Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture.

Autor: Boutet I; Sorbonne Université, CNRS, UMR 7144 Station Biologique de Roscoff Roscoff France., Alves Monteiro HJ; National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark., Baudry L; Institut Pasteur Unité Régulation Spatiale des Génomes, CNRS Paris France., Takeuchi T; Marine Genomics Unit Okinawa Institute of Science and Technology Graduate University Okinawa Japan., Bonnivard E; Sorbonne Université, CNRS, UMR 7144 Station Biologique de Roscoff Roscoff France., Billoud B; Sorbonne Université, CNRS UMR 8227, Station Biologique de Roscoff Roscoff France., Farhat S; Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York USA., Gonzales-Araya R; Centre Régional de la Conchyliculture Bretagne Nord Morlaix France., Salaun B; Centre Régional de la Conchyliculture Bretagne Nord Morlaix France., Andersen AC; Sorbonne Université, CNRS, UMR 7144 Station Biologique de Roscoff Roscoff France., Toullec JY; Sorbonne Université, CNRS, UMR 7144 Station Biologique de Roscoff Roscoff France., Lallier FH; Sorbonne Université, CNRS, UMR 7144 Station Biologique de Roscoff Roscoff France., Flot JF; Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium., Guiglielmoni N; Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium., Guo X; Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences Rutgers University Port Norris New Jersey USA., Li C; Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China., Allam B; Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York USA., Pales-Espinosa E; Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York USA., Hemmer-Hansen J; National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark., Moreau P; Institut Pasteur Unité Régulation Spatiale des Génomes, CNRS Paris France., Marbouty M; Institut Pasteur Unité Régulation Spatiale des Génomes, CNRS Paris France., Koszul R; Institut Pasteur Unité Régulation Spatiale des Génomes, CNRS Paris France., Tanguy A; Sorbonne Université, CNRS, UMR 7144 Station Biologique de Roscoff Roscoff France.
Jazyk: angličtina
Zdroj: Evolutionary applications [Evol Appl] 2022 Oct 10; Vol. 15 (11), pp. 1730-1748. Date of Electronic Publication: 2022 Oct 10 (Print Publication: 2022).
DOI: 10.1111/eva.13462
Abstrakt: 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.
Competing Interests: The authors declare no conflicts of interest.
(© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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