http://lod.bco-dmo.org/id/dataset/958631
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
2025-04-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas
2025-04-10
publication
2025-04-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-04-11
publication
https://doi.org/10.26008/1912/bco-dmo.958631.1
Erik Sotka
Grice Marine Laboratory - College of Charleston
principalInvestigator
Allan Strand
Grice Marine Laboratory - 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., Strand, A. (2025) NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.958631.1 [access date]
SRA archive of Magallana gigas Dataset Description: Methods and Sampling: <p>Sampling was conducted at several locations: South Korea, Japan, USA, European coastlines, Argentina, and Chile.</p>
<p>At each site, we collected approximately 20 individuals at least 1 meter apart from natural and artificial substrata outside of obvious aquacultural infrastructure to target naturally-settled spat. The two exceptions were in Chile, which were a mix of aquacultural (n=17) and feral (n=3) samples collected from the same estuary (Estero Tongoy), and New Zealand, where oysters were naturally settled within aquaculture farms. Shells were pulled by hand off of hard substrata. Whole or mantle tissue was preserved in 95% ethanol and shipped to Charleston, South Carolina (USA) for DNA extraction using Macherey-Nagel Nucleospin Tissue kits, using the manufacturer's instructions.</p>
<p>To generate libraries for RADseq (restriction-site associated DNA sequencing), we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10 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® to isolate the 300 – 450 bp fraction. This fraction was then single-read sequenced (100 or 150 basepairs) with Illumina Novaseq, HiSeq 2500 and/or HiSeq 4000 machines. We used custom scripts to demultiplex into sample-specific FASTQ-formatted files.</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
completed
Erik Sotka
Grice Marine Laboratory - College of Charleston
843-953-9191
Grice Marine Laboratory 205 Fort Johnson Road
Charleston
SC
29412
USA
SotkaE@cofc.edu
pointOfContact
Allan Strand
Grice Marine Laboratory - College of Charleston
843-953-9189
Grice Marine Laboratory, 66 George St. Room 216
Charleston
SC
29424
USA
stranda@cofc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
accession
bioproject_accession
biosample_accession
pop
Population
Region
Region2
NatNon
Collection_Date
CollectionMonth
CollectionYear
Latitude
Longitude
Collector
theme
None, User defined
sample identification
accession number
NCBI BioProject accession
NCBI BioSample accession
sample description
site
date
month of year
year
latitude
longitude
person name
featureType
BCO-DMO Standard Parameters
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
-124.023696
175.11
-40.5394
58.8684
2005-07-01
2021-11-30
Global
0
BCO-DMO catalogue of parameters from NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas
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/958682.rdf
Name: sample_name
Units: unitless
Description: <p>Individual ID (3 letter pop name and 3-digit identifier)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958683.rdf
Name: accession
Units: unitless
Description: <p>GenBank SRA accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/958684.rdf
Name: bioproject_accession
Units: unitless
Description: <p>GenBank BioProject number</p>
http://lod.bco-dmo.org/id/dataset-parameter/958685.rdf
Name: biosample_accession
Units: unitless
Description: <p>GenBank BioSample number</p>
http://lod.bco-dmo.org/id/dataset-parameter/958686.rdf
Name: pop
Units: unitless
Description: <p>3 letter Population abbreviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/958687.rdf
Name: Population
Units: unitless
Description: <p>Full population name</p>
http://lod.bco-dmo.org/id/dataset-parameter/958688.rdf
Name: Region
Units: unitless
Description: <p>shorted region name</p>
http://lod.bco-dmo.org/id/dataset-parameter/958689.rdf
Name: Region2
Units: unitless
Description: <p>region name</p>
http://lod.bco-dmo.org/id/dataset-parameter/958690.rdf
Name: NatNon
Units: unitless
Description: <p>Native (nat) and non-native (non)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958691.rdf
Name: Collection_Date
Units: unitless
Description: <p>Population collection date (Year-Month)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958692.rdf
Name: CollectionMonth
Units: unitless
Description: <p>Population collection Month (when available)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958693.rdf
Name: CollectionYear
Units: unitless
Description: <p>Population collection Year</p>
http://lod.bco-dmo.org/id/dataset-parameter/958694.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of population collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/958695.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of opulation collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/958696.rdf
Name: Collector
Units: unitless
Description: <p>Scientist that collected the dataset</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
106205
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/5881d725-62f6-4993-8074-ba0c9ea19a5e/content
download
https://doi.org/10.26008/1912/bco-dmo.958631.1
download
onLine
dataset
<p>Sampling was conducted at several locations: South Korea, Japan, USA, European coastlines, Argentina, and Chile.</p>
<p>At each site, we collected approximately 20 individuals at least 1 meter apart from natural and artificial substrata outside of obvious aquacultural infrastructure to target naturally-settled spat. The two exceptions were in Chile, which were a mix of aquacultural (n=17) and feral (n=3) samples collected from the same estuary (Estero Tongoy), and New Zealand, where oysters were naturally settled within aquaculture farms. Shells were pulled by hand off of hard substrata. Whole or mantle tissue was preserved in 95% ethanol and shipped to Charleston, South Carolina (USA) for DNA extraction using Macherey-Nagel Nucleospin Tissue kits, using the manufacturer's instructions.</p>
<p>To generate libraries for RADseq (restriction-site associated DNA sequencing), we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10 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® to isolate the 300 – 450 bp fraction. This fraction was then single-read sequenced (100 or 150 basepairs) with Illumina Novaseq, HiSeq 2500 and/or HiSeq 4000 machines. We used custom scripts to demultiplex into sample-specific FASTQ-formatted files.</p>
Specified by the Principal Investigator(s)
<p>These data are the demultiplexed files from Illumina sequencing.</p>
Specified by the Principal Investigator(s)
- Imported original file "meta_forBIODMO.csv" into the BCO-DMO system.
- Created column for collection date in YYYY-MM format.
- Saved final file as "958631_v1_m_gigas_sra.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