RT Journal Article SR Electronic T1 Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic ressource for aquaculture JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.06.26.497643 DO 10.1101/2022.06.26.497643 A1 Isabelle Boutet A1 Homère J. Alves Monteiro A1 Lyam Baudry A1 Takeshi Takeuchi A1 Eric Bonnivard A1 Bernard Billoud A1 Sarah Farhat A1 Ricardo Gonzales-Haraya A1 Benoit Salaun A1 Ann Andersen A1 Jean-Yves Toullec A1 François Lallier A1 Jean-François Flot A1 Nadège Guiglielmoni A1 Ximing Guo A1 Li Cui A1 Bassem Allam A1 Emmanuelle Pales-Espinoza A1 Jakob Hemmer-Hansen A1 Martial Marbouty A1 Romain Koszul A1 Arnaud Tanguy YR 2022 UL http://biorxiv.org/content/early/2022/06/28/2022.06.26.497643.abstract AB The European flat oyster (Ostrea edulis L.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds. O. edulis has been the subject of numerous studies and programs in population genetics and on the presence of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which 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 on the foreshore, obtaining a reference genome has proved to be 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 technology, 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 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response of O. edulis to M. refringens. This genome will serve as a reference for genomic studies on O. edulis to better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.Competing Interest StatementThe authors have declared no competing interest.