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Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone

  • Objective: A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism’s remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but vary-ing results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).Results: Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation atObjective: A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism’s remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but vary-ing results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).Results: Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine–cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeog-enomic studies, providing sufficient material is available.show moreshow less

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Metadaten
Author details:Nikolas BaslerORCiD, Georgios Xenikoudakis, Michael V. WestburyORCiDGND, Lingfeng Song, Guilian Sheng, Axel BarlowORCiDGND
URN:urn:nbn:de:kobv:517-opus4-428151
DOI:https://doi.org/10.25932/publishup-42815
ISSN:1866-8372
Title of parent work (German):Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
Publication series (Volume number):Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (715)
Publication type:Postprint
Language:English
Publication year:2017
Publishing institution:Universität Potsdam
Release date:2019/05/28
Tag:Ailuropoda melanoleuca; ancient DNA (aDNA); bleach; endogenous content; giant panda; next generation sequencing (NGS); palaeogenomics; paleogenomics; pre-digestion
Issue:715
Number of pages:7
Source:BMC Research Notes 10 (2017) Art. 754 DOI: 10.1186/s13104-017-3061-3
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät
DDC classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Peer review:Referiert
Publishing method:Open Access
Grantor:BioMed Central
License (German):License LogoCC-BY - Namensnennung 4.0 International
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