Canadian Forest Service Publications

Improved detection and identification of the sudden oak death pathogen Phytophthora ramorum and the Port Orford cedar root pathogen Phytophthora lateralis. 2019. Feau, N., Ojeda, D. I., Beauseigle, S., Bilodeau, G.J., Brar, A., Cervantes‐Arango, S., Dale, A.L., Dhillon, B., Hammett, C., Herath, P., Shamoun, S.F., Tsui, C.K.M., Tanguay, P., Hamelin, R.C. Plant Pathology. 68:878-888.

Year: 2019

Available from: Pacific Forestry Centre

Catalog ID: 39813

Language: English

CFS Availability: PDF (download)

Available from the Journal's Web site.
DOI: 10.1111/ppa.13015

† This site may require a fee.

Abstract

Early detection provides the best way to prevent introduction and establishment of alien plant pathogens. Amplification of DNA by PCR has revolutionized the detection and monitoring of plant pathogens. Most of those assays rely on the amplification of a fraction of the genome of the targeted species. With the availability of whole genomes for a growing number of fungi and oomycetes it is becoming possible to compare genomes and discover regions that are unique to a target organism. This study has applied this pipeline to develop a set of hierarchical TaqMan real-time PCR detection assays targeting DNA of all four Phytophthora ramorum lineages, and a closely related species, P. lateralis. Nine assays were generated: three targeting DNA of all P. ramorum lineages, one for each lineage of P. ramorum, one for P. lateralis and one targeting DNA of P. ramorum and P. lateralis. These assays were very accurate and sensitive, ranging from 98.7% to 100% detection accuracy of 2–10 gene copies of the targeted taxa from pure cultures or inoculated tissues. This level of sensitivity is within the lowest theoretical limit of detection of DNA. It is expected that these assays will be useful because of their high level of specificity and the ease with which they can be multiplexed because of the inherent flexibility in primer and probe design afforded by their lack of conservation in non-target species.

Plain Language Summary

The objective of this research article is to develop improved genomic-based detection and identification of two invasive alien forest pathogens- Phytophthora ramorum (causal agent of sudden oak death) and Phytophthora lateralis (causal agent of Port-Orford cedar root rot disease). In this study, we applied this pipeline to develop a set of hierarchical TaqMan real-time PCR detection assays targeting DNA of all four P. ramorum lineages, and a closely related species, P. lateralis. Nine assays were generated: three targeting DNA of all P. ramorum lineages, one for each lineage of P. ramorum, one for P. lateralis and one targeting DNA of P. ramorum and P. lateralis. These assays were very accurate and sensitive, ranging from 98.7% to 100% detection accuracy of 2–10 gene copies of the targeted taxa from pure cultures or inoculated tissues. This level of sensitivity is within the lowest theoretical limit of detection of DNA. These assays will be useful because of their high level of specificity to detect and accurately identify P. ramorum and P. lateralis. Early detection provides the best way to prevent introduction and establishment of alien plant pathogens in Canadian urban and natural forest ecosystems.

Date modified: