A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models

Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.

Neoplasia in captive Tsushima leopard cats (Prionailurus bengalensis euptilurus)

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) is a subspecies of the mainland leopard cat that lives on the small island of Tsushima, Japan. Captive breeding has been attempted in zoos in Japan because only approximately 100 animals remain in the wild and the Tsushima leopard cat is an endangered species. There are very few reports on diseases, including tumours, of this species. We analysed the deaths of 58 Tsushima leopard cats and confirmed that nine had neoplastic disease. The average age at death of the animals with neoplasia was 14 years and tumours were the primary cause of death in all animals. Eight of the nine cases involved primary tumours of the pancreas, liver, gallbladder, tongue and salivary glands, suggesting that Tsushima leopard cats may have a predilection for digestive system tumours. This is the first report of neoplastic disease in the Tsushima leopard cat.

Quality of cauda epididymal sperm immediately after collection and after freezing-thawing from Amur leopard cats (Prionailurus bengalensis euptilurus) and a local population of the subspecies Tsushima leopard cats

In this study, cauda epididymal sperm were collected from Amur leopard cats with various causes of death as well as Tsushima leopard cats that underwent castration surgery, and sperm quality was compared with that in domestic cats. A sufficient number of sperm similar to those in domestic cats could be collected from the cauda epididymis of Amur leopard cats. However, in old leopard cats, no or very few cauda epididymal sperm were recovered, although there were no differences in sperm motility and sperm abnormality. There were no significant differences in sperm quality immediately after collection and after freezing-thawing of cauda epididymal sperm compared with corresponding estimates in domestic cats.

Increased Risk of Infection with Severe Fever with Thrombocytopenia Virus among Animal Populations on Tsushima Island, Japan, Including an Endangered Species, Tsushima Leopard Cats

To investigate the seroprevalence of severe fever with thrombocytopenia syndrome (SFTS) among wild and companion animals on Tsushima Island, Japan, SFTS virus (SFTSV)-specific ELISA and virus-neutralizing tests were conducted on 50 wild boars, 71 Sika deer, 84 dogs, 323 domestic cats, and 6 Tsushima leopard cats. In total, 1 wild boar (1.8%), 2 dogs (2.4%), 7 domestic cats (2.2%), and 1 Tsushima leopard cat (16.7%) were positive for anti-SFTSV antibodies. Among the 11 positive animals, 10 were collected after 2019, and all were found on the southern part of the island. SFTSV, thus far, seems to be circulating within a limited area of Tsushima Island. To protect humans and animals, including endangered Tsushima leopard cats, from SFTSV infection, countermeasures are needed to prevent the spread of SFTSV on Tsushima Island.

Systemic amyloidosis derived from EFEMP1 in a captive Tsushima leopard cat

In animals, most cases of systemic amyloidosis are of amyloid A type, and the other types of systemic amyloidoses are rare. This study analyzed systemic amyloidosis in a 15-year-old female Tsushima leopard cat. Amyloid deposits strongly positive for Congo red staining were observed in the arterial walls as well as the interstitium in multiple organs. Mass spectrometry-based proteomic analysis with laser microdissection of amyloid deposits identified epidermal growth factor-containing fibulin-like extracellular matrix protein 1 (EFEMP1) as a prime amyloidogenic protein candidate. Immunohistochemistry showed that the amyloid deposits were positive for the N-terminal region of EFEMP1. From these results, the present case was diagnosed as EFEMP1-derived amyloidosis. It is the first such case in an animal. EFEMP1-derived amyloidosis in humans has recently been reported as a systemic amyloidosis, and it is known as an age-related venous amyloidosis. The present case showed different characteristics from human EFEMP1-derived amyloidosis, including the amyloid deposition sites and the amyloidogenic region of the EFEMP1 protein, suggesting a different pathogenesis between Tsushima leopard cat and human EFEMP1-derived amyloidosis.

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Simple Summary

The Tsushima leopard cat, Prionailurus bengalensis euptilurus, is a small regional population of the Amur leopard cat and is only found on Tsushima Island in Japan. A breeding program will require adequate information on parentage, kinship, and inbreeding for this population. Hence, there is an urgent need to develop this information in order to conserve the population and its genetic diversity. We performed GRAS-Di analysis to investigate the genetic diversity and genetic structure of the Tsushima leopard cat. We identified between 133 and 158 single-nucleotide polymorphism (SNP) markers in three different genotyping methods. These SNP markers can be used in identification of individuals and parentage. In addition, structure analysis using these markers demonstrated the similar genetic composition of the samples from 48 Tsushima leopard cats, and indicated Tsushima leopard cats have no subpopulations. We have provided genetic markers that are useful for conservation of the Tsushima leopard cat, such as individual identification and parentage. Moreover, we have also clarified units for conservation of the Tsushima leopard cat population from structure analysis.

Abstract

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.

The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation

We examined genetic diversity of the wild Tsushima leopard cat-a regional population of the Amur leopard cat-using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.

Efficient immortalization of cells derived from critically endangered Tsushima leopard cat (Prionailurus bengalensis euptilurus) with expression of mutant CDK4, Cyclin D1, and telomerase reverse transcriptase

Tsushima leopard cat is the subspecies of Amur cats, and it is classified as the most highest class of critically endangered animals. Although the protection activity is highly recognized, the number of animals is decreasing due to the human activity and invasion of domestic cats and infectious disease. In this study, we succeeded primary culture of normal fibroblasts derived from the Tsushima leopard cat (Prionailurus bengalensis euptilurus). Furthermore, we introduced the human derived mutant Cyclin Dependent Kinase 4, Cyclin D1, and telomere reverse transcriptase. We showed that the expression of these three genes efficiently immortalized cells derived from Tsushima leopard cat. Furthermore, we showed that the chromosome pattern of the established cells is identical with the original one. These data indicate that our method of immortalization is useful to establish cell lines from critically endangered cats, which potentially contributes to the re-generation of critically endangered animals from cultured cell with reproductive technique, such as somatic cloning.

Identification of Felis catus Gammaherpesvirus 1 in Tsushima Leopard Cats (Prionailurus bengalensis euptilurus) on Tsushima Island, Japan

Felis catus gammaherpesvirus 1 (FcaGHV1) is a widely endemic infection of domestic cats. Current epidemiological data identify domestic cats as the sole natural host for FcaGHV1. The Tsushima leopard cat (TLC; Prionailurus bengalensis euptilurus) is a critically endangered species that lives only on Tsushima Island, Nagasaki, Japan. Nested PCR was used to test the blood or spleen of 89 TLCs for FcaGHV1 DNA; three (3.37%; 95% CI, 0.70⁻9.54) were positive. For TLC management purposes, we also screened domestic cats and the virus was detected in 13.02% (95% CI, 8.83⁻18.27) of 215 cats. Regarding phylogeny, the partial sequences of FcaGHV1 from domestic cats and TLCs formed one cluster, indicating that similar strains circulate in both populations. In domestic cats, we found no significant difference in FcaGHV1 detection in feline immunodeficiency virus-infected (p = 0.080) or feline leukemia virus-infected (p = 0.163) cats, but males were significantly more likely to be FcaGHV1 positive (odds ratio, 5.86; 95% CI, 2.27⁻15.14) than females. The higher frequency of FcaGHV1 detection in domestic cats than TLCs, and the location of the viral DNA sequences from both cats within the same genetic cluster suggests that virus transmission from domestic cats to TLCs is likely.

EBSTEIN ANOMALY IN THE TSUSHIMA LEOPARD CAT (PRIONAILURUS BENGALENSIS EUPTILURUS)

Ebstein anomaly is a rare congenital heart disease that has been described in domestic dogs, a meerkat, a pygmy goat, and a lion. An 11-mo-old Tsushima leopard cat presented to Osaka Prefecture University Veterinary Hospital for diagnosis and treatment of right-sided congestive heart failure. Echocardiography showed a dilated right atrium and ventricle with an enlarged tricuspid valve annulus and apical displacement of the tricuspid valve leaflets. The cat was diagnosed with Ebstein anomaly. To the best of our knowledge, this is the first report of this type of congenital heart disease in a Tsushima leopard cat.

Molecular survey of arthropod-borne pathogens in ticks obtained from Japanese wildcats

The Iriomote cat (IC), Prionailurus bengalensis iriomotensis, and the Tsushima leopard cat (TLC), Prionailurus bengalensis euptilurus, are endangered subspecies of leopard cats in Japan. In addition to habitat destruction and road kills, infectious diseases may threaten their populations, and infection with arthropod-borne pathogens has been reported in both subspecies. Infestations with ectoparasites, especially ticks, have frequently been observed in ICs and TLCs. In the present study, ticks collected from captured ICs and TLCs between November 2011 and January 2012 were morphologically identified and the prevalence of the pathogens Bartonella sp., Babesia sp., Ehrlichia sp., Anaplasma sp., Hepatozoon sp., and hemoplasmas in the ticks was molecularly evaluated. The ticks Haemaphysalis longicornis, H. hystricis, and Amblyomma testudinarium were obtained from ICs, and H. megaspinosa, Ixodes tanuki, H. campanulata, and A. testudinarium were collected from TLCs. The pathogens Hepatozoon felis, Babesia sp., and Anaplasma bovis were detected in ticks obtained from ICs, while H. felis. Babesia sp., Ehrlichia sp., E. muris, 'Candidatus Mycoplasma haemominutum', and Bartonella henselae were found in ticks from TLCs. To protect and conserve these endangered animals, continuous monitoring and additional surveys will be necessary to understand the role of ticks as disease vectors in Japanese wildcats.

Molecular epidemiologic survey of Bartonella, Ehrlichia, and Anaplasma infections in Japanese Iriomote and Tsushima leopard cats

The Iriomote cat (IC; Prionailurus iriomotensis) and the Tsushima leopard cat (TLC; Prionailurus bengalensis euptilura) are endangered wild felids in Japan. As a part of ongoing conservation activities, we conducted a molecular, epidemiologic survey of Bartonella, Ehrlichia, and Anaplasma infections in wild IC and TLC populations. Blood samples (47 from 33 individual IC; 22 from 13 TLC) were collected between August 2002 and January 2011. Using PCR analysis, we confirmed the presence of Bartonella henselae in ICs and Bartonella clarridgeiae in TLCs, with prevalences of 6% and 8%, respectively. Using PCR and basic local alignment search tool analyses, we identified Ehrlichia canis in both cats and Anaplasma bovis in TLCs. The prevalence of E. canis was 12% in ICs and 8% in TLCs, and the prevalence of A. bovis was 15% in TLCs. This is the first report, to our knowledge, of B. henselae, B. clarridgeiae, E. canis, and A. bovis infections in these two endangered species. Continuous monitoring of these pathogens is needed for their conservation.