Comparison of target enrichment strategies for ancient pathogen DNA

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA, and targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – (1) array-based hybridization capture and in-solution capture using either (2) RNA or (3) DNA baits – have different characteristics that may influence the capture efficiency, specificity, and reproducibility. Here, we compared their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum of 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens, and RNA baits usually perform better than DNA baits. Method summary We compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity, and reproducibility for ancient and modern Mycobacterium leprae and Treponema pallidum samples. Array-based capture and in-solution capture with RNA and DNA baits were all tested in three independent replicates.