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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
True single-molecule DNA sequencing of a pleistocene horse bone
Genome Research, Volume 21, No. 10, Year 2011
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Description
Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules, as required for second-generation sequencing, introduce biases into the data that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by threefold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 39 ends of ancient templates, indicating the presence of 39-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches. © 2011 by Cold Spring Harbor Laboratory Press.
Authors & Co-Authors
Orlando, Ludovic A.A.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Ginolhac, Aurélien
Denmark, Copenhagen
Statens Naturhistoriske Museum
Raghavan, Maanasa
Denmark, Copenhagen
Statens Naturhistoriske Museum
Vilstrup, Julia T.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Rasmussen, Morten
Denmark, Copenhagen
Statens Naturhistoriske Museum
Magnussen, Kim
Denmark, Copenhagen
Statens Naturhistoriske Museum
Steinmann, Kathleen E.
United States, Cambridge
Applications
Kapranov, Philipp
United States, Cambridge
Applications
Thompson, John F.
United States, Cambridge
Applications
Zazula, Grant D.
Canada, Whitehorse
Gouvernement du Yukon
Froese, Duane
Canada, Edmonton
University of Alberta
Moltke, Ida
Denmark, Copenhagen
Københavns Universitet
Shapiro, Beth
United States, University Park
Pennsylvania State University
Hofreiter, Michael
United Kingdom, York
University of York
Al-Rasheid, Khaled A.S.
Saudi Arabia, Riyadh
College of Sciences
Gilbert, Thomas M.P.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Willerslev, Eske
Denmark, Copenhagen
Statens Naturhistoriske Museum
Statistics
Citations: 149
Authors: 17
Affiliations: 8
Identifiers
Doi:
10.1101/gr.122747.111
ISSN:
10889051
e-ISSN:
15495469
Research Areas
Genetics And Genomics
Health System And Policy