NEW YORK (GenomeWeb News) – An international team led by investigators at BGI-Shenzhen, Lanzhou University, and the Chinese Academy of Sciences has sequenced and started analyzing a draft version of the domestic yak genome, uncovering genetic adaptations that appear to assist the animal with life at high altitudes.
As they reported online yesterday in Nature Genetics, the researchers did genome and transcriptome sequencing on a female yak that had lived in a high altitude Chinese province neighboring Tibet. They also did transcriptome sequencing on samples from five different tissue types collected from the same animal.
Along with its identification of SNPs and predicted protein-coding genes in the yak, the group did comparative genomic analyses between yak and cattle, a closely related animal that typically lives at much lower altitudes. The analyses uncovered expansions to sensory perception and energy metabolism-related gene families in the yak. In addition, it pointed to signs of positive selection in yak metabolic genes and genes related to low oxygen conditions, or hypoxia.
Going forward, researchers say, such insights are expected to not only clarify the genetic features behind agriculturally important traits in the yaks and other animals living under similar conditions, but could also fuel research into human conditions linked to altitude sickness or hypoxia.
"The identification of genes required for natural high-altitude adaptation may help to improve current understanding, treatment, and prevention of altitude sickness and other hypoxia-related diseases in humans," they noted.
"In addition, this report of the yak genome sequence, together with the many [single nucleotide variants] identified will facilitate genetic dissection of agronomically important traits in the species and will accelerate the genetic improvement of milk and meat production in this animal that is essential to the lifestyle and economy of the Tibetan people," they added.
The researchers sequenced the yak genome with the Illumina HiSeq 2000 using genomic DNA from the liver of a female yak from the Qinghai-Tibetan Plateau in China's Qinghai Province. With this sequence data, they put together an almost 2.7 billion base draft yak genome assembly that had 65 times coverage, on average, and at least 20-fold coverage over 98 percent of the assembly.
They also used the HiSeq 2000 to sequence RNA from fresh heart, liver, brain, stomach, and lung samples collected from the same yak.
Based on this RNA-sequence data, combined with gene prediction models and sequence homology information, the team estimated that the yak genome contains 22,282 protein-coding genes. They also tracked down some 2.2 million heterozygous SNPs within the female yak's genome.
When they compared the genome to those of other animals, the researchers identified 362 gene families that were shared between yak and cattle, but missing from the genomes of dogs and humans.
Within other 100 gene families that were specific to yak alone, meanwhile, the team saw a slew of genes contributing to scent detection, defense, and immunity.
Almost 600 more gene families were expanded in the yak genome compared to those of cattle, humans, dogs, and several other mammals, meanwhile. Again, olfactory genes were over-represented, as were genes contributing to other types of sensory and taste perception and energy metabolism.
Such features are consistent with some of the traits that have been described for the yak in the past, such as their high metabolism, acute senses, impressive foraging ability, enlarged hearts and lungs, and a lack of blood vessel constriction in the lungs when faced with relatively low oxygen conditions.
Patterns in the domestic yak and cattle genome indicate that the animals diverged from one another around 4.9 million years ago — around the same time as the human-chimpanzee split, the study's authors noted. Since then, many of the yak and cattle genes have remained very similar, with the two animals sharing 45 percent protein identity and 99.5 percent protein similarity.
Nevertheless, the researchers did track down intriguing signals of selection in yak and cattle genes. In the yak, for instance, genes involved in hypoxia response, energy metabolism, and nutrition were over-represented amongst genes showing signs of positive selection.
Follow-up functional analyses of such genes are expected to offer even more insights into animal adaptation to life at high altitude, according to the study's authors, as are studies comparing yak response to high altitude with those of other animals living in similar conditions.
The team has submitted whole-genome shotgun sequence data from the study to GenBank, The European Molecular Biology Laboratory, and the DNA Data Bank of Japan. Mitochondrial sequence data, short-read data, and transcriptome data from the yak genome study are being made available through GenBank, the Short Read Archive, and the Gene Expression Omnibus, respectively.