Optimizing ancient DNA recovery from archaeological plant seeds

Area of Science:

• Paleogenomics
• Archaeobotany
• Ancient DNA (aDNA) recovery

Background:

• Recovering ancient DNA (aDNA) from archaeobotanical remains is difficult due to DNA fragmentation, low copy numbers, and inhibitors.
• Existing methods often struggle with the low quality and quantity of DNA from ancient plant samples.

Purpose of the Study:

• To develop and evaluate a novel protocol for enhanced ancient DNA (aDNA) recovery from archaeobotanical remains.
• To improve the efficiency of downstream processes like Next-Generation Sequencing (NGS) library production.

Main Methods:

• Utilized a soil inhibitor-optimized reagent combined with an aDNA-specific silica binding step.
• Applied the protocol to ancient grape pips from two distinct archaeological sites.
• Assessed extract suitability for NGS library construction and sequencing.

Main Results:

• The new protocol demonstrated higher and more consistent aDNA yields compared to previous methods.
• Significantly improved NGS library production, especially for challenging samples.
• Successfully incorporated highly fragmented and damaged endogenous aDNA into sequencing libraries, preserving key metrics.

Conclusions:

• The developed protocol effectively enhances ancient DNA (aDNA) recovery from archaeobotanical samples.
• This advancement is crucial for future paleogenomic studies on historical and ancient plant remains.
• The method offers improved library production and sequencing outcomes for degraded DNA sources.