Data from: Environmental sampling of turfgrass using Oxford Nanopore Technologies reveals two new <i>Pythium</i> species and a confirmed report of <i>Pythiogeton ramosum</i> confirmed by molecular barcoding
As part of the testing of a new oomycete specific primer set designed to amplify the cox2–spacer–cox1 region and sequenced using an Oxford Nanopore Technologies (ONT) device, environmental samples were taken from symptomatic turfgrass sites in North Brunswick, NJ and Clayton, NC. Phylogenetic analysis revealed the presence of new Pythium species in the New Jersey samples and the presence of a species of the poorly understood genus Pythiogeton in the North Carolina sample. All three taxa were baited out of the turf cores and their colony morphology characterized on corn meal agar, V-8 agar and potato-carrot agar. Isolates were grown on V-8 agar at 0, 5, 10, 15, 20, 25, 30, 35 and 40 °C to determine their optimal growth temperatures. All taxa were inoculated onto autoclaved grass blades in sterile soil extract water and incubated at 5, 10, 15, 20 or 25 °C and observed for sporangia, zoospore release, hyphal swellings, oogonia, antheridia and mature oospores. The Pythiogeton isolate matched the description of P. ramosum. One of the new species of Pythium (Pythium quipu) released zoospores from undifferentiated hyphae and had frequent hyphal swellings and infrequent thick-walled oospores, while the other (P. japamala) produces swollen, lobed sporangia and pleurotic oospores with mostly monoclinous antheridia. No symptoms of root or crown lesions were seen in pathogenicity tests inoculating these species on tall fescue or creeping bentgrass.
Resources
7 resources available
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Supplemetal_Fasta_1_Four_Gene_Tree.fasta
FASTA -
Supplemetal_Fasta_CO1_alignment.fasta
FASTA -
Supplemetal_Fasta_COX2_alignment.fasta
FASTA -
Supplemetal_Fasta_ITS_alignment.fasta
FASTA -
Supplemetal_Fasta_LSU_alignment.fasta
FASTA -
Supplemental_Figure_1_Environmental_Results_5-1.tif
TIF -
Supplemental_Table_1_Pythium_NCBI_Accession.csv
CSV
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| accrualPeriodicity | irregular |
| bureauCode |
[ "005:18" ] |
| contactPoint |
{ "fn": "Groben, Glen", "hasEmail": "mailto:glen.groben@usda.gov" } |
| description | <p dir="ltr">As part of the testing of a new oomycete specific primer set designed to amplify the <i>cox</i>2–spacer–<i>cox</i>1 region and sequenced using an Oxford Nanopore Technologies (ONT) device, environmental samples were taken from symptomatic turfgrass sites in<b> </b>North Brunswick, NJ and Clayton, NC. Phylogenetic analysis revealed the presence of new <i>Pythium</i> species in the New Jersey samples and the presence of a species of the poorly understood genus <i>Pythiogeton</i> in the North Carolina sample. All three taxa were baited out of the turf cores and their colony morphology characterized on corn meal agar, V-8 agar and potato-carrot agar. Isolates were grown on V-8 agar at 0, 5, 10, 15, 20, 25, 30, 35 and 40 °C to determine their optimal growth temperatures. All taxa were inoculated onto autoclaved grass blades in sterile soil extract water and incubated at 5, 10, 15, 20 or 25 °C and observed for sporangia, zoospore release, hyphal swellings, oogonia, antheridia and mature oospores. The <i>Pythiogeton</i> isolate matched the description of <i>P. ramosum</i>. One of the new species of <i>Pythium</i> (<i>Pythium quipu</i>) released zoospores from undifferentiated hyphae and had frequent hyphal swellings and infrequent thick-walled oospores, while the other (<i>P.</i> <i>japamala</i>) produces swollen, lobed sporangia and pleurotic oospores with mostly monoclinous antheridia. No symptoms of root or crown lesions were seen in pathogenicity tests inoculating these species on tall fescue or creeping bentgrass.</p> |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Supplemetal_Fasta_1_Four_Gene_Tree.fasta", "format": "fasta", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/64770822" }, { "@type": "dcat:Distribution", "title": "Supplemetal_Fasta_CO1_alignment.fasta", "format": "fasta", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/64770825" }, { "@type": "dcat:Distribution", "title": "Supplemetal_Fasta_COX2_alignment.fasta", "format": "fasta", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/64770828" }, { "@type": "dcat:Distribution", "title": "Supplemetal_Fasta_ITS_alignment.fasta", "format": "fasta", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/64770831" }, { "@type": "dcat:Distribution", "title": "Supplemetal_Fasta_LSU_alignment.fasta", "format": "fasta", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/64770834" }, { "@type": "dcat:Distribution", "title": "Supplemental_Figure_1_Environmental_Results_5-1.tif", "format": "tif", "mediaType": "image/tiff", "downloadURL": "https://ndownloader.figshare.com/files/64770837" }, { "@type": "dcat:Distribution", "title": "Supplemental_Table_1_Pythium_NCBI_Accession.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/65095650" } ] |
| identifier | 10.15482/USDA.ADC/32348121.v1 |
| keyword |
[ "Environmental Sequencing", "Metabarcoding", "Molecular Diagnostics", "New Jersey", "North Carolina", "Oomycetes", "Oxford Nanopore Technologies", "Phylogenetics", "Pythiogeton ramosum", "Pythium", "Pythium japamala", "Pythium quipu", "Turfgrass" ] |
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2026-06-08 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2023-08-13/2024-07-15 |
| title | Data from: Environmental sampling of turfgrass using Oxford Nanopore Technologies reveals two new <i>Pythium</i> species and a confirmed report of <i>Pythiogeton ramosum</i> confirmed by molecular barcoding |
