Products
Services
Applications
Resources Get started
Resource Centre
Back

Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences

Publication

Date: 12th December 2019 | Source: Phytopathology

Authors: Marco Enrique Mechan Llontop, Parul Sharma, Marcela Aguilera Flores, Shu Yang, Jill Pollok, Long Tian, Chengjie Huang, Steven Rideout, Lenwood S Heath, Song Li, Boris Alexander Vinatzer.

Routine strain-level identification of plant pathogens directly from symptomatic tissue could significantly improve plant disease control and prevention. Here we tested the Oxford Nanopore Technologies (ONT) MinIONTM sequencer for metagenomic sequencing of tomato plants either artificially inoculated with a known strain of the bacterial speck pathogen Pseudomonas syringae pv. tomato (Pto), or collected in the field and showing bacterial spot symptoms caused by either one of four Xanthomonas species. After species-level identification using ONT’s WIMP software and the third party tools Sourmash and MetaMaps, we used Sourmash and MetaMaps with a custom database of representative genomes of bacterial tomato pathogens to attempt strain-level identification. In parallel, each metagenome was assembled and the longest contigs were used as query with the genome-based microbial identification Web service LINbase. Both the read-based and assembly-based approaches correctly identified Pto strain T1 in the artificially inoculated samples. The pathogen strain in most field samples was identified as a member of Xanthomonas perforans group 2. This result was confirmed by whole genome sequencing of colonies isolated from one of the samples. Although in our case, metagenome-based pathogen identification at the strain-level was achieved, caution still needs to be exerted when interpreting strain-level results because of the challenges inherent to assigning reads to specific strains and the error rate of nanopore sequencing.

Read the full text Find out more about WIMP

Recommended for you

Open a chat to talk to our sales team
FAQs

FAQs

Search