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

PeerJ 2018 22;6:e4392. Epub 2018 Feb 22.

Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada.

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.

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Source
http://dx.doi.org/10.7717/peerj.4392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825881PMC
February 2018
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References

(Supplied by CrossRef)
Genetic diversity and origins of the homoploid-type hybrid Phytophthora× alni
Aguayo et al.
Applied and Environmental Microbiology 2016
Plant pathology: sudden larch death
Brasier et al.
Nature 2010
Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen
Dhillon et al.
Proceedings of the National Academy of Sciences of the United States of America 2015
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
Duplessis et al.
Proceedings of the National Academy of Sciences of the United States of America 2011

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