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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article numbere0253248
JournalPLOS one
Issue number12 December
Publication statusPublished - 1 Dec 2021

Bibliographical note

Publisher 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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