Journal article
A New Oomycete Metabarcoding Method Using the rps10 Gene
Phytobiomes journal, Vol.6(3), pp.214-226
2022
Abstract
Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause plant and animal diseases. Improved methods are needed for rapid and accurate characterization of oomycete communities using DNA metabarcoding. We have evaluated the mitochondrial 40S ribosomal protein S10 (rps10) gene as a locus for oomycete metabarcoding and provide primers predicted to amplify this region from all oomycetes based on a wide range of available reference sequences. We evaluated its utility relative to the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a mock community using Illumina MiSeq. Amplified sequence variants (ASVs) and operational taxonomic units (OTUs) were identified per community. Observed sequences and predicted taxonomy of ASVs and OTUs were compared with the known composition of the mock community. Both rps10 and ITS yielded ASVs with sequences matching 21 of the 24 species in the mock community and matching all 24 when allowing for a 1-bp difference. Taxonomic classifications of ASVs included 23 members of the mock community for rps10 and 17 for ITS1. Sequencing results for the environmental samples suggest that the rps10 locus results in substantially less amplification of nontarget organisms than the ITS1 method. The amplified rps10 region also has higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete metabarcoding. The rps10 barcode and methods described herein provide an effective tool for metabarcoding oomycetes using short-read sequencing.
Details
- Title
- A New Oomycete Metabarcoding Method Using the rps10 Gene
- Authors/Creators
- Zachary S. L. Foster - Oregon State UniversityFelipe E. Albornoz - Oregon State UniversityValerie J. Fieland - Oregon State UniversityMeredith M. Larsen - Horticultural Crops Research LaboratoryF. Andrew Jones - Oregon State UniversityBrett M. Tyler - Oregon State UniversityHai D. T. Nguyen - Agr & Agrifood Canada, Ottawa, ON K1A 0C6, CanadaTreena I. Burgess - Murdoch UniversityCarolyn Riddell - Forest ResearchHermann Voglmayr - University of ViennaFrank N. Martin - Agricultural Research ServiceNiklaus J. Grunwald - Horticultural Crops Research Laboratory
- Publication Details
- Phytobiomes journal, Vol.6(3), pp.214-226
- Publisher
- Amer Phytopathological Soc
- Number of pages
- 13
- Grant note
- 2072-22000-039-00D; 2038-22000-015-00D / United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Current Research Information System Project USDA-ARS Floriculture Nursery Initiative research programs DEB-1542681 / National Science Foundation; National Science Foundation (NSF)
- Identifiers
- 991005579903107891
- Murdoch Affiliation
- Centre for Terrestrial Ecosystem Science and Sustainability; Harry Butler Institute
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.97 Plant Pathology
- 3.97.1439 Phytophthora Management
- Web Of Science research areas
- Microbiology
- Plant Sciences
- ESI research areas
- Microbiology