Abstract
ABSTRACTDNA extraction and library preparation are crucial steps in any ancient DNA study. Although palaeogenomic researchers are facing a growing choice of DNA extraction and sequencing library preparation methods, how their performance varies with DNA preservation remains unclear. To help elucidate this question, we compared the performance of two common DNA extraction and Illumina library preparation methods on a set of archaeological human samples, considered to contain ancient DNA of intermediate to good preservation (5–50% endogenous DNA). Results indicate that while the levels of contamination and endogenous DNA recovered are comparable for both silica-in-solution and silica-column based extractions, the ability of the former to accommodate larger starting quantities of sample material confers notable benefits with regards to library complexity, and furthermore seems to aid with the recovery of shorter endogenous DNA molecules. While our observations gained from comparing the single-stranded with double-stranded DNA library construction methods largely replicate earlier observations, the combination of our data with previously published datasets demonstrate that the benefits gained using single-stranded methods are inversely proportional to the endogenous DNA content in the ancient sample.
Highlights
IntroductionSequencing (HTS) technologies and associated developments in laboratory methodologies dedicated to the generation of palaeogenomic data from archaeological and historic samples
The research potential offered by ancient DNA has expanded enormously over the last decade thanks to the introduction of High-ThroughputSequencing (HTS) technologies and associated developments in laboratory methodologies dedicated to the generation of palaeogenomic data from archaeological and historic samples
To help elucidate this question, we compared the performance of two common DNA extraction and Illumina library preparation methods on a set of archaeological human samples, considered to contain ancient DNA of intermediate to good preservation (5–50% endogenous DNA)
Summary
Sequencing (HTS) technologies and associated developments in laboratory methodologies dedicated to the generation of palaeogenomic data from archaeological and historic samples While these innovations have revolutionized the field by enabling genomicscale analyses (Shapiro and Hofreiter 2014; Der Sarkissian et al 2015; Orlando et al 2015), optimization of all steps in the data generation and analytical process can further reduce costs and increase data output. DNA extraction and HTS library preparation methods stand at the beginning of any palaeogenomic study. In both cases, ideal methods should maximize the potential for sequencing endogenous DNA, at the exclusion of contaminants and exogenous sources of DNA.
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