Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture
2022
Boutet, Isabelle | Alves Monteiro, Homère | Baudry, Lyam | Takeuchi, Takeshi | Bonnivard, Eric | Billoud, Bernard | Farhat, Sarah | Gonzales-Araya, Ricardo | Salaun, Benoit | Andersen, Ann | Toullec, Jean‐yves | Lallier, François | Flot, Jean‐françois | Guiglielmoni, Nadège | Guo, Ximing | Li, Cui | Allam, Bassem | Pales-Espinosa, Emmanuelle | Hemmer-Hansen, Jakob | Moreau, Pierrick | Marbouty, Martial | Koszul, Romain | Tanguy, Arnaud | Station biologique de Roscoff = Roscoff Marine Station (SBR) ; Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) | Adaptation et diversité en milieu marin (ADMM) ; Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR) ; Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) | Danmarks Tekniske Universitet = Technical University of Denmark (DTU) | Régulation spatiale des Génomes - Spatial Regulation of Genomes ; Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS) | Collège Doctoral ; Sorbonne Université (SU) | Okinawa Institute of Science and Technology Graduate University (OIST) | School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS) ; Stony Brook University [SUNY] (SBU) ; State University of New York (SUNY)-State University of New York (SUNY) | Centre Régional de la Conchyliculture Bretagne Nord | Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE) ; Adaptation et diversité en milieu marin (ADMM) ; Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR) ; Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR) ; Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) | Université libre de Bruxelles (ULB) | Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon) ; AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Haskin Shellfish Research Laboratory (HSRL) ; Rutgers, The State University of New Jersey [New Brunswick] (RU) ; Rutgers University System (Rutgers)-Rutgers University System (Rutgers) | Chinese Academy of Sciences [Beijing] (CAS) | Marine Sciences Research Center ; Stony Brook University [SUNY] (SBU) ; State University of New York (SUNY)-State University of New York (SUNY) | This study was funded by the Roscoff_O.edulis-V1 Fonds Européen pour les Affaires Maritimes et la Pêche (FEAMP) (grant code: PFEA470017FA1000016).
International audience
Mostrar más [+] Menos [-]Inglés. The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.
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