Detection of Seagrass Pathogens Using Environmental DNA (eDNA), North Pacific, 2016-present
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove) Japan, Safety Sound, Izembek Lagoon, Port Moller, Chignik Lagoon, and Frederick Sound, Alaska and cloacal swabs from waterfowl hunted near Cold Bay Alaska. Replicate samples and multiple sampling dates of the same location were included. Highly conserved primers which could differentiate species of interest were developed for four portions of mtDNA genes (5.8S, 18S, ITS, and COI). The reference list and conserved primer sets to identify species present were developed using publicly available data https://www.ncbi.nlm.nih.gov/genbank/
Complete Metadata
| accessLevel | public |
|---|---|
| bureauCode |
[
"010:12"
]
|
| contactPoint |
{
"fn": "U.S. Geological Survey, Alaska Science Center",
"@type": "vcard:Contact",
"hasEmail": "mailto:gs-ak_asc_datamanagers@usgs.gov"
}
|
| description | This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove) Japan, Safety Sound, Izembek Lagoon, Port Moller, Chignik Lagoon, and Frederick Sound, Alaska and cloacal swabs from waterfowl hunted near Cold Bay Alaska. Replicate samples and multiple sampling dates of the same location were included. Highly conserved primers which could differentiate species of interest were developed for four portions of mtDNA genes (5.8S, 18S, ITS, and COI). The reference list and conserved primer sets to identify species present were developed using publicly available data https://www.ncbi.nlm.nih.gov/genbank/ |
| distribution |
[
{
"@type": "dcat:Distribution",
"title": "Digital Data",
"format": "XML",
"accessURL": "https://doi.org/10.5066/P9T69I3V",
"mediaType": "application/http",
"description": "Landing page for access to the data"
},
{
"@type": "dcat:Distribution",
"title": "Original Metadata",
"format": "XML",
"mediaType": "text/xml",
"description": "The metadata original format",
"downloadURL": "https://data.usgs.gov/datacatalog/metadata/USGS.ASC265.xml"
}
]
|
| identifier | http://datainventory.doi.gov/id/dataset/USGS_ASC265 |
| keyword |
[
"Alaska",
"Animals/Vertebrates",
"Aquatic ecosystems",
"Biological informatics",
"Biota",
"Birds",
"DNA Primers",
"DNA, Mitochondrial",
"Databases, Nucleic acid",
"Decline (Plant disease)",
"Disease detection",
"Disease spread",
"Disease vectors",
"Ducks/Geese/Swans",
"Ecological processes",
"Ecosystem",
"Ecosystem diversity",
"Environment",
"Environmental DNA",
"Feasibility studies",
"Field sampling",
"Halophytophthora",
"Hokkaido",
"Izembek National Wildlife Refuge",
"Japan",
"Labyrinthula sp.",
"Labyrinthula zosterae",
"Marine biology",
"Marine environment monitoring",
"Mitochondrial DNA",
"Ocean circulation",
"Oceans and Seas",
"Phytophthora gemini",
"Plants",
"Species/Population Interactions",
"USGS:ASC265",
"Zostera marina",
"eDNA"
]
|
| modified | 2024-08-02T00:00:00Z |
| publisher |
{
"name": "U.S. Geological Survey",
"@type": "org:Organization"
}
|
| spatial | 145.2334, 43.5834, -132.9831, 64.4917 |
| theme |
[
"Geospatial"
]
|
| title | Detection of Seagrass Pathogens Using Environmental DNA (eDNA), North Pacific, 2016-present |
