http://lod.bco-dmo.org/id/dataset/998297
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2026-05-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Decorator worm Diopatra cuprea single nucleotide polymorphism (SNP) genotypes from collections in the Gulf of Mexico and eastern United States estuaries from 2009 to 2022
2026-05-08
publication
2026-05-08
revision
BCO-DMO Linked Data URI
2026-05-08
creation
http://lod.bco-dmo.org/id/dataset/998297
Erik Sotka
College of Charleston
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Sotka, E. (2026) Decorator worm Diopatra cuprea single nucleotide polymorphism (SNP) genotypes from collections in the Gulf of Mexico and eastern United States estuaries from 2009 to 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998297 [access date]
Dataset Description: <p>See "Related Datasets" for&nbsp;sanger-sequenced a mitochondrial locus (COI) metadata and accession information at NCBI's Genbank database.</p> Methods and Sampling: <p>Note: This metadata section includes description of a related dataset (sanger-sequenced a mitochondrial locus (COI) that was generated as part of this study. See "Related Datasets" section for metadata and NCBI Genbank accession identifiers in that dataset.&nbsp;<br />
<br />
<em>Diopatra cuprea</em> were sampled from 19 locations on the United States east coast, from Duxbury MA (the genus’ northern limit) to St. Teresa Beach FL. Tubes were excavated with a shovel, the worm removed, and antennae clipped off and preserved in 95% ethanol for later DNA extraction. or 2022 samples, twenty-five randomly selected individuals from each population were extracted for DNA, with the exception of Broad River Estuary populations from which 20 and 22 samples were collected. Approximately 25&nbsp;mg of tissue wet weight was&nbsp;rinsed of ethanol with deionized water and extracted with the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s extraction protocol. Extractions were screened with 1.5% agarose gels and DNA was quantified using a NanoDrop 200 spectrophotometer (Thermo Scientific, Waltham, MA, USA) to obtain concentration values and purity.&nbsp;</p>
<p>A portion of the COI gene was then PCR amplified using the protocol in Berke, et al. (2010, doi:10.1111/j.1466-8238.2009.00509.x). These were cleaned with an EXO-SAP-IT protocol and sent for Sanger sequencing with these same primers at a private company.</p>
<p>Double digest restriction-associated DNA sequencing (or ddRADSeq) library was prepared on 312 samples following the protocol in Parchman et al. (2012,doi: 10.1111/j.1365-294X.2012.05513.x).&nbsp;Briefly, we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10&nbsp;bp barcodes to the digested DNA of each individual. The products were then PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility or the Tufts University Core Facility, which used Pippin Prep<sup>®</sup> to isolate the 300–450&nbsp;bp fraction. This fraction was then single-read sequenced (100 basepairs) with Illumina HiSeq 4000 machine. FASTQ sequences were demultiplexed using custom Unix code. 510&nbsp;million reads contained barcode sequence (range = 39 to 6.8&nbsp;million (M) reads per sample; mean = 1.6&nbsp;M reads), and 234 individuals had at least 200&nbsp;K reads that were analyzed.<br />
<br />
FASTQ files were uploaded to the NCBI's Sequence Read Archive (SRA) that were generated as described above.&nbsp; See the "Related Datasets" section&nbsp;for SRA metadata and accessions.&nbsp;<br />
<br />
Organism identifier (Life Science Identifier (LSID)):<br />
Diopatra cuprea, Bosc, 1802, LSID(urn:lsid:marinespecies.org:taxname:157339)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924599 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924599
onGoing
Erik Sotka
College of Charleston
843-953-9191
Grice Marine Laboratory 205 Fort Johnson Road
Charleston
SC
29412
USA
sotkae@cofc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
year_collected
sample_id
pop_defined
geographic_location
state_name
estuary_local
mt_haplotype
mt_hap_group
mt_hap_subgroup
collector
SRA_Run
SRA_Study
version
BioSample
site_lat
site_lon
sites_collector
Assay_Type
AvgSpotLen
Bases
BioProject
BioSampleModel
Bytes
Experiment
Instrument
isolate
isolation_source
Library_Name
LibraryLayout
LibrarySelection
LibrarySource
Organism
Platform
tissue
Illumina sequencing machine
theme
None, User defined
year
sample identification
site
region
site description
sample description
person name
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
No BCO-DMO term
NCBI BioSample accession
latitude
longitude
NCBI BioProject accession
NCBI SRA experiment accession (SRX)
instrument
taxon
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
The genetic legacy of an Asian oyster introduction and its disease-causing parasite
https://osprey.bco-dmo.org/project/820200
The genetic legacy of an Asian oyster introduction and its disease-causing parasite
<p><em>NSF abstract:</em></p>
<p>During the 20th century, the Pacific oyster <em>Crassostrea gigas</em> was deliberately introduced from its native range of coastal Asia to the estuaries of six continents. While the introduced Pacific oysters are widely aquacultured and thus can generate local economic wealth, they sometimes outcompete native oysters, and can carry microbial, animal and plant hitchhikers that negatively impact local economies and the ecological functioning of local estuaries. This study comprehensively assesses the pathways and sources of Pacific oyster introductions using a worldwide, population genetic survey. Simultaneously, the study also assesses the pathways and source of one hitchhiking protist (<em>Haplosporidium nelsoni</em>) that causes the disease MSX (multinucleated sphere X) in the Virginia oyster (<em>Crassostrea virginica</em>) along the eastern seaboard of the United States. One goal of this research is to generate management strategies that combat the negative impacts of the Pacific oyster and its associated invaders, and minimize future invasions. A second goal is to minimize some uncertainty about the population biology of the devastating Haplosporidium parasite, and thus, increase confidence of policy makers who are managing shellfish health, restoration and commerce. By quantifying the pathways and sources of <em>C. gigas</em>, this project may inform strategies to combat negative impacts of <em>C. gigas</em> and its associated invaders, as well as minimize future invasions. Moreover, quantifying dispersal within and among populations of <em>H. nelsoni</em> along the US East Coast will provide perspective on the effectiveness of regional biosecurity measures in preventing the ongoing dispersal of this destructive pathogen via aquaculture. In addition, the project lends itself well to programs that foster critical thinking and research experience among both undergraduate and K-12 students. The project provides opportunities for 6-9 undergraduates to perform research, includes a 2-day workshop on bioinformatics for the wider undergraduate community, and facilitates ongoing opportunities for K-12 students to participate in citizen-science research.</p>
<p>There is a wealth of information on the source, pathways and vectors of <em>C. gigas</em> based largely on historical documents but no study has comprehensively tested whether these historical accounts are correct using a worldwide, population genetic survey. Using >14K single-nucleotide polymorphisms (SNPs) from 41 populations across five continents a high level of spatial genetic differentiation was found within the native range and differences in source populations among non-native regions. Preliminary genetic data indicated that the parasitic protist, <em>Haplosporidium nelsoni </em>arrived with C. gigas imports to the US Atlantic coastline and then infected the native C. virginica, however the native source populations, the pathways and vector from which <em>H. nelsoni </em>arrived remain unknown. This project couples high-throughput sequencing technologies and Approximate Bayesian Computing (ABC)-based models to answer the following: What are the population genomic patterns among <em>C. gigas</em> from native and non-native regions? What are the population genomic patterns of <em>Haplosporidium nelsoni </em>among Asian and North American Crassostrea gigas and eastern North American <em>C. virginica</em>? What were the source populations and invasion pathways of <em>C. gigas</em> and <em>H. nelsoni</em>? Identifying source locations, pathways and vectors of introduction of C. gigas will provide researchers with a null-model of invasion history for dozens of other non-native species that were transported with <em>C. gigas</em>. Currently, there are no verified 'vector maps' for historical shipments of <em>C. gigas</em> that are similar to those generated from modern-day or historical shipping records.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Oyster historical genetics
largerWorkCitation
project
eng; USA
oceans
-84.51061
-69.99714
27.4575
42.04647
2009-01-01
2022-12-31
Global
0
BCO-DMO catalogue of parameters from Decorator worm Diopatra cuprea single nucleotide polymorphism (SNP) genotypes from collections in the Gulf of Mexico and eastern United States estuaries from 2009 to 2022
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/999357.rdf
Name: year_collected
Units: unitless
Description: <p>Year sample was collected (yyyy)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999358.rdf
Name: sample_id
Units: unitless
Description: <p>individual sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999359.rdf
Name: pop_defined
Units: unitless
Description: <p>Popular name of site</p>
http://lod.bco-dmo.org/id/dataset-parameter/999360.rdf
Name: geographic_location
Units: unitless
Description: <p>Sample Site</p>
http://lod.bco-dmo.org/id/dataset-parameter/999361.rdf
Name: state_name
Units: unitless
Description: <p>State name (USA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999362.rdf
Name: estuary_local
Units: unitless
Description: <p>Coastal vs Inland</p>
http://lod.bco-dmo.org/id/dataset-parameter/999363.rdf
Name: mt_haplotype
Units: unitless
Description: <p>mtDNA haplotype from Sotka et al. 2023 doi.org/10.3390/biology12040521</p>
http://lod.bco-dmo.org/id/dataset-parameter/999364.rdf
Name: mt_hap_group
Units: unitless
Description: <p>mtDNA haplotype from Sotka et al. 2023 doi.org/10.3390/biology12040521</p>
http://lod.bco-dmo.org/id/dataset-parameter/999365.rdf
Name: mt_hap_subgroup
Units: unitless
Description: <p>mtDNA haplotype from Sotka et al. 2023 doi.org/10.3390/biology12040521</p>
http://lod.bco-dmo.org/id/dataset-parameter/999366.rdf
Name: collector
Units: unitless
Description: <p>Person</p>
http://lod.bco-dmo.org/id/dataset-parameter/999367.rdf
Name: SRA_Run
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) Run accession in the Sequence Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/999368.rdf
Name: SRA_Study
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) study accession in the Sequence Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/999369.rdf
Name: version
Units: unitless
Description: <p>SRA accession version number</p>
http://lod.bco-dmo.org/id/dataset-parameter/999370.rdf
Name: BioSample
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/999371.rdf
Name: site_lat
Units: decimal degrees
Description: <p>Site latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/999373.rdf
Name: site_lon
Units: decimal degrees
Description: <p>Site longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/999375.rdf
Name: sites_collector
Units: unitless
Description: <p>co-author that collected samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/999376.rdf
Name: Assay_Type
Units: unitless
Description: <p>Assay Type</p>
http://lod.bco-dmo.org/id/dataset-parameter/999377.rdf
Name: AvgSpotLen
Units: count
Description: <p>Average Spot Length (SRA metadata from NCBI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999378.rdf
Name: Bases
Units: count
Description: <p>Bases</p>
http://lod.bco-dmo.org/id/dataset-parameter/999379.rdf
Name: BioProject
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioProject identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/999380.rdf
Name: BioSampleModel
Units: unitless
Description: <p>BioSample model (e.g. Invertebrate)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999381.rdf
Name: Bytes
Units: bytes
Description: <p>Size in bytes</p>
http://lod.bco-dmo.org/id/dataset-parameter/999382.rdf
Name: Experiment
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) Experiment accession in the Sequence Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/999383.rdf
Name: Instrument
Units: unitless
Description: <p>Instrument name</p>
http://lod.bco-dmo.org/id/dataset-parameter/999384.rdf
Name: isolate
Units: unitless
Description: <p>Isolate</p>
http://lod.bco-dmo.org/id/dataset-parameter/999385.rdf
Name: isolation_source
Units: unitless
Description: <p>isolation source</p>
http://lod.bco-dmo.org/id/dataset-parameter/999386.rdf
Name: Library_Name
Units: unitless
Description: <p>Library Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/999387.rdf
Name: LibraryLayout
Units: unitless
Description: <p>Library Layout</p>
http://lod.bco-dmo.org/id/dataset-parameter/999388.rdf
Name: LibrarySelection
Units: unitless
Description: <p>Library Selection</p>
http://lod.bco-dmo.org/id/dataset-parameter/999389.rdf
Name: LibrarySource
Units: unitless
Description: <p>Library Source</p>
http://lod.bco-dmo.org/id/dataset-parameter/999390.rdf
Name: Organism
Units: unitless
Description: <p>organism sampled (Diopatra cuprea)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999391.rdf
Name: Platform
Units: unitless
Description: <p>platform</p>
http://lod.bco-dmo.org/id/dataset-parameter/999392.rdf
Name: tissue
Units: unitless
Description: <p>tissue sample location</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/998297/data/download
download
onLine
dataset
<p>Note: This metadata section includes description of a related dataset (sanger-sequenced a mitochondrial locus (COI) that was generated as part of this study. See "Related Datasets" section for metadata and NCBI Genbank accession identifiers in that dataset.&nbsp;<br />
<br />
<em>Diopatra cuprea</em> were sampled from 19 locations on the United States east coast, from Duxbury MA (the genus’ northern limit) to St. Teresa Beach FL. Tubes were excavated with a shovel, the worm removed, and antennae clipped off and preserved in 95% ethanol for later DNA extraction. or 2022 samples, twenty-five randomly selected individuals from each population were extracted for DNA, with the exception of Broad River Estuary populations from which 20 and 22 samples were collected. Approximately 25&nbsp;mg of tissue wet weight was&nbsp;rinsed of ethanol with deionized water and extracted with the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s extraction protocol. Extractions were screened with 1.5% agarose gels and DNA was quantified using a NanoDrop 200 spectrophotometer (Thermo Scientific, Waltham, MA, USA) to obtain concentration values and purity.&nbsp;</p>
<p>A portion of the COI gene was then PCR amplified using the protocol in Berke, et al. (2010, doi:10.1111/j.1466-8238.2009.00509.x). These were cleaned with an EXO-SAP-IT protocol and sent for Sanger sequencing with these same primers at a private company.</p>
<p>Double digest restriction-associated DNA sequencing (or ddRADSeq) library was prepared on 312 samples following the protocol in Parchman et al. (2012,doi: 10.1111/j.1365-294X.2012.05513.x).&nbsp;Briefly, we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10&nbsp;bp barcodes to the digested DNA of each individual. The products were then PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility or the Tufts University Core Facility, which used Pippin Prep<sup>®</sup> to isolate the 300–450&nbsp;bp fraction. This fraction was then single-read sequenced (100 basepairs) with Illumina HiSeq 4000 machine. FASTQ sequences were demultiplexed using custom Unix code. 510&nbsp;million reads contained barcode sequence (range = 39 to 6.8&nbsp;million (M) reads per sample; mean = 1.6&nbsp;M reads), and 234 individuals had at least 200&nbsp;K reads that were analyzed.<br />
<br />
FASTQ files were uploaded to the NCBI's Sequence Read Archive (SRA) that were generated as described above.&nbsp; See the "Related Datasets" section&nbsp;for SRA metadata and accessions.&nbsp;<br />
<br />
Organism identifier (Life Science Identifier (LSID)):<br />
Diopatra cuprea, Bosc, 1802, LSID(urn:lsid:marinespecies.org:taxname:157339)</p>
Specified by the Principal Investigator(s)
- Loaded TSV file SRAattributes+meta.txt as table 998297_v1_diopatra-sra-metadata, with empty string, "nd", and "NA" treated as missing values
- Renamed column: accession to BioSample
- Applied metadata (descriptions, standard name IDs, units) to 14 columns in 998297_v1_diopatra-sra-metadata including sample_ID, geographic.location, sites.Lat, sites.Lon, mtHaplotype, and related fields
- Renamed 13 columns in 998297_v1_diopatra-sra-metadata: sample_ID to sample_id, Pop.Defined to pop_defined, geographic.location to geographic_location, State.Name to state_name, EstuaryLocal to estuary_local, mtHaplotype to mt_haplotype, mtHap.Group to mt_hap_group, mtHap.Subgroup to mt_hap_subgroup, Year.Collected to year_collected, Collector to collector, sites.Lat to site_lat, sites.Lon to site_lon, sites.Collector to sites_collector
- Negated site_lon values (multiplied by -1) using a computed field mathematical operation (longitudes W are negative)
- Rounded site_lat and site_lon to 5 decimal places with trailing zeros preserved
- Loaded CSV file SraRunTable_PRJNA1103840.csv (output from NCBI Run Selector Tool) using filename as table name, with empty string and "nd" treated as missing values
- Joined SRA metadata from the NCBI Run selector into provided metadata table using BioSample as the join key. Tables both were checked first that they were unique by BioSample. Added SRA metadata not present in the attributes file including Assay Type, AvgSpotLen, Bases, BioProject, BioSampleModel, Bytes, Experiment, Instrument, Library Name, LibraryLayout, LibrarySelection, LibrarySource, Organism, Platform, SRA Run, SRA Study, isolate, isolation_source, tissue, and version
- Reordered 34 columns, placing year_collected and sample_id first, followed by sample metadata, SRA identifiers, and sequencing metadata
- Renamed columns: Assay Type to Assay_Type, Library Name to Library_Name
- Applied updated metadata (descriptions, standard name IDs, units) to all 34 columns
- Set final data types for columns
- Output written to 998297_v1_diopatra-sra-metadata.csv
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina sequencing machine
Illumina sequencing machine
PI Supplied Instrument Name: Illumina sequencing machine PI Supplied Instrument Description:Illumina HiSeq 4000 or Illumina NovaSeq 6000 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.