Advancing DNA extraction from experimental resin-preserved specimens

DNA extraction preserved in resin-like viscous materials still represents a challenge due to the presence of inhibitory substances, leading to the lack of standardized protocols. Nevertheless, these materials have the potential to offer a wide range of information, e.g. in modern and archaeological samples. Here, three different extraction approaches based on phenol/chloroform/treatment were tested. We tested: (a) the performance of the PB buffer of the Qiagen MinElute PCR Purification Kit versus a homemade Dabney binding buffer, (b) the effect of a treatment with bleach solution, and (c) different final elution volumes. The samples studied were made of adhesive material from pine resin, crushed pine charcoal, and beeswax, obtained from experimental sickles which were replicated from Neolithic specimens. The resin was sampled before and after using the experimental sickles on the field to harvest Triticum aestivum. To evaluate the efficiency of the protocol we measured the DNA concentration for each test and performed a metagenomic analysis on the retrieved high-throughput shotgun sequencing data. Higher DNA concentration levels were found on the outer layer of the resin obtained after harvesting. Moreover, no significant differences were found between tests with PB buffer and Dabney buffer. On the other hand, those samples that were subjected to bleach treatment, yielded the smallest amounts of DNA, while reducing the elution buffer volume had a positive effect. Metagenomic analyses revealed a strong presence of wheat DNA together with commonly associated microorganisms. In this study we provide an efficient method for extracting DNA from adhesive resin-like viscous material. Taxonomic analysis of the retrieved genetic material showed that DNA was acquired exclusively during harvesting, highlighting the potential of molecular analysis on similar materials, not only in an ecological but also in an archaeological context.