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

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

Fersiynau electronig

Dangosydd eitem ddigidol (DOI)

  • Nikolas Basler
    University of Potsdam
  • Georgios Xenikoudakis
    University of Potsdam
  • Michael V. Westbury
    University of Potsdam
  • Lingfeng Song
    China University of Geosciences, Wuhan
  • Guilian Sheng
    China University of Geosciences, Wuhan
  • Axel Barlow
    University of Potsdam
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 varying 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 palaeogenomic studies, providing sufficient material is available
Iaith wreiddiolSaesneg
Rhif yr erthygl754
CyfnodolynBMC Research Notes
Cyfrol10
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 20 Rhag 2017
Cyhoeddwyd yn allanolIe
Gweld graff cysylltiadau