The Earth is presently experiencing its sixth mass extinction event, largely propelled by human-induced habitat loss. This poses the most significant threat to global biodiversity. While minimizing the impacts of habitat loss is the primary strategy to counter this detrimental reality and prevent further ecosystem loss, genomic methods offer additional opportunities to preserve and sustain remaining species. While directly examining wild populations remains crucial, zoological facilities affiliated with organizations like the Association of Zoos and Aquariums (AZA) play a vital role in species conservation, offering more opportunities to study animals more accessible than their wild counterparts. Through meticulously designed management strategies such as Species Survival Plans (SSPs) and studbook management, these facilities actively promote conservation efforts.

 Although most zoo-managed species may not be suitable for reintroduction, maintaining genetic diversity and minimizing disease risk is a top priority. With sequencing technologies becoming increasingly more affordable, the power of genomics can enhance management strategies for both wild and human-managed populations, precisely addressing the conservation needs of various wildlife. Generating reference genomes is one way to accomplish this as it enables researchers to analyze a species' genetic makeup, aiding in assessing fitness, monitoring diseases, and understanding evolutionary history, thereby contributing to species sustainability.

The fishing cat (Prionailurus viverrinus) is a smaller felid found in the marshlands throughout Southeast Asia. Aptly named, this cat has adapted to primarily hunt in its surrounding waterways, a distinctive behavior uncommon among other felid species. The fishing cat's conservation status was last classified as “vulnerable” by the International Union for Conservation of Nature (IUCN) in 2016 due to ongoing population decline. Human activities, including habitat loss for agriculture, aquaculture, and urbanization, as well as logging and retaliatory killings, pose significant threats to the feline’s survival. If this rapid habitat degradation persists in these regions, numerous species reliant on these ecosystems, particularly aquatic systems vital for the fishing cat, will continue to disappear.

North American zoos affiliated with the AZA manage a small population of fishing cats. Over the past few decades, an increased prevalence of bladder cancer known as transitional cell carcinoma (TCC) has been observed in older cats. Despite TCC being well-documented in numerous species including humans, the exact cause remains unknown. To enhance the longevity of this zoo-managed population, we generated a reference genome and conducted whole-genome sequencing (WGS) of both healthy and TCC-affected cats. This high-quality reference genome now serves as a genetic blueprint for the fishing cat species. By mapping the WGS cats to this reference, our aim was to identify harmful gene mutations present in the cancer-afflicted cats.

In this study, we generated a highly accurate chromosome level reference genome and WGS data from 11 zoo-managed fishing cats. Additionally, we utilized this genome to verify the close genetic relationship with another Prionailurus species, the Asian leopard cat. By evaluating the reference genome alongside the 11 WGS cats, we classified various genetic variants, enhancing our understanding of genetic diversity in this cohort. Through the analysis of these genetic variants and evaluating cancer causing genes, we identified potential genetic factors contributing to TCC occurrence. While our findings suggest a greater presence of harmful gene mutations in cancer cats, particularly in BRCA2, further research with a larger cat sample size is needed for validation. Moreover, our study includes a detailed illustration of the current North American zoo-population pedigree. Combined with the new knowledge of potential harmful genes associated with TCC, this study offers additional insight for zoological facilities in managing and breeding programs for fishing cats, especially those at risk of developing cancer as they age.

 We hope that our findings will help further address the issue of bladder cancer occurrence in the fishing cat, and provide additional evidence to the power of genomics when it comes to managing species at risk of extinction. Although not as well-known as some of the larger cats such as the tiger or lion, the conservation of this smaller, elusive feline species is just as crucial, as the loss of any species, particularly a feline apex predator, would be detrimental to the natural ecosystems to which it inhabits. By generating a reference genome for the fishing cat, further genetic evaluation into both wild and zoo-managed populations is now a possibility and necessary for the preservation of this species. Ultimately, by leveraging genomic advancements to understand and protect species like the fishing cat, we not only safeguard individual populations, but contribute to the broader conservation efforts essential for ensuring Earth's biodiversity for generations to come.

Title Image: Fishing cat "Puddles" at the Oklahoma City Zoo. Image provided by Dr. Jennifer D'Agostino, director of OKC Zoo veterinary services.