http://lod.bco-dmo.org/id/dataset/998962
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
2026-05-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
RADseq SNP genotypes of Perkinsus marinus and Crassostrea virginica from the Gulf of Mexico and eastern Atlantic shorelines collected from 2011-2019
2026-05-19
publication
2026-05-19
revision
BCO-DMO Linked Data URI
2026-05-19
creation
http://lod.bco-dmo.org/id/dataset/998962
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) RADseq SNP genotypes of Perkinsus marinus and Crassostrea virginica from the Gulf of Mexico and eastern Atlantic shorelines collected from 2011-2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998962 [access date]
Methods and Sampling: <p>For each oyster sampled, animals were cleaned, measured and shucked to expose soft tissues. Gill and mantle were extracted from each oyster and preserved in 95% ethanol for genetic analysis. DNA was extracted using a QIAGEN QIAamp DNA Mini Kit. Genomic DNA concentration was measured with a Nanodrop spectrophotometer to ensure the concentration was ≥100&nbsp;ng&nbsp;<em>μ</em>L<sup>−1</sup>. All positive samples in microcentrifuge tubes were randomly mixed before transport in case there was an error in future sequencing steps that could cause a loss in representation of an entire population. Once the microcentrifuge tubes containing the extracted DNA were thoroughly mixed, 20&nbsp;<em>μ</em>L of each of the 64 samples were used in subsequent library construction. The DNA of each individual oyster was digested separately with 2 restriction enzymes, EcoRI and MseI. The digested DNA fragments were then ligated to Illumina adaptors at the MseI end and with Illumina adaptors coupled with an 8–10&nbsp;bp unique barcode to the EcoRI end to allow identification of the individual <em>in silico</em>. The restriction-ligation products were then PCR-amplified in 2 separate reactions using standard Illumina primers. The final PCR products were pooled and shipped for sequencing.</p>
<p>Fifty-nine <em>P. marinus</em>-positive samples were sequenced in 2020 at the Tufts University Genomic Services (200–400&nbsp;bp fraction; single-end sequencing on an Illumina HiSeq 2500 using SE125), 42 samples were sequenced in 2022 at the University of Texas Genomic Sequencing and Analysis Facility (300–450&nbsp;bp fraction; single-end sequencing on an Illumina NovaSeq SP using SR100) and 37 of each of those samples were sequenced in both runs.<br />
<br />
Organism identifiers (Life Science Identifier (LSID)):<br />
Crassostrea virginica (urn:lsid:marinespecies.org:taxname:140657)<br />
Perkinsus marinus&nbsp; (urn:lsid:marinespecies.org:taxname:562957)</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
BioSample
sample_name
organism
isolate
host
isolation_source
geo_loc_name
tissue
date_collection
siteName
State
Region
Region2
Storage
Lat
Lon
Accesion
BioProject
Illumina Sequencing machine (HiSeq 2500)
Illumina NovaSeq SP
384-well thermocycler (Eppendorf)
theme
None, User defined
NCBI BioSample accession
sample identification
taxon
sample description
site description
region
No BCO-DMO term
site
latitude
longitude
NCBI SRA run accession (SRR)
NCBI BioProject accession
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Thermal Cycler
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
-90
-75.66
29.24
37.81
2011-10-06
2019-10-24
Global
0
BCO-DMO catalogue of parameters from RADseq SNP genotypes of Perkinsus marinus and Crassostrea virginica from the Gulf of Mexico and eastern Atlantic shorelines collected from 2011-2019
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/999034.rdf
Name: BioSample
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioSample accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/999035.rdf
Name: sample_name
Units: unitless
Description: <p>sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999036.rdf
Name: organism
Units: unitless
Description: <p>'Crassostrea virginica' LSID(urn:lsid:marinespecies.org:taxname:140657), or 'Perkinsus marinus' LSID(urn:lsid:marinespecies.org:taxname:562957)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999037.rdf
Name: isolate
Units: unitless
Description: <p>sample ID v2</p>
http://lod.bco-dmo.org/id/dataset-parameter/999038.rdf
Name: host
Units: unitless
Description: <p>parasite or none (missing data identifier will vary by file type accessed. Blank in csv files).</p>
http://lod.bco-dmo.org/id/dataset-parameter/999039.rdf
Name: isolation_source
Units: unitless
Description: <p>Estuary</p>
http://lod.bco-dmo.org/id/dataset-parameter/999040.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Country:State</p>
http://lod.bco-dmo.org/id/dataset-parameter/999041.rdf
Name: tissue
Units: unitless
Description: <p>gill/mantle or Culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/999042.rdf
Name: date_collection
Units: unitless
Description: <p>Collection Date</p>
http://lod.bco-dmo.org/id/dataset-parameter/999043.rdf
Name: siteName
Units: unitless
Description: <p>SiteName long</p>
http://lod.bco-dmo.org/id/dataset-parameter/999044.rdf
Name: State
Units: unitless
Description: <p>US State</p>
http://lod.bco-dmo.org/id/dataset-parameter/999045.rdf
Name: Region
Units: unitless
Description: <p>Bay or Eastern Shore (VA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999046.rdf
Name: Region2
Units: unitless
Description: <p>Atlantic or Gulf</p>
http://lod.bco-dmo.org/id/dataset-parameter/999047.rdf
Name: Storage
Units: unitless
Description: <p>DNA stored in FFPE or Fresh</p>
http://lod.bco-dmo.org/id/dataset-parameter/999048.rdf
Name: Lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/999049.rdf
Name: Lon
Units: decimal degrees
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/999050.rdf
Name: Accesion
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) Run accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/999051.rdf
Name: BioProject
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioProject identifier.</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/998962/data/download
download
onLine
dataset
<p>For each oyster sampled, animals were cleaned, measured and shucked to expose soft tissues. Gill and mantle were extracted from each oyster and preserved in 95% ethanol for genetic analysis. DNA was extracted using a QIAGEN QIAamp DNA Mini Kit. Genomic DNA concentration was measured with a Nanodrop spectrophotometer to ensure the concentration was ≥100&nbsp;ng&nbsp;<em>μ</em>L<sup>−1</sup>. All positive samples in microcentrifuge tubes were randomly mixed before transport in case there was an error in future sequencing steps that could cause a loss in representation of an entire population. Once the microcentrifuge tubes containing the extracted DNA were thoroughly mixed, 20&nbsp;<em>μ</em>L of each of the 64 samples were used in subsequent library construction. The DNA of each individual oyster was digested separately with 2 restriction enzymes, EcoRI and MseI. The digested DNA fragments were then ligated to Illumina adaptors at the MseI end and with Illumina adaptors coupled with an 8–10&nbsp;bp unique barcode to the EcoRI end to allow identification of the individual <em>in silico</em>. The restriction-ligation products were then PCR-amplified in 2 separate reactions using standard Illumina primers. The final PCR products were pooled and shipped for sequencing.</p>
<p>Fifty-nine <em>P. marinus</em>-positive samples were sequenced in 2020 at the Tufts University Genomic Services (200–400&nbsp;bp fraction; single-end sequencing on an Illumina HiSeq 2500 using SE125), 42 samples were sequenced in 2022 at the University of Texas Genomic Sequencing and Analysis Facility (300–450&nbsp;bp fraction; single-end sequencing on an Illumina NovaSeq SP using SR100) and 37 of each of those samples were sequenced in both runs.<br />
<br />
Organism identifiers (Life Science Identifier (LSID)):<br />
Crassostrea virginica (urn:lsid:marinespecies.org:taxname:140657)<br />
Perkinsus marinus&nbsp; (urn:lsid:marinespecies.org:taxname:562957)</p>
Specified by the Principal Investigator(s)
<p>Reads were aligned to the <em>P. marinus</em> genome (GCA_000006405.1) and the <em>C. virginica</em> genome (GCF_002022765.2). The median number of reads aligned to the <em>P. marinus</em> genome (0.13&nbsp;M; a range of 0.10–1.01&nbsp;M) was 0.37% of the median number aligned to the <em>C. virginica</em> genome (34&nbsp;M; a range of 3.52–66.89&nbsp;M). This yielded a ratio of 265 <em>C. virginica</em> to <em>P. marinus</em> reads per sample. Of the total number of reads per sample, a median of 0.80 and 91.30% of reads were <em>P. marinus</em> and <em>C. virginica</em>, respectively.</p>
<p>After alignment of 64 samples to the <em>P. marinus</em> genome, we kept 35 samples that had between 100&nbsp;K and 1&nbsp;M <em>P. marinus</em> reads. Another sample identified as 6837–16, from VA had 1.1&nbsp;M reads, from which we randomly downsampled 500&nbsp;K reads using samtools view.&nbsp;</p>
<p>For <em>P. marinus</em>, we found all single-nucleotide polymorphisms, or SNPs [set minor allele frequency (MAF) threshold at 0] and then a custom script to find SNPs that had at least 1 read across 50% of individuals. This yielded 772 SNPs. An analysis of allele frequencies indicated that 393 SNPs were polymorphic between or within samples. Thus, all subsequent analyses are based on phred-scale genotype likelihoods of 393 polymorphic SNPs at 36 individuals. For <em>C. virginica</em>, we created genotypes from the same 36 individuals, and included SNPs with MAF&nbsp;&gt;&nbsp;1% and at least 1 read per sample, yielding genotypes at 52&nbsp;100 SNPs.<br />
<br />
Organism name, Life Science Identifier (LSID):<br />
Crassostrea virginica, urn:lsid:marinespecies.org:taxname:140657<br />
Perkinsus marinus, urn:lsid:marinespecies.org:taxname:562957</p>
Specified by the Principal Investigator(s)
- Loaded CSV file "meta_forBCODMO.csv" into table "998962_v1_perkinsus-crassostrea-co-phylogeny"; empty strings and "NA" treated as missing values
- Set types for 18 columns: Accesion, BioProject, BioSample, geo_loc_name, host, isolate, isolation_source, organism, sample_name, siteName, State, Storage, tissue, Region, Region2 as string; Lat, Lon as number; date_collection as string
- Updated field metadata (descriptions, standard name IDs, supplied units) for all 18 columns, including NCBI accession identifiers (Accesion, BioProject, BioSample), geographic coordinates (Lat, Lon), collection date, organism (Crassostrea virginica and Perkinsus marinus), tissue type, storage method, and location fields
- Converted date_collection from format "%m/%d/%y" to ISO 8601 string format "%Y-%m-%d"
- Set date_collection type to date with format "%Y-%m-%d"
- Renamed column Accesion to Accession (correcting spelling)
- Output final table as "998962_v1_perkinsus-crassostrea-co-phylogeny.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 (HiSeq 2500)
Illumina Sequencing machine (HiSeq 2500)
PI Supplied Instrument Name: Illumina Sequencing machine (HiSeq 2500) 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.
Illumina NovaSeq SP
Illumina NovaSeq SP
PI Supplied Instrument Name: Illumina NovaSeq SP 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.
384-well thermocycler (Eppendorf)
384-well thermocycler (Eppendorf)
PI Supplied Instrument Name: 384-well thermocycler (Eppendorf) Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)