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Sequencing Entering the ancient world: Paleogenomics is on the rise

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As next-generation sequencing technologies emerge on the market, experts believe they will be used for projects other than medical sequencing. This notion was reinforced in late December when scientists announced the first genome sequences from a woolly mammoth, which became extinct about 10,000 years ago. The project could signal the start of a sequencing trend in the nascent field of paleogenomics.

“The academic interest of being able to go back in time and recover potentially fairly complete genomic sequences for these Ice Age mammals
is huge,” says mammoth project participant

Ross MacPhee, curator of vertebrate zoology at the American Museum of Natural History.

The woolly mammoth was sequenced using 454 Life Sciences’ Genome Sequencer 20. Pennsylvania State University, which owns an instrument, collaborated with seven other partners to complete the project, including McMaster University in Canada and research institutions in Russia, the United Kingdom, France, and Germany.

Stephan Schuster, an associate professor at Penn State, says they wouldn’t have been able to do the project without the high-throughput instrument.

“There is a lot of bacterial contamination [in fossils], so typically you have to sequence an awful lot of bacteria in order to get your target,” says

Chris McLeod, chief operating officer and president of 454. Of the 28 million base pairs sequenced from the woolly mammoth sample, a little less than half, or around 13 million, actually belonged to the mammoth.

Ancient DNA is also highly fragmented, making it a nice fit for 454’s read length, which runs around 100 bases. And the sequencer compartmentalizes single DNA molecules prior to the amplification step in a lipid vesicle. “This way we avoid any amplification bias that occurs in pools of DNA,” Schuster says.

MacPhee says that through his museum’s collaboration with Penn, musk ox and woolly rhinoceros may be next in line for sequencing. He believes most ancient DNA sequencing will be done through collaborations between institutions that own a sequencer and those with expertise in ancient DNA. Leaders in ancient DNA research include the University of Adelaide in Australia, Lawrence Berkeley National Laboratory, Stanford University, Max Planck Institute for Evolutionary Anthropology, University College of London, and Oxford University. “These are the ones that ... would be expected to get on this paleogenomics high horse,” MacPhee says.

Some have already started.

Eddy Rubin, director of the Genomics Division at LBNL and director of the Joint Genome Institute, says he has started using 454’s instrument to “sequence several ancient samples.”
— Kate O’Rourke
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