DNA Barcoding of Nematodes Using the MinION

Frontiers in Ecology and Evolution

Ineke E. Knot¹  George D. Zouganelis²  Robbie Rae²  Gareth D. Weedall²  Serge A. Wich² 

[1] Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands;School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom;

关键词: MinION;    DNA barcoding;    biomonitoring;    18S (SSU) rRNA gene;    Anisakis simplex;    Panagrellus redivivus;   

DOI  :  10.3389/fevo.2020.00100

来源: DOAJ

【 摘 要 】

Many nematode species are parasitic and threaten the health of plants and animals, including humans, on a global scale. Advances in DNA sequencing techniques have allowed for the rapid and accurate identification of many organisms including nematodes. However, the steps taken from sample collection in the field to molecular analysis and identification can take many days and depend on access to both immovable equipment and a specialized laboratory. Here, we present a protocol to genetically identify nematodes using 18S SSU rRNA sequencing using the MinION, a portable third generation sequencer, and proof that it is possible to perform all the molecular preparations on a fully portable molecular biology lab – the Bentolab. We show that both parasitic and free-living nematode species (Anisakis simplex, Panagrellus redivivus, Turbatrix aceti, and Caenorhabditis elegans) can be identified with a 96–100% accuracy compared to Sanger sequencing, requiring only 10–15 min of sequencing. This protocol is an essential first step toward genetically identifying nematodes in the field from complex natural environments (such as feces, soil, or marine sediments). This increased accessibility could in turn improve global information of nematode presence and distribution, aiding near-real-time global biomonitoring.

【 授权许可】

Unknown