The tiger genome and comparative analysis with lion and snow leopard genomes

Abstract

Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.

Figure 1. Relationship of the tiger to other mammalian species.

(a) Orthologous gene clusters in mammalian species. The Venn diagram shows the number of unique and shared gene families among seven mammalian genomes. (b) Gene expansion or contraction in the tiger genome. Numbers designate the number of gene families that have expanded (green, +) and contracted (red, −) after the split from the common ancestor. The most recent common ancestor (MRCA) has 17,841 gene families. The time lines indicate divergence times among the species.

Figure 2. EGLN1 and TYR mutations related to hypoxia in snow leopard and white fur in white lion.

(a) Alignment of mammalian EGLN1 amino-acid sequences. Amino acids unique to the snow leopard (216th residue in human EGLN1), naked mole rat and rodents are shown in red, grey and blue, respectively. The number of individuals genotyped in this study is listed in parentheses. (b) Alignment of mammalian TYR sequences. Amino-acid sequences unique to the white lion (87th residue in human TYR) are shown in red, and tawny lion having heterozygous allele (G/A) are shown in grey; X represents amino acid of R/Q. The numbers in parentheses are number of individuals. ‘w’ denotes white type and ‘wt’ denotes wild type.

Figure 3. Synteny blocks between tiger and cat genomes.

Domestic cat chromosomes are shown as grey bars (in Mb scales). The other six color bars (in Mb scales) are tiger scaffolds with syntenic break between tiger and cat (2 inter- and 4 intra-chromosomal rearrangements). The tiger and cat rearrangements were detected using dog genome as an out-group.

Figure 4. Genetic diversity and population size history in Panthera species.

(a) Rate of heterozygous SNVs in Panthera species. The heterozygous SNVs rates (y axis) were calculated by dividing the total number of heterozygous SNVs by genome size. Individuals that are white colored in nature (white tiger and white lion) are shown in grey. Tigers, lions, cat, gorilla, giant panda, chimpanzee and naked mole rat are captive bred. Snow leopard, orang-utans and Tasmanian devil are wild caught individuals. (b) Estimated big cat population sizes and climate history from 2.5 kyr BP to 3 Myr BP. Tsuf, atmospheric surface air temperature; RSL, relative sea level; 10 m.s.l.e., 10 m sea level equivalent; TG, Amur tiger; LN, African lion; SL, snow leopard; WTG, white tiger; WLN, white African lion. ‘F’ after the species abbreviation means the data were generated from comparison with Felis_catus-6.2 as a reference genome in SNV calling.