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Metadata: Laboratory data for experimental exposure of Pacific Oysters (Crassostrea (Magallana) gigas) to Ostreid herpesvirus (OsHV-1) in 2016
Abstract:
Laboratory data for experimental exposure of 1,000 Pacific Oysters (Crassostrea (Magallana) gigas) to Ostreid herpesvirus (OsHV-1) in 2016 for the purpose of collecting survival vs mortality and viral load data to estimate heritability of resistance to Ostreid herpesvirus (OsHV-1) using single nucleotide polymorphism (SNP) analysis of the challenged oysters. The dataset take the form of: - Quantitative PCR (qPCR) data for Pacific oysters challenged with OsHV-1. V- iral load was measured in viral copies per mg of tissue, AND the raw data is CT (cycle threshold) values. - Survival and mortality data for the disease challenge, and the position of each oyster within the challenge system - Disease challenge parameters, including feeding, temperature and water quality measurements - Illumina MiSeq derived sequencing data produced from a single oyster experimentally infected with OsHV-1
Data holder:
Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)
| Other details | ||
| Internal code | Internally assigned metadata identifier | 10453 |
| Title | The title is used to provide a brief and precise description of the dataset such as 'Date', 'Originating organisation/programme', 'Location' and 'Type of survey'. All acronyms and abbreviations should be reproduced in full. | Laboratory data for experimental exposure of Pacific Oysters (Crassostrea (Magallana) gigas) to Ostreid herpesvirus (OsHV-1) in 2016 |
| File Identifier | The File Identifier is a code, preferably a GUID, that is globally unique and remains with the same metadata record even if the record is edited or transferred between portals or tools. | CEFASaa56c787-3714-47c3-9253-80da10586242 |
| Resource Identifier | This is the code assigned by the data owner. | CEFAS22009 |
| Resource type | The resource type will likely be a dataset but could also be a series (collection of datasets with a common specification) or a service. | dataset |
| Start date | This describes the date the resource starts. This may only be the year if month and day are not known | 2016 |
| End date | This describes the date the resource ends. This may only be the year if month and day are not known | 2025-10-13 |
| Frequency of updates | This describes the frequency with which the resource is modified or updated i.e. a monitoring programme that samples once per year has a frequency that is described as 'annually'. | notPlanned |
| Abstract | The abstract provides a clear and brief statement of the content of the resource. | Laboratory data for experimental exposure of 1,000 Pacific Oysters (Crassostrea (Magallana) gigas) to Ostreid herpesvirus (OsHV-1) in 2016 for the purpose of collecting survival vs mortality and viral load data to estimate heritability of resistance to Ostreid herpesvirus (OsHV-1) using single nucleotide polymorphism (SNP) analysis of the challenged oysters. The dataset take the form of: - Quantitative PCR (qPCR) data for Pacific oysters challenged with OsHV-1. V- iral load was measured in viral copies per mg of tissue, AND the raw data is CT (cycle threshold) values. - Survival and mortality data for the disease challenge, and the position of each oyster within the challenge system - Disease challenge parameters, including feeding, temperature and water quality measurements - Illumina MiSeq derived sequencing data produced from a single oyster experimentally infected with OsHV-1 |
| Lineage | Lineage includes the background information, history of the sources of data, data quality statements and methods. | The data (survival vs mortality and low vs high viral load) were used alongside medium density SNP (single nucleotide polymorphism) data to estimate heritability of resistance to Ostreid herpesvirus (OsHV-1) to identify genomic regions containing putative resistance genes and to inform the use of genomics to enhance efforts to breed for resistance. Oysters used in this study were obtained from multiple crosses of parents provided by Guernsey Sea Farms (UK) and reared at Cefas facilities. The oysters comprised three pair crosses that were created at Cefas (from 3 sires and 2 dams) and each reared separately, while the rest of the crosses (from 14 sires and 14 dams) were obtained as spat from Guernsey Sea Farms and combined into a mixed culture tank at Cefas. Oysters were held at 20 (+/- 2°C) during post-settlement and fed with a combination of Isocrysis, Tetraselmis, Chaetoceros, *Pavlova sp*., and ‘Shellfish Diet 1800’ (a unique mix of five marine microalgae - *Isochrysis, Pavlova, Tetraselmis, Thalassiosira weissflogii & Thalassiosira pseudonana*.), until they reached an appropriate size (>5 mm) at approximately eight months of age. A subsample of approximately 1,000 oysters were then transferred to the challenge tank at 20 (+/- 2°C) for two days for acclimation and then experimentally challenged with a virulent form of OsHV, with samples taken from mortalities and survivors for genotyping and qPCR (quantitative polymerase chain reaction) measurement of viral load. The viral count of all samples is determined by qPCR according to (`Martenot et al. 2010`_), with the additional use of a plasmid-based standard curve cloned for absolute quantification. The estimated copy number was then divided by the weight of the animal (mg) to obtain a measure of the viral load. Viral load values were then normalized by transformation to the logarithmic scale for further analyses. The samples were genotyped using a multi-species oyster SNP array, and the genotype data were used to reconstruct the pedigree. DNA extracted from single oyster experimentally infected with OsHV-1 was subjected to Nextera XT library preparation and sequencing on an Illumina MiSeq, using 2 x 300 bp read length. These data were sent to Ifremer for whole genome assembly of OsHV-1 and comparison to other OsHV-1 genomes collected by Ifremer. Please see the below papers for more detailed information below; `A Genome-Wide Association Study for Host Resistance to Ostreid Herpesvirus in Pacific Oysters (Crassostrea gigas)`_ `Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species`_ .. _`martenot et al. 2010`: https://www.sciencedirect.com/science/article/abs/pii/S0166093410003162?via%3Dihub .. _`a genome-wide association study for host resistance to ostreid herpesvirus in pacific oysters (crassostrea gigas)`: https://academic.oup.com/g3journal/article/8/4/1273/5941681?login=true .. _`genomic diversity of the ostreid herpesvirus type 1 across time and location and among host species`: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.711377/full |
| Related keywords | ||
| Keyword | General subject area(s) associated with the resource, uses multiple controlled vocabularies | Aquaculture |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Agricultural and aquaculture facilities | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Marine Environmental Data and Information Network | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | data.gov.uk | |
| Geographical coverage | ||
| North | The northern-most limit of the data resource in decimal degrees | 52.4595 |
| East | The eastern-most limit of the data resource in decimal degrees | 1.74086 |
| South | The southern-most limit of the data resource in decimal degrees | 52.4581 |
| West | The western-most limit of the data resource in decimal degrees | 1.73881 |
| Responsible organisations | ||
| Role | The point of contact is person or organisation with responsibility for the creation and maintenance of the metadata for the resource. | pointOfContact |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The originator is the person or organisation who created, collected or produced the resource. | originator |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The custodian is the person or organisation that accepts responsibility for the resource and ensures appropriate care and maintenance. If a dataset has been lodged with a Data Archive Centre for maintenance then this organisation is be entered here. | custodian |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The distributor is the person or organisation that distributes the resource. | distributor |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The owner is the person or organisation that owns the resource. | owner |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| data.manager@cefas.co.uk | ||
| Resource locators | ||
| Locator URL | Web address (URL) that links to the resource | https://data.cefas.co.uk/view/22009 |
| Locator name | Name of the web resource | Cefas Data Portal |
| Dataset constraints | ||
| 20.1 Limitations on Public Access - Access constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 20.2 Limitations on Public Access - Other constraints | noLimitations | |
| 21.1 Conditions for Access and Use - Use constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 21.2 Conditions for Access and Use - Other constraints | http://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_RestrictionCode | |
| Version info | ||
| Date of publication | The publication date of the resource or if previously unpublished the date that the resource was made publicly available via the MEDIN network. | 2024-08-21 |
| Date of last revision | The most recent date that the resource was revised. | 2025-10-13 |
| Date of creation | The date that the resource was created. | 2024-08-21 |
| Harvest date | The date which this record has been (re)harvested from the provider. | 2026-04-19 |
| Metadata date | The date when the content of this metadata record was last updated. | 2025-10-13 |
| Metadata standard name | The name of the metadata standard used to create this metadata | MEDIN |
| Metadata standard version | The version of the MEDIN Discovery Metadata Standard used to create the metadata record | 3.1.1 |