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Published Online December 20, 2005
Science DOI: 10.1126/science.1123360

Reports

Submitted on December 2, 2005
Accepted on December 15, 2005

Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Hendrik N. Poinar 1*, Carsten Schwarz 2, Ji Qi 3, Beth Shapiro 4, Ross D. E. MacPhee 5, Bernard Buigues 6, Alexei Tikhonov 7, Daniel Huson 8, Lynn P. Tomsho 3, Alexander Auch 3, Markus Rampp 9, Webb Miller 3, Stephan C. Schuster 3*

1 McMaster Ancient DNA Center; Department of Anthropology; Pathology & Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
2 McMaster Ancient DNA Center; Department of Anthropology
3 Penn State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA.
4 Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, South Parks Road, Oxford, OX1 3PS, UK.
5 Division of Vertebrate Zoology/Mammalogy American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024, USA.
6 #2 Avenue de la Pelouse, F-94160 St Mandé France.
7 Zoological Institute, Russian Academy of Sciences, Universitetskaya nab.1, Saint-Petersburg 199034, Russia.
8 Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany.
9 Garching Computing Center (RZG), Boltzmannstrasse 2, D-85748 Garching, Germany.

* To whom correspondence should be addressed.
Hendrik N. Poinar , E-mail: poinarh{at}mcmaster.ca
Stephan C. Schuster , E-mail: scs{at}bx.psu.edu

We sequenced 28 million base pairs of DNA in a metagenomics approach using a woolly mammoth (Mammuthus primigenius) sample from Siberia. Thanks to exceptional sample preservation and use of a novel emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.


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