Data from: Oxford nanopore-based cox1-spacer-cox2 amplicon sequencing enables high-resolution molecular identification of oomycetes from environmental samples

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>