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Comparative Genomics Offers Hints to Molecular Adaptations in Woolly Mammoth Genomes

NEW YORK (GenomeWeb) – A Pennsylvania State University-led team is using comparative genomics to start untangling molecular features that may have contributed to the woolly mammoth's characteristic traits and ability to withstand chilly Arctic environments.

As they reported online today in Cell Reports, the researchers sequenced the complete genomes of two woolly mammoths and three Asian elephants. By comparing the mammoth and elephant sequences to one another, they were able to start picking out and functionally validating derived alleles suspected of being functionally important in the mammoth.

The search led to variants in genes from lipid, adipose tissue, skin, and hair development pathways, for example, along with components of pathways contributing to circadian rhythm and temperature sensation.

The study's authors are interested in tackling other ancient genomes in the future, provided sufficient funding falls into place.

"We want to parlay this into a large operation to sequence ancient genomes," co-corresponding author Webb Miller, a comparative genomics and bioinformatics researcher at Pennsylvania State University, told GenomeWeb. "There are many scientific … and other forensic issues one can address if one knows how to sequence and analyze DNA this old."

The work is the latest in a series of ancient DNA sequencing studies focused on the woolly mammoth, which lived in cold, northern sites where preservation was more prone to occur.

In a study published earlier this year in Current Biology, for example, researchers from the Swedish Museum of Natural History and elsewhere did genome sequencing on a 45,000-year-old mammoth from Siberia and a 4,300-year-old mammoth from Wrangel Island to get a look at population patterns in the mammoth leading up to its extinction.

In contrast, authors of the current analysis focused on finding molecular features in the mammoth genome that could offer clues to the animal's distinctive features, such as the lush fur, small ears and tails, and suspected differences in temperature detection that made it adept at surviving extreme cold.

Because Asian elephants and mammoths are thought to belong to a lineage that split off from the African Savannah elephant lineage roughly 7 million years ago, Miller and colleagues reasoned that sequences conserved in African elephants, Asian elephants, and other animals — but altered in the woolly mammoth — likely represent derived mammoth alleles.

For their sequencing effort, the researchers focused on woolly mammoth from two clades that are thought to have diverged from one another some 1.5 million years ago — long after the Asian elephant and woolly mammoth lineages separated some 5 million years ago.

Miller and colleagues sequenced DNA from the same 20,000-year-old and 60,000-year-old mammoth individuals for a study published in Nature in 2008.

They have since used Illumina sequencing instruments to generate 20-fold coverage of each mammoth genome, on average, while sequencing three living Asian elephant genomes to average depths of around 30-fold apiece.

By aligning these sequences to an African elephant reference genome, the team detected tens of millions of apparent SNPs across the three species. That collection included more sequences encoding more than 2,000 apparent amino acid substitutions and dozens of early stop codons that were derived in the mammoths but found in their ancestral form in Asian and African elephants.

When the researchers looked more closely at the mammoth-derived alleles, they saw functional enrichment for pathways involved in everything from skin, hair, and adipose tissue development to circadian cycles, fat digestion, lipid metabolism, insulin signaling, and temperature sensing.

The team was particularly intrigued by mammoth-specific changes in a handful of genes coding for so-called "temperature-sensitive, receptor potential channel" (thermoTRP)-coding genes, which code for pore proteins that respond to temperature.

Following modeling of temperature-responsive channels containing woolly mammoth substitutions in such proteins, the researchers did more detailed analyses on the thermoTRP-coding gene TRPV3, which showed ties to temperature sensation, skin composition, and hair growth in past studies.

In that protein, they uncovered a woolly mammoth substitution at a site conserved in the Asian elephant, African elephant, and dozens of other animals, Miller noted. "To me, that says, 'This is really doing something, and it's doing something different in the woolly mammoth.'"

Indeed, the team's functional assays in a human embryonic cell line suggested the mammoth-derived form of TRPV3 produced a channel protein with diminished temperature sensation, hinting that such searches can uncover authentic woolly mammoth molecular adaptations.

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