2026-10-07T22:27:47Z https://api.figshare.com/v2/oai

oai:figshare.com:article/32620011 2026-10-02T16:21:14Z category_31025 category_30569 category_30950 category_31061 category_31022 portal_1059 item_type_3 month_year_10_2026

Data from: Oxford nanopore-based cox1-spacer-cox2 amplicon sequencing enables high-resolution molecular identification of oomycetes from environmental samples GLEN GROBEN (23838564) Jo Anne Crouch (17478222) Plant and fungus systematics and taxonomy Agricultural biotechnology diagnostics (incl. biosensors) Sequence analysis Genomics Phylogeny and comparative analysis Oomycota Environmental sequencing Oxford Nanopore Technologies long-read sequencing Molecular Diagnostics Population Genetics Metabarcoding Phylogenetics <p dir="ltr">Oomycete plant pathogens threaten global food security, agriculture, and environmental health. Molecular identification of oomycetes typically relies on short high-copy number DNA markers (~500-bp or less), such as ribosomal DNA or mitochondrial cytochrome oxidase subunits, but these markers may lack species- or subspecies-level resolution due to factors like insufficient nucleotide variation or inconsistent amplification. We developed a primer set that amplifies ~92.5% of the <i>cox</i>1-spacer-<i>cox</i>2 region and report a long-read amplicon approach using Oxford Nanopore Technologies to sequence 2.0-2.3 kbp amplicons. Oomycete specificity was tested with positive amplification from 24 oomycete genera and 88 oomycete species obtained from axenic cultures and plant tissue. Tested fungi did not yield amplicons, and environmental sequences were limited to oomycetes, confirming marker specificity. Phylogenetic analysis showed taxonomic resolution consistent with multi-locus and genome-scale datasets. Environmental testing showed direct oomycete species identification from three different systems. Turfgrass samples identified novel taxa of a new <i>Pythium</i> species and a new genus of oomycetes basal to <i>Albugo</i>. Sequencing of 52 diseased corn and sugarcane leaves differentiated <i>Peronosclerospora philippinensis </i>from <i>P. sacchari</i>, resolving a previously difficult taxonomic distinction. Metabarcoding of Florida citrus orchards roots and soils identified seven oomycete species including two major citrus pathogens (<i>Phytophthora</i> <i>palmivora</i> and <i>P</i>. <i>nicotianae</i>). This <i>cox</i>1-spacer-<i>cox</i>2 protocol enables high resolution oomycete species identification directly from environmental samples and is comparable with existing <i>cox</i>1 and <i>cox</i>2 molecular datasets. Overall, the COX1-2 primer set and sequencing approach provides enhanced identification of oomycetes across agricultural and horticultural systems.</p> 2026-10-02T16:21:14Z Dataset Dataset 10.15482/USDA.ADC/32620011.v1 https://figshare.com/articles/dataset/Data_from_Oxford_nanopore-based_cox1-spacer-cox2_amplicon_sequencing_enables_high-resolution_molecular_identification_of_oomycetes_from_environmental_samples/32620011 CC0