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Journal article
Comparison of primers for the detection of Phytophthora (and other oomycetes) from environmental samples
Journal of Fungi, Vol.8(9), Art. 980
2022
Abstract
Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 primer combinations have been designed to amplify oomycetes, or more specifically, Phytophthora species, from environmental samples. We used the Illumina sequencing platform to compare 13 primer combinations on mock communities and environmental samples. The primer combinations tested varied significantly in their ability to amplify Phytophthora species in a mock community and from environmental samples; this was due to either low sensitivity (unable to detect species present in low concentrations) or a lack of specificity (an inability to amplify some species even if they were present in high concentrations). Primers designed for oomycetes underestimated the Phytophthora community compared to Phytophthora-specific primers. We recommend using technical replicates, primer combinations, internal controls, and a phylogenetic approach for assigning a species identity to OTUs or ASVs. Particular care must be taken if sampling substrates where hybrid species could be expected. Overall, the choice of primers should depend upon the hypothesis being tested.
Details
- Title
- Comparison of primers for the detection of Phytophthora (and other oomycetes) from environmental samples
- Authors/Creators
- T.I. Burgess (Author/Creator) - Phytophthora Science and Management, Harry Butler Institute, Murdoch 6150, AustraliaD. White (Author/Creator)S.J. Sapsford (Author/Creator)
- Publication Details
- Journal of Fungi, Vol.8(9), Art. 980
- Publisher
- MDPI
- Identifiers
- 991005542061207891
- Copyright
- © 2022 by the authors
- Murdoch Affiliation
- Harry Butler Institute; Centre for Phytophthora Science and Management
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.97 Plant Pathology
- 3.97.1439 Phytophthora Management
- Web Of Science research areas
- Microbiology
- Mycology
- ESI research areas
- Plant & Animal Science