Optimizing ancient DNA recovery from archaeological plant seeds

Paleogenomics has recently expanded its applications, including studies on plant remains to trace evolution and domestication. However, recovering ancient DNA (aDNA) from archaeobotanical remains is challenging due to the highly fragmented nature of endogenous aDNA, low copy numbers and inhibitors that hinder further manipulation and analysis. In this study, we explored the application of a reagent optimized against soil inhibitors, typically used in sediment DNA extraction, coupled with an aDNA-specific silica binding step, to improve and maximize the recovery of processable aDNA. Ancient grape pips were used as starting material. The approach was evaluated in two archaeological contexts, assessing the suitability of extracts for downstream processing, including NGS library production and sequencing. In conclusion, we demonstrated the protocol was effective in recovering aDNA, achieving higher yields and more consistent performance across sites compared to previous extraction methods. It significantly improved the library production step, particularly in challenging sites. Finally, we have shown it successfully allowed to incorporate into sequencing libraries the highly fragmented and damaged endogenous aDNA from ancient samples, while preserving read yield, library complexity and other sequencing metrics. Future studies on historical and ancient plant remains will benefit from these advancements in high-quality aDNA recovery.