resources for the study of adaptation, trait evolution, species divergence, and population structure analyses. Currently, more than 120 genome assemblies and many more whole genome re-sequencing data are available for the mammalian taxa. These data will be used for furthering conservation efforts and for good management practices of endangered wild species. Felidae, the family of cats, includes the most iconic and much threatened wild species such as the tiger, lion, cheetah, and leopard. Felidae species are the top predators and eat only meat to survive. As a hyper-carnivore, the felids have acquired several key diet-related traits such as digestive enzymes, shortened digestive tracts, and alteration of taste bud sensitivities to sugar. This extreme genetic adaptation endows us to generate invaluable insight and practical bio-markers in the future, for human disease and health studies as a genome diversity resource. The morphology of cats is highly adapted for hunting, powered by flexible bodies, fast reflexes, and strong muscular limbs. They also possess highly developed senses of night vision, hearing, and smell. The leopard, Panthera pardus, is among the most widely distributed big cats, inhabiting from Africa to Russian Far East. Of the nine genetically distinguished subspecies, the Amur leopard faces the most serious threat of extinction, with only 60–70 individuals remaining in the wild, mostly due to the increasing human population expansion, habitat loss, hunting, and poaching. Felidae genomes are well-studied from a genomic perspective. Genome assemblies have been available for four species in Felidae, i.e., domestic cat (Felis catus), tiger (Panthera tigris), cheetah (Acinonyx jubatus), and lion (P. leo). In addition, whole genome sequences for snow leopard (P. uncia) and additional individuals of tiger and