CEFASaa56c787-3714-47c3-9253-80da10586242 English dataset Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk pointOfContact 2025-10-13T01:33:30 EPSG Geodetic Parameter Registry 2022-01-07 revision WGS 84 Laboratory data for experimental exposure of Pacific Oysters (Crassostrea (Magallana) gigas) to Ostreid herpesvirus (OsHV-1) in 2016 2024-08-21 publication 2025-10-13 revision 2024-08-21 creation CEFAS22009 https://data.cefas.co.uk 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 Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk originator Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk custodian Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk distributor Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) data.manager@cefas.co.uk owner notPlanned Aquaculture GEMET, version 1.0 2008-06-01 publication Agricultural and aquaculture facilities GEMET - INSPIRE themes, version 1.0 2008-06-01 publication Marine Environmental Data and Information Network MEDIN metadata record availability 2012-01-11 publication data.gov.uk MEDIN metadata record availability 2012-01-11 publication otherRestrictions noLimitations otherRestrictions Public data - no limitations to reuse English farming 1.73881 1.74086 52.4581 52.4595 2016 2025-10-13 Unknown https://data.cefas.co.uk/view/22009 Cefas Data Portal information The Cefas Data Portal contains metadata records and data sets available to download and connect to in support of our commitment to open science. dataset INSPIRE Data Specification on Agricultural and Aquaculture Facilities – Technical Guidelines 2013-12-10 publication false See the referenced specification Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services 2010-12-08 publication true See the referenced specification 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 MEDIN 3.1.1