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

X W Barton; S S Tobe; J B Fontaine; C L Oskam

doi:10.1007/s00436-025-08583-0

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

Journal article

Open access

Peer reviewed

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

X W Barton, S S Tobe, J B Fontaine and C L Oskam

Parasitology research (1987), Vol.125(1), 5

2026

DOI: https://doi.org/10.1007/s00436-025-08583-0

PMID: 41493496

Appears in Open Access via Read & Publish Agreements

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Abstract

Amblyomma - genetics

Animals

DNA - genetics

DNA - isolation & purification

Ixodidae - genetics

Sequence Analysis, DNA - methods

Specimen Handling - methods

Advanced sequencing technologies require strict standards for DNA input and integrity. This study addresses the challenge of extracting high-quality, endogenous DNA from smaller arthropods with mixed DNA sources (arthropod, host, and microbiome), using Amblyomma triguttatum as a model organism. We evaluated three tissue types (Whole, Bisected, and Legs), three disruption methods (Undisrupted, Sliced, and liquid nitrogen bead Homogenisation), and two extraction kits (Qiagen DNeasy Blood & Tissue and MagAttract HMW) to optimise DNA yield, quality, and composition. The Qiagen MagAttract High Molecular Weight Kit significantly increased the proportion of large DNA fragments (20-48.5 kbp) by 11-fold compared to the Qiagen DNeasy Blood & Tissue Kit. Aggressive homogenisation methods produced the highest proportion of short fragments (97%, 1-10 kbp). Whole-Homogenised specimens yielded the highest DNA concentration (198 ng µL⁻¹), whereas Bisected-Undisrupted specimens achieved 146 ng µL⁻¹ with a greater proportion of large fragments (3.15%). Bacterial DNA content remained consistent across treatments. Our findings highlight the importance of selecting appropriate extraction methods to ensure optimal DNA quality for advanced sequencing applications. These results provide useful guidelines for optimising DNA extractions from smaller-bodied arthropods (~ 10-20 mg) and establish a framework for future studies to consider DNA quantity, quality, and composition.

Details

Title: A framework for optimising arthropod DNA quality and quantity for modern sequencing tools using hard ticks (Ixodidae)
Authors/Creators: X W Barton - Murdoch University
S S Tobe - Centre for One Health and Biosecurity, Harry Butler Institute, Murdoch University, Perth, 6150, Australia
J B Fontaine - Murdoch University, School of Environmental and Conservation Sciences
C L Oskam - Murdoch University, Centre for Biosecurity and One Health
Publication Details: Parasitology research (1987), Vol.125(1), 5
Publisher: Springer Nature; NEW YORK
Number of pages: 16
Identifiers: 991005851088007891
Murdoch Affiliation: Centre for Biosecurity and One Health; Harry Butler Institute; School of Environmental and Conservation Sciences; School of Medical, Molecular and Forensic Sciences; College of Environmental and Life Sciences
Language: English
Resource Type: Journal article

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Citation topics: 1 Clinical & Life Sciences; 1.258 Zoonotic Diseases; 1.258.227 Tick-borne Pathogens
Web Of Science research areas: Parasitology
ESI research areas: Microbiology