Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
Hendrik N. Poinar,1,2,3*
Carsten Schwarz,1,2
Ji Qi,4
Beth Shapiro,5
Ross D. E. MacPhee,6
Bernard Buigues,7
Alexei Tikhonov,8
Daniel H. Huson,9
Lynn P. Tomsho,4
Alexander Auch,9
Markus Rampp,10
Webb Miller,4
Stephan C. Schuster4*
We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed 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.
1 McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
2 Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
3 Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
4 Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA.
5 Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, South Parks Road, Oxford, OX1 3PS, UK.
6 Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024, USA.
7 #2 Avenue de la Pelouse, F-94160 St. Mandé, France.
8 Zoological Institute, Russian Academy of Sciences, Universitetskaya nab.1, Saint Petersburg 199034, Russia.
9 Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany.
10 Garching Computing Center (RZG), Boltzmannstrasse 2, D-85748 Garching, Germany.
* To whom correspondence should be addressed. E-mail: poinarh{at}mcmaster.ca (H.N.P.); scs{at}bx.psu.edu (S.C.S.)
