Article (Scientific journals)
Improving the performance of true single molecule sequencing for ancient DNA.
Ginolhac, Aurélien; Vilstrup, Julia; Stenderup, Jesper et al.
2012In BMC Genomics, 13, p. 177
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Keywords :
Animals; Base Composition/genetics; Base Sequence; DNA/genetics; DNA, Mitochondrial/genetics; Fossils; Genome/genetics; Horses/genetics; Nucleotidases/metabolism; Nucleotides/genetics; Phylogeny; Sequence Analysis, DNA/methods/standards
Abstract :
[en] BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. RESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. CONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Ginolhac, Aurélien  ;  University of Copenhagen > Centre for Geogenetics
Vilstrup, Julia
Stenderup, Jesper
Rasmussen, Morten
Stiller, Mathias
Shapiro, Beth
Zazula, Grant
Froese, Duane
Steinmann, Kathleen E.
Thompson, John F.
Al-Rasheid, Khaled A. S.
Gilbert, Thomas M. P.
Willerslev, Eske
Orlando, Ludovic
More authors (4 more) Less
External co-authors :
yes
Language :
English
Title :
Improving the performance of true single molecule sequencing for ancient DNA.
Publication date :
2012
Journal title :
BMC Genomics
ISSN :
1471-2164
Publisher :
BioMed Central, United Kingdom
Volume :
13
Pages :
177
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 30 March 2016

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