Genome-enhanced detection and identification of fungal pathogens responsible for pine and poplar rust diseases

Abstract

Biosurveillance is a proactive approach that may help to limit the spread of invasive fungal pathogens of trees, such as rust fungi which have caused some of the world’s most damaging diseases of pines and poplars. Most of these fungi have a complex life cycle, with up to five spore stages, which is completed on two different hosts. They have a biotrophic lifestyle and may be propagated by asymptomatic plant material, complicating their detection and identification. A bioinformatics approach, based on whole genome comparison, was used to identify genome regions that are unique to the white pine blister rust fungus, Cronartium ribicola, the poplar leaf rust fungi Melampsora medusae and Melampsora larici-populina or to members of either the Cronartium and Melampsora genera. Species- and genus-specific real-time PCR assays, targeting these unique regions, were designed with the aim of detecting each of these five taxonomic groups. In total, twelve assays were developed and tested over a wide range of samples, including different spore types, different infected plant parts on the pycnio-aecial or uredinio-telial host, and captured insect vectors. One hundred percent detection accuracy was achieved for the three targeted species and two genera with either a single assay or a combination of two assays. This proof of concept experiment on pine and poplar leaf rust fungi demonstrates that the genome-enhanced detection and identification approach can be translated into effective real-time PCR assays to monitor tree fungal pathogens.

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

“…Given the paucity of sequenced genomes for invasive species, this genome will serve as an important resource to study invasive species at the genomic level. Due to the varying abilities of introduced species to establish in a new environment, decision-making regarding resource allocation, mitigation, and management has always been uncertain; availability of genomic information for non-native species may provide new solutions (Hamelin and Roe, 2019). Whole-genome information expedites downstream population genomic studies on the role of multiple introductions, admixture, and adaptive ramifications of novel genotypes allowing ‘exploration’ of novel phenotypic space, phenologies, and ecological interactions (Bertolotti et al, 2020).…”

“…North et al 2021, DeGiorgio et al, 2016; Nielsen et al, 2005). With improved understanding and forecasting at each stage of the invasion process, managers can make decisions on invasions much more accurately than in the past (Bergeron et al 2019, Keriö et al 2020). Hence, sequencing whole genomes for these non-model organisms provide crucial tools to efficiently manage and predict future invasions.…”

Improved detection and identification of the sudden oak death pathogenPhytophthora ramorumand the Port Orford cedar root pathogenPhytophthora lateralis

“…To estimate the accuracy of each assay in detecting DNA from the target taxon, C t values obtained in the previous experiments with DNA from pure cultures and infected plant material were interpreted using the naïve Bayes classifier described by Bergeron et al . (). Briefly, the classifier is trained on C t values obtained from collections of ‘positive’ (i.e.…”

“…Briefly, the classifier is trained on C t values obtained from collections of ‘positive’ (i.e. DNA from target taxa) and ‘negative’ (DNA from non‐target taxa) samples to provide a probability for an unknown sample of being positive and negative (Bergeron et al ., ). For each assay, 10 000 training sets were built by randomly picking 79 C t values taken (either from positive or negative samples) from the set of 158 C t values obtained with the qPCR tests made on DNA from cultures and from infected plant material.…”

Fast and reliable molecular methods to detect fungal pathogens in woody plants

“…The major pathway of non-native plant pathogen introduction is the international trade of plants, mainly ornamental (Liebhold et al 2012;Santini et al 2013). For these reasons, biosecurity protocols for plant protection have been developed to prevent the spread and assist in the eradication of invasive species (Bergeron et al 2019;Wittenberg and Cock 2001). Previous experience from EU-funded projects identified critical points that should be tackled to improve the efficacy of the EU plant health regime.…”