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Identification of individual root-knot nematodes using low coverage long-read sequencing

Sellers, Graham S.; Jeffares, Daniel C.; Lawson, Bex; Prior, Tom; Lunt, David H.


Graham S. Sellers

Daniel C. Jeffares

Bex Lawson

Tom Prior


Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.


Sellers, G. S., Jeffares, D. C., Lawson, B., Prior, T., & Lunt, D. H. (2021). Identification of individual root-knot nematodes using low coverage long-read sequencing. PLoS ONE, 16(12), Article e0253248.

Journal Article Type Article
Acceptance Date Oct 27, 2021
Online Publication Date Dec 1, 2021
Publication Date Dec 1, 2021
Deposit Date Apr 1, 2022
Publicly Available Date Apr 1, 2022
Journal PLoS ONE
Print ISSN 1932-6203
Electronic ISSN 1932-6203
Publisher Public Library of Science
Peer Reviewed Peer Reviewed
Volume 16
Issue 12
Article Number e0253248
Public URL


Published article (2 Mb)

Copyright Statement
Copyright: © 2021 Sellers et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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