Genome-Enhanced Detection and Identification (GEDI) of plant pathogens.

Nicolas Feau,Monique L Sakalidis,Braham Dhillon,Richard C Hamelin,Adnan Uzunovic,Philippe Tanguay,Stéphanie Beauseigle,Inanc Birol,Angela L Dale,Hesther Yueh,Marie-Josée Bergeron,Greg Taylor,Sandra Cervantes-Arango,Padmini Herath,Clement K.M Tsui,Steven J.M Jones,Dario I Ojeda,Guillaume J Bilodeau,Josyanne Lamarche

doi:10.7717/peerj.4392

Abstract

Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.

Highlights

Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems
When genomic distances between target and non-target taxa are short, rejection of candidate by the BLASTn filter can rapidly increase with diminution of the e-value cutoff (Fig. S3B)
The filtering step in Module 3 decreased the number of candidates to 37 for P. ramorum and 180 for P. lateralis, suggesting that about 97% of the putative unique candidate clusters predicted in the OrthoMCL analysis were false positives according to our filtering criteria (Table 2)

Summary

Introduction

Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. To prevent and manage those emerging diseases, rapid detection and identification of the causal pathogens are crucial This is important for tree diseases where large contiguous forest ecosystems can be threatened by invasive and emerging pathogens, resulting in ecosystem-wide irreversible damage when prevention and management fail (Pautasso, Schlegel & Holdenrieder, 2015). Plant pathogens can be transmitted by a variety of means, including natural dispersal in water, rain and wind. The intensification of drivers such as international trade, combined with climate change contribute to the emergence and rapid increase of the threat that plant pathogens may cause to ecosystems (Desprez-Loustau et al, 2016; Pautasso, Schlegel & Holdenrieder, 2015; Santini et al, 2013)

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