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

TY - JOUR

T1 - Identification of individual root-knot nematodes using low coverage long-read sequencing

AU - Sellers, Graham S.

AU - Jeffares, Daniel C.

AU - Lawson, Bex

AU - Prior, Tom

AU - Lunt, David H.

N1 - 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.

PY - 2021/12/1

Y1 - 2021/12/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85120420204&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0253248

DO - 10.1371/journal.pone.0253248

M3 - Article

AN - SCOPUS:85120420204

SN - 1932-6203

VL - 16

JO - PLOS one

JF - PLOS one

IS - 12 December

M1 - e0253248

ER -