Nematode-specific SSU primers are usually used for amplifications from genomic DNAs purified from complex soil nematodes

-Nematode-specific primers

-18S rRNA primers

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DNA Barcoding of Nematodes Using the MinION

📷Ineke E. Knot 📷George D. Zouganelis 📷Gareth D. Weedall 📷Serge A. Wich 📷Robbie Rae

Front. Ecol. Evol., 30 April 2020 Sec. Environmental Informatics and Remote Sensing Volume 8 - 2020 | https://doi.org/10.3389/fevo.2020.00100

"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."

"Generally, NF1-18Sr2b has been the preferred choice for soil nematodes and the SSUF04-SSUR22 for marine nematodes (Creer et al. 2010, Porazinska et al. 2010b, 2010a, Fonseca et al. 2014, Holovachov et al. 2017)."

But Primer pair: Nemf/18Sr2b is much better than NF1/18Sr2b, because you will receive higher coverage and larger read length.

Article Evaluation of Metabarcoding Primers for Analysis of Soil Nem...