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Tiger, lion and leopard genomes revealed assisting big cats' conservation

23.09.2013
The latest study was published online in Nature Communications

An international team led by South Korea's Personal Genomics Institute and BGI unraveled the first whole genome of a 9-year-old male Amur tiger (Panthera tigris altaica), and compared it with the genomes of other big cats including the white Bengal tiger, lions, and snow leopards. The genomic data from this study provides an invaluable resource for the future studies of big cats and their whole family's conservation. The latest study was published online in Nature Communications.

Despite big cats' reputation for ferocity, these majestic species face more danger than they pose: All are endangered, mainly due to habitat loss, poaching, and dwindling food supplies. As the largest felid species on earth, tiger has become one of the world's most endangered species. Understanding of tiger's genetic diversity and demography has been very limited without the whole-genome sequence of tiger, or any of the Panthera species.

In this study, researchers sequenced the whole genome of an Amur tiger, also known as the Siberian tiger, and assembled it using BGI self-developed software SOAPdenovo. The Amur tiger genome was predicted to contain 20,226 protein-coding genes and 2,935 non-coding RNAs, and was enriched in olfactory receptor sensitivity, amino-acid transport, and metabolic-related genes, among others. Additionally, researchers found that the Amur tiger genome showed more than 95 percent similarity to the genome of domestic cat.

Researchers also sequenced the genomes of other Panthera-a white Bengal tiger, an African lion, a white African lion, and a snow leopard-using next-gen sequencing technology, and aligned them using the genome sequences of tiger and domestic cat. They discovered a number of Panthera lineage-specific and felid-specific amino acid changes that may affect the metabolism pathways. These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet.

Furthermore, the team revealed the evidence that the 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.

Previous studies showed that the human loci EGLN1 (Egl nine homologue 1) and EPAS1 (endothelial PAS domain-containing protein 1) are two key factors for mediating high-altitude adaptation. In this study, the team found that the snow leopard had unique amino-acid changes in both genes that may have contributed to snow leopard's acquisition of an alpine, high altitude ecological niche.

In addition, researchers found that white lions contain a variant in the TYR gene. Variants in TYR were previously reported to be related with white coat color in domestic cats as well as with 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.

When observing the species' genetic diversity, researchers found the genetic diversity of tiger and lion were similar to that of human. Interestingly, the diversity of snow leopard genome was nearly half that of the other Panthera species and slightly lower than that of the Tasmanian devil.

The Amur tiger genome is the first reference genome sequenced from the Panthera lineage and the second from the Felidae species. The data from tigers, lions and snow leopards provides a rich and diverse genome resource that could be used in future studies of conservation and population genomics. Genetics underpins the 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.

About BGI

BGI was founded in Beijing, China, in 1999 with the mission to become a premier scientific partner for the global research community. The goal of BGI is to make leading-edge genomic science highly accessible, which it achieves through its investment in infrastructure, leveraging the best available technology, economies of scale, and expert bioinformatics resources. BGI, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.

BGI has a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research: research that has generated over 200 publications in top-tier journals such as Nature and Science. BGI's many accomplishments include: sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, more recently, have sequenced the human Gut Metagenome, and a significant proportion of the genomes for the1000 Genomes Project. For more information about BGI, please visit http://www.genomics.cn.

Contact information:

Bicheng Yang
Public Communication Officer
BGI
+86-755-82639701
yangbicheng@genomics.cn

Jia Liu | EurekAlert!
Further information:
http://www.genomics.cn

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