The tiger proteome contained 14,954 orthologous gene families. To create a detailed annotation of the tiger proteome, gene clusters were constructed using seven mammalian genomes (tiger, cat, human, dog, mouse, giant panda and opossum). The assembled Amur tiger genome was predicted to contain 20,226 protein-coding genes ( Supplementary Tables S19–S23, Supplementary Methods) and 2,935 non-coding RNAs ( Supplementary Table S24, Supplementary Methods). For comparative genomic analysis of big cats, we also sequenced four other Panthera genomes ( Table 1, Supplementary Tables S1 and S18): a white Bengal tiger ( Panthera tigris tigris), an African lion, a white African lion and a snow leopard their genome sequences were aligned with the domestic cat and tiger genomes. S5, Supplementary Tables S12–S17, Supplementary Methods). This high similarity allowed us to improve the assembly of the tiger genome by using the recently completed high coverage (12 × coverage) domestic cat genome ( Supplementary Fig. The tiger genome sequence shows 95.6% similarity to the domestic cat ( Supplementary Table S11) from which it diverged approximately 10.8 million years ago (MYA) 15 human and gorilla have 94.8% similarity and diverged around 8.8 MYA (from TimeTree). Additionally, analysis of the tiger draft genome assembly for core eukaryotic genes 14 revealed homologues for >93.4% of conserved genes in the assembly ( Supplementary Table S10). Assembly quality was assessed by aligning the assembled tiger blood transcripts and cat EST sequences onto the tiger scaffolds (>96% coverage and 98.9% mapping rate, respectively), and heterozygous single nucleotide variants (SNVs) were validated by the Sanger method ( Supplementary Tables S6–S9, Supplementary Methods). Sequence reads were assembled using SOAPdenovo 13 into scaffolds (2.4 Gb in length) having an N50 length of 8.84 Mb (contig N50 length of 29.8 kb Table 1, Supplementary Figs S2–S4, Supplementary Tables S4 and S5, Methods). The DNA of a 9-year-old male Amur tiger from Everland Zoo in Korea was sequenced by Illumina HiSeq2000 ( Supplementary Fig. Panthera whole-genome sequences provide valuable information on genome organization, evolutionary divergence and overall endemic diversity.
We describe genotypic variation and genotype association analyses with species-specific phenotypes and adaptation. We report the first tiger genome sequence assembly and annotation as well as a comparative analysis of the lion ( Panthera leo) and snow leopard ( Panthera uncia) genomes. However, no whole-genome reference sequence has been reported for the tiger, or any of the Panthera species, thus limiting current understanding of genetic diversity and demography 10, 11, 12. Previous genetic studies using mitochondrial and nuclear loci have helped to elucidate the phylogeography and population genetics of tigers 1, 5, 6, 7, and the low coverage genome (1.8 × ) of the domestic cat ( Felis catus) has provided insights into felid evolution 8, 9. The Amur tiger ( Panthera tigris altaica) is the largest in overall size and the only subspecies inhabiting snow-covered regions.
Four of these went extinct in the wild during the last century (Javan, Balinese, South China and Caspian tigers), leaving five extant subspecies (Amur, Bengal, Indochinese, Malayan and Sumatran tigers) 5. Tigers comprise of nine genetically validated subspecies 1, 5, 6. It is postulated that without conservation measures tigers will soon become extinct in the wild, thus turning the preservation of existing wild tiger populations into a major goal of conservation efforts 3, 4. The current estimates of wild tigers range from just 3,050 to 3,950 individuals. Tigers are a keystone species and natural indicators of the health of the ecological communities in which they are found 2.
The tiger ( Panthera tigris), the largest felid species on Earth and a widely recognized symbol for wildlife conservation 1, is one of the world’s most endangered species.
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