Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

Area of Science:

• Ancient DNA (aDNA) research
• Next-generation sequencing (NGS)
• Molecular biology techniques

Background:

• Second-generation sequencing technologies have advanced ancient DNA (aDNA) studies.
• Targeted capture-enrichment methods can enhance aDNA recovery from degraded samples with low endogenous DNA content.

Purpose of the Study:

• To evaluate the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems for ancient DNA (aDNA) enrichment.
• To identify factors influencing aDNA capture experiments using ancient maize samples.

Main Methods:

• Construction of Illumina sequencing libraries from ancient maize.
• Application of Agilent SureSelect and Mycroarray MySelect in-solution capture systems.
• Analysis of target enrichment efficiency and biases introduced by sample characteristics.

Main Results:

• High levels of clonality and the presence of multi-copy sequences in targets caused data biases, irrespective of the capture method used.
• Neither SureSelect nor MySelect consistently outperformed the other in average target enrichment.
• No significant difference in performance was observed between two different tiling designs.

Conclusions:

• Targeted capture-enrichment is a viable method for recovering aDNA from ancient plant materials like maize.
• Clonality and repetitive sequences are critical factors to consider, as they can introduce biases in aDNA capture experiments.
• The study provides practical recommendations for optimizing targeted sequencing strategies in aDNA research.