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Researchers Present Genomic Analysis of Tiger and Other Big Cat Genomes

NEW YORK (GenomeWeb News) – The genomes of big cats like tigers, lions, and snow leopards show hints of genetic changes that allow them to subsist on a largely carnivorous diet as well as other adaptations, researchers from South Korea's Personal Genomics Institute, BGI-Shenzhen in China, and elsewhere reported in Nature Communications today.

According to the International Union for Conservation of Nature, there are some 3,200 tigers living in the wild. Other big cats are also listed as vulnerable or endangered species and have similarly low population numbers, with about 39,000 lions and approximately 5,000 snow leopards in the wild.

Through sequencing the whole genome of an Amur tiger, also known as the Siberian tiger, and comparing it with sequences from a white Bengal tiger, an African lion, a white African lion, and a snow leopard, the researchers, led by BGI's Jun Wang and the Personal Genomics Institute's Jong Bhak, also glimpsed other molecular adaptations belonging to the cats, such as a snow leopard-specific variant that may enable it to live at higher altitudes and a variant that may be behind the color of the white lion's coat.

"This genetic variation comparison using whole genomes among species and subspecies can thus provide valuable insight and information for the whole family's conservation," Wang, Bhak, and their colleagues wrote.

To generate a genome sequence and assembly for the Amur tiger, Panthera tigris altaica, the researchers collected DNA from a male, nine-year-old tiger living in Everland Zoo in Korea and sequenced it to nearly 84x coverage using the Illumina HiSeq 2000. They then assembled it using SOAPdenovo and found that it shows more than 95 percent similarity to the domestic cat genome.

Additionally, they predicted the Amur tiger genome to contain 20,226 protein-coding genes and 2,935 non-coding RNAs. The tiger genome is, the researchers noted, enriched in olfactory receptor sensitivity, amino-acid transport, and metabolic-related genes, among others. The tiger and cat genomes also appeared to contain similar numbers of repeats and transposable elements.

The investigators also sequenced genomes from other Panthera — a white Bengal tiger, an African lion, a white African lion, and a snow leopard —using the HiSeq 2000, and aligned them using the tiger and domestic cat genomes.

From this, they uncovered a number of Panthera lineage-specific and felid-lineage specific amino acid changes, including ones predicted to have a functional impact. For example, genes with Panthera-specific changes were enriched in protein, fatty acid, and amino acid metabolic pathways.

"These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet," the researchers noted.

Further, genes related to muscle strength as well as energy metabolism and sensory nerves, including olfactory receptor activity and visual perception, appeared to be undergoing rapid evolution in the tiger.

The researchers also investigated traits of the other big cats. As snow leopards typically live in higher altitudes, they examined whether they harbored variants in the EGLN1 and EPAS2 genes, which have been linked to high-altitude living.

Snow leopards, they found, have unique amino acid changes in the proteins those genes encode that the other cats lack. For instance, they uncovered a methionine to lysine change in EGLN1 that appears to lead to a difference in protein charge that the researchers say may affect its function.

"[T]hese EGLN1 and possibly EPAS1 variants are provocative candidates that may have contributed to the snow leopard's acquisition of an alpine, high altitude ecological niche," the researchers added.

In addition, the researchers found that white lions contain a variant in the TYR gene — variants in TYR previously had been linked to white coat color in domestic cats as well as to a form of albinism in people. The white lion variant appeared to lead to an amino acid change that seems to affect the charge of the resulting protein.

For the tiger, the researchers also noted that the within-species diversity appeared to be similar to that of people, but the snow leopard had low diversity levels, closer to that of the Tasmanian devil.

"Our data from tigers, lions, and snow leopard can provide a rich and diverse genome resource that could be used in future studies of conservation and population genomics so that the genetic underpinnings of local adaptation and potential inbreeding and/or outbreeding in wild and captive populations can be illuminated and thereby help ensure the future survival of these majestic species," Wang, Bhak, and their colleagues added.