A framework for optimising arthropod DNA quality and quantity for modern sequencing tools using hard ticks (Ixodidae)

Area of Science:

• Genomics
• Molecular Biology
• Arthropod Research

Background:

• Advanced sequencing technologies demand high-quality DNA input and integrity.
• Extracting pure, endogenous DNA from small arthropods with mixed DNA sources (arthropod, host, microbiome) presents a significant challenge.

Purpose of the Study:

• To optimize DNA extraction methods for small arthropods, focusing on yield, quality, and composition.
• To identify the best combination of tissue types, disruption methods, and extraction kits for DNA suitable for advanced sequencing.

Main Methods:

• Evaluated three tissue types: Whole, Bisected, and Legs.
• Assessed three disruption methods: Undisrupted, Sliced, and liquid nitrogen bead Homogenisation.
• Compared two DNA extraction kits: Qiagen DNeasy Blood & Tissue and MagAttract High Molecular Weight.

Main Results:

• The MagAttract HMW kit increased large DNA fragments (20-48.5 kbp) 11-fold compared to the DNeasy kit.
• Aggressive homogenization yielded more short DNA fragments (97%, 1-10 kbp).
• Whole-Homogenised specimens gave the highest DNA concentration (198 ng µL⁻¹), while Bisected-Undisrupted specimens had more large fragments (3.15%).

Conclusions:

• Selecting appropriate DNA extraction kits and methods is vital for obtaining optimal DNA quality for advanced sequencing.
• Provides guidelines for DNA extraction from small arthropods (10-20 mg), considering DNA quantity, quality, and composition.