SNP panels genotyping data for the genetic characterization of cupped oyster resources in Europe

Date 2020-02-21
Author(s) Lapegue SylvieORCID1, 2, 3, Heurtebise Serge3, Cornette Florence1, 2, 3, Guichoux Erwan4, Gagnaire Pierre-Alexandre5
Affiliation(s) 1 : IFREMER, UMR MARBEC,Montpellier, France
2 : MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
3 : IFREMER SG2M-LGPMM, La Tremblade, France
4 : BIOGECO, INRA, Univ. Bordeaux, Cestas, France
5 : ISEM - CNRS, UMR5554, SMEL, Montpellier, France
DOI 10.17882/71545
Publisher SEANOE
Keyword(s) cupped oysters, population genetics, introgression, conservation, shellfisheries
Abstract

The Pacific oyster, Crassostrea gigas, has been voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry following a severe disease outbreak. Since then, the two species are in contact in southern Europe and therefore have the potential to exchange genes in a new environment. Whether C. gigas and C. angulata truly represent biological species, semi-isolated species of populations of the same species has been largely discussed. This has been recently clarified by a genome-wide approach providing empirical evidence for highly heterogeneous divergence patterns across the genome, attributed to reduced introgression in low-recombining regions since secondary contact. Up to now only one mitochondrial and one nuclear marker have been used to differentiate C. gigas and C. angulata. Here, we selected a subset of ancestry informative makers from existing genomic resources in order to (1) easily differentiate C. gigas and C. angulata, and (2) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic coasts. In this context several datasets were produced using 15 to 80 SNP markers.

Licence CC-BY
Acknowledgements We are very grateful to all our colleagues who contributed to the collection of samples: F. Batista, S. Pouvreau, H. Palvadeau, J.F. Bouget, P. Soletchnik, J.-L. Seugnet, P. Geairon, F. D’Amico, F. Lagarde. We thank J. Haure, M. Chapat, and the hatchery team of Ifremer La Tremblade for their help in the production of some biological material. MassARRAY genotyping was performed at the Genome Transcriptome Facility of Bordeaux with the help of Adline Delcamp and Marie Massot. This work was supported by Ifremer, the ANR project HYSEA (no. ANR-12-BSV7-0011) and DPMA (Direction des Pêches Maritimes et de l’Aquaculture) project ECOSCOPA. The Genome Transcriptome Facility of Bordeaux received grants from Investissements d’Avenir, Convention attributive d’aide EquipEx Xyloforest ANR-10-EQPX-16-01.
Data
File Size Format Processing Access
Genotypes obtained in the development of the ancestry informative panel (Study 1) 8 KB CSV Quality controlled data Open access
Genotypes obtained to confirm the power of the ancestry informative panel (Study 2) 16 KB CSV Quality controlled data Open access
Genotypes obtained to characterize the Euopean cupped oyster diversity (Study 3) 219 KB CSV Quality controlled data Open access
List and characteristics of all the samples used 18 KB DOC, DOCX Quality controlled data Open access
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How to cite 

Lapegue Sylvie, Heurtebise Serge, Cornette Florence, Guichoux Erwan, Gagnaire Pierre-Alexandre (2020). SNP panels genotyping data for the genetic characterization of cupped oyster resources in Europe. SEANOE. https://doi.org/10.17882/71545