DNA Barcoding of Nematodes Using the MinION
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-04-01
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| Series: | Frontiers in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fevo.2020.00100/full |
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| author | Ineke E. Knot George D. Zouganelis Gareth D. Weedall Serge A. Wich Serge A. Wich Robbie Rae |
| author_facet | Ineke E. Knot George D. Zouganelis Gareth D. Weedall Serge A. Wich Serge A. Wich Robbie Rae |
| author_sort | Ineke E. Knot |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T16:05:59Z |
| format | Article |
| id | doaj.art-c0cf0df0bc5643e9ada2737c59d45b7c |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-12-13T16:05:59Z |
| publishDate | 2020-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-c0cf0df0bc5643e9ada2737c59d45b7c2022-12-21T23:39:02ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2020-04-01810.3389/fevo.2020.00100477311DNA Barcoding of Nematodes Using the MinIONIneke E. Knot0George D. Zouganelis1Gareth D. Weedall2Serge A. Wich3Serge A. Wich4Robbie Rae5Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsSchool of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United KingdomSchool of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United KingdomInstitute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsSchool of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United KingdomSchool of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United KingdomMany 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.https://www.frontiersin.org/article/10.3389/fevo.2020.00100/fullMinIONDNA barcodingbiomonitoring18S (SSU) rRNA geneAnisakis simplexPanagrellus redivivus |
| spellingShingle | Ineke E. Knot George D. Zouganelis Gareth D. Weedall Serge A. Wich Serge A. Wich Robbie Rae DNA Barcoding of Nematodes Using the MinION Frontiers in Ecology and Evolution MinION DNA barcoding biomonitoring 18S (SSU) rRNA gene Anisakis simplex Panagrellus redivivus |
| title | DNA Barcoding of Nematodes Using the MinION |
| title_full | DNA Barcoding of Nematodes Using the MinION |
| title_fullStr | DNA Barcoding of Nematodes Using the MinION |
| title_full_unstemmed | DNA Barcoding of Nematodes Using the MinION |
| title_short | DNA Barcoding of Nematodes Using the MinION |
| title_sort | dna barcoding of nematodes using the minion |
| topic | MinION DNA barcoding biomonitoring 18S (SSU) rRNA gene Anisakis simplex Panagrellus redivivus |
| url | https://www.frontiersin.org/article/10.3389/fevo.2020.00100/full |
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