Applied population genomics in the native European flat oyster (<i>Ostrea edulis</i>)

The native European flat oyster (Ostrea edulis) has been facing challenges since ancient times. Originally found in Europe, we have evidence of important fisheries for the species since the Mesolithic. Cultivation was practiced by the Romans as early as the 2nd century AD. And O. edulis wild stocks continued to be commercially exploited during the Renaissance, leading to overfishing and causing local extinction. Anthropogenic activities have also played a significant role in the spread of lethal disease that further depleted natural populations. Today, multiple projects are underway to restore the O. edulis habitat and overcome its decline.This Phd thesis participates in advancing our understanding of the restoration success for the native European flat oyster, by examining the genetic diversity of the species wild and cultured populations, and offering recommendations for genetic monitoring and hatchery production protocols.Initial findings, grounded in the assembly of a high-quality O. edulis genome, elucidates the population structure of wild remnants O. edulis populations and sheds light on the structural variation in their genomes, including the discovery of previously unidentified genetic clusters of natural population in Scandinavia. We also probed into the potential effects of local adaptation and analyzed geographical heterogeneity in genomic regions linked to resistance to Bonamia ostrea, a parasite significantly affecting local populations and restoration programmes.Then, investigations into the best protocols for maintaining genetic diversity reveal that active management, combined with genetic monitoring of spat production methods, is critical in preventing the loss of genetic diversity in hatchery strains. The findings underscore the Ryman-Laikre effects as a substantial challenge in flat oyster restoration. In response, we propose a method to estimate parentage, relatedness, and genetic variation in both wild and hatchery scenarios as an effective tool to control and implement new hatchery protocols.Lastly, the implications of hatchery-reared oyster supplementation for population genetic diversity were investigated. We observe profound genomic changes even after a few generations, emphasizing the necessity for genetic diversity monitoring in hatcheries. Consequently, we propose the implementation of production protocols that aim to limit genomic change away from origin source populations and suggest a focus on natural recruitment processes for local biodiversity. The outcomes of this research contribute to the knowledge base required for effective restoration programmes of O. edulis, ultimately enhancing ecosystem function and supporting sustainable, low-carbon emission food resources

Genetic parentage reconstruction as a practical tool applied to aquaculture and restoration programs for the European flat oyster, <i>Ostrea edulis</i>

Preserving and maximizing genetic diversity in conservation programs, including for restocking, are of high importance. The threatened European flat oyster (Ostrea edulis) is currently the subject of several applied conservation and restocking programs, but concerns have been raised over potential negative side effects of these programs, for example due to our limited knowledge about the genetic effects in natural populations of releasing offspring of hatchery origin. Here, we developed an effective, easily applicable and highly reliable method to assess the genetic diversity and parental contributions in flat oyster hatchery production based on analyses of 17 microsatellite loci. We analysed four broodstocks and their hatchery-reared spat (total n = 354) and compared diversity to that in wild samples of adults and spat from the broodstock source in the Limfjorden (total n = 138). Based on four hatchery tank experiments with fully resolved parentage assignments, we found that five swarming events (larval releases) were characterized by a single maternal and multiple paternal contributions, and that the number of contributing parents varied greatly both among individual tanks, and between swarming events within tank. On average, the effective number of breeders was only one third of the actual broodstock size. Although the broodstock exhibited high genetic variation, the high reproductive skew resulted in produced offspring representing only a relatively small subset of this variation. The work demonstrates potential impact of hatchery reared offspring on decreasing genetic diversity in wild populations, but also that genetic monitoring can be integrated in conservation programs to minimize negative effects on restoration and supplementary restocking programs that utilize hatchery reared spats to support natural populations

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

International audienceThe 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

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

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