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

Basler, N., Xenikoudakis, G., Westbury, M.V., Song, L., Sheng, G. and Barlow, A. ORCID: 0000-0002-5532-9458, 2017. Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone. BMC Research Notes, 10 (1): 754. ISSN 1756-0500

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Abstract

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.

Item Type: Journal article
Publication Title: BMC Research Notes
Creators: Basler, N., Xenikoudakis, G., Westbury, M.V., Song, L., Sheng, G. and Barlow, A.
Publisher: Springer
Date: 20 December 2017
Volume: 10
Number: 1
ISSN: 1756-0500
Identifiers:
NumberType
10.1186/s13104-017-3061-3DOI
1233243Other
Divisions: Schools > School of Science and Technology
Depositing User: Jonathan Gallacher
Date Added: 13 Nov 2019 11:43
Last Modified: 13 Nov 2019 11:43
URI: http://irep.ntu.ac.uk/id/eprint/38245

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