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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
A New Oomycete Metabarcoding Method Using the rps10 Gene
Phytobiomes Journal, Volume 6, No. 3, Year 2022
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Description
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. © 2022 American Phytopathological Society. All rights reserved.
Authors & Co-Authors
Albornoz, Felipe E.
United States, Corvallis
Oregon State University
Jones, Franklin Andrew
United States, Corvallis
Oregon State University
United States, Washington, D.c.
Smithsonian Tropical Research Institute
Tyler, Brett M.
United States, Corvallis
Oregon State University
Nguyen, Hai D.T.
Canada, Ottawa
Agriculture and Agri-food Canada
Burgess, Treena Isobel
Australia, Perth
Murdoch University
Voglmayr, Hermann
Austria, Vienna
Universität Wien
Martin, Frank N.
United States, Washington, D.c.
United States Department of Agriculture
Grünwald, Niklaus J.
United States, Washington, D.c.
United States Department of Agriculture
Statistics
Citations: 7
Authors: 8
Affiliations: 6
Identifiers
Doi:
10.1094/PBIOMES-02-22-0009-R
ISSN:
24712906
Research Areas
Genetics And Genomics
Study Design
Case-Control Study