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.

Abstract

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.

Citation

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. https://doi.org/10.1371/journal.pone.0253248

• 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
• DOI: https://doi.org/10.1371/journal.pone.0253248
• Public URL: https://hull-repository.worktribe.com/output/3894899