Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Area of Science:

• Marine biology
• Paleogenomics
• Molecular ecology

Background:

• Marine sedimentary ancient DNA (sedaDNA) is crucial for reconstructing past ocean ecosystems.
• Low DNA preservation in subseafloor sediments and a lack of authentication tools limit sedaDNA studies.
• Metagenomic data analysis for sedaDNA presents significant bioinformatic challenges.

Purpose of the Study:

• To improve the detection and authentication of marine eukaryote sedaDNA in subseafloor sediments.
• To develop and validate new bioinformatic tools and techniques for sedaDNA analysis.
• To investigate DNA damage profiles in marine phytoplankton over geological timescales.

Main Methods:

• Application of hybridization capture baits (Planktonbaits1 and HABbaits1) to target marine eukaryote sedaDNA.
• Utilizing the bioinformatics tool HOPS for sedaDNA authentication.
• Development of a new proxy, "% eukaryote sedaDNA damage", correlated with subseafloor depth.

Main Results:

• Hybridization capture increased eukaryote relative abundance by 4-fold (Planktonbaits1) and 9-fold (HABbaits1) compared to shotgun sequencing.
• The HOPS tool and the new damage proxy successfully authenticated sedaDNA components.
• The first DNA damage profiles for the marine phytoplankton Emiliania huxleyi were reported, showing correlation with depth.

Conclusions:

• The developed hybridization capture and bioinformatics approach significantly enhances marine eukaryote sedaDNA recovery and authentication.
• The "% eukaryote sedaDNA damage" proxy provides a reliable measure of sedaDNA authenticity and its relationship with depositional depth.
• This study opens new possibilities for studying the long-term evolution and ecological changes of marine eukaryotes across geological time.