The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids

Abstract

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.

Keywords: black-footed cat; conservation; inbreeding; introgression.

Fig. 1.

Phylogeny of Felis. (A) The geographical distribution of current Felis species based on IUCN data. (B) The distribution of the ratio (Z axis) of home range size (Y axis) to weight (X axis) shows F. nigripes is the highest among Felidae species. (C) Circos plots between the domestic cat (Right) and the BFC (Left). The circles from outside to inside represent karyotypes, GC contents, gene density, and repeats elements (LINE, SINE, LTR), respectively. (D) Each bar represents a chromosome of the domestic cat (felcat9.0). Colored bands represent tree topologies of 50-kb per window; colors correspond to the upright topologies, with white regions showing missing data. (E) The reconstructed time-scaled species tree of the genus Felis with Asian leopard cat, Prionailurus bengalensis, as outgroup. Colored lines represent the introgression between the BFC and other Felis species. (F) The schematic shows the current distribution area of the BFC (Left) and the estimated historically adaptative geographic space according to the historical climate conditions in the last glacial maximum period (Right). The black dots represent the locations of the observations of the BFCs, and the color bar indicates gradient of the probability of presence in the BFCs.

Fig. 2.

Genomic signatures of genetic adaptation in the BFC. (A) Gene family expansion/contraction of the compared species of the genus Felis and outgroups. (B) KEGG enrichment items of the expanded family genes in BFC. (C) The results of KEGG functional enrichment test of detected PSGs and REGs. (D) The metabolic related functional genes with the tested significant selection signals in digestive system BFC. (E) Three PSGs have defined functions in stereocilia connections and mechanosensory transduction (PCDH15 and PTPRQ) and regulation of actin polymerization within stereocilia (DIAPH1), while one REG (HOMER2) is a receptor involved in transduction of nerve impulses. (F) BFC-specific amino acid mutations at the conserved structures (FNIII: Fibronectin type III domain, cadherin domain, and Polar residues) in PCDH15 and PTPRQ genes compared with different felid species and outgroups. These two genes are involved in the function of inner hair cells’ stereocilia movement.

Fig. 3.

A comparison of genomic selection between the BFC and other Felis species. (A) Plots of principal components 1, 2, and 3 from PCA analysis of Felis spp. (B) Distribution of ln (pi ratios) and Fst values calculated in 50-kb sliding windows with 25-kb increments between BFCs group and control group (including jungle cat, sand cat, and other five wildcat species). The data points in blue [corresponding to the top 5% of the empirical ln(pi ratios) distribution with values < = -3.485 and the top 5% of the empirical Fst distribution with values > 0.406] are genomic regions under selection in BFC group. (C) The top 20 KEGG pathways were identified by the functional enrichment tests on genes that are under selection from Tajima’s D test, and the most significant item is the metabolic pathway (P: 4.76E-05). The KEGG items with different colors were associated with metabolism (red), immune (blue), and nervous system (orange). (D) A region with significant genetic divergence and selection (Fst = 4.793 and π ratio = 2.652) between BFC and other contains three genes: MRPL30, MITD1 and LIPT1, and the pattern of genotypes shows the different between BFC (major allele) in yellow and others (minor allele) in blue.

Fig. 4.

Conservation genetics of the BFC. (A) PMSC analysis of the population history of eight Felis species during three major glacial periods, i.e. the LGM, Penultimate Glacial (PG) and Naynayxungla Glaciation (NG). (B) The levels of heterozygosity (Left) of small Felis species and big cats (Right). (C) The levels of FROHs (Left) of small Felis species compared with those of three big cats (Right). (D) The histogram exhibits the total ROH lengths of all 15 BFCs, and the landscape of the distribution of ROH fragments on 18 autosomes of the BFC individual BFC6 which was used for de novo genome assembly. (E) The 67 alleles of missense mutations detected in 29 amyloidosis-associated genes carried by 15 BFCs. The red colored boxes represent the missense SNPs compared with the reference genome of the BFC. The histogram at left shows the frequencies of the mutated alleles in 67 alleles of 15 BFCs. (F) The gene structure of TTR contains four exons in BFC with four SNPs. The missense deleterious mutation (ChrD3 52,756,499 G/A Gly23Ser) found at the first position of codon23 in the second exon of the TTR gene. The bottom diagram simply shows the process that abnormal deposits of TTR protein in various tissues and organs throughout the body.