Bivalves of the family Lucinidae, Loripes orbiculatus and Lucinoma borealis , are sympatric species inhabiting coastal seagrass beds in Roscoff Bay. These bivalves harbor chemoautotrophic symbionts within their gills that provide autotrophic nutrition to the host by oxidizing hydrogen sulfide (H₂S) present in the sediment. Although Lucinidae are typically considered fully autotrophic in these environments, seagrass beds are subject to fluctuations in sulfide availability due to tides, seasonal changes, and anthropogenic disturbances. This study investigates how Lucinidae cope with periods of low sulfide availability by exploring their nutritional strategies under sulfide starvation. Lucinidae species were incubated for 15 days in the presence of sediment bacteria or a mixture of two phytoplankton species labeled with ¹⁵N and ¹³C, with or without addition of sulfide, to trace assimilation pathways into the gill and visceral mass. Results show that both ¹⁵N and ¹³C were incorporated into tissues within seven days, indicating that lucinids are capable of assimilating both autotrophy- and heterotrophy-derived sources of nutrition. Composition of their associated bacterial communities was not affected. These findings provide evidence of mixotrophy in coastal Lucinidae, indicating that they can shift to filter-feeding under low sulfide availability, probably contributing to their ecological success. Nutritional plasticity of the Lucinidae may be key to their resilience in fluctuating coastal environments.

The European flat oyster Ostrea edulis, the European native species presents a major ecological, economic, and cultural importance. O. edulis populations have experienced a severe decline due to overfishing, habitat destruction, parasitic diseases, and invasive species. This decline led to its classification as a threatened species under the OSPAR Convention. Despite this status, O. edulis plays a crucial role in coastal ecosystems by forming oyster reefs that enhance biodiversity, improve water filtration, and contribute to carbon storage. O. edulis is a protandrous sequential hermaphrodite, alternating between male and female phases in response to environmental conditions, particularly temperature and food availability. Populations are generally characterized by a male-biased sex ratio, which reduces reproductive success. Sex identification remains challenging due to the lack of reliable non-destructive methods. To improve sustainable seed production and support ecological restoration, a deeper understanding of the molecular mechanisms governing gametogenesis is required. This study combines histological and transcriptomic analyses of simultaneously hermaphroditic gonadal tissues of O. edulis to characterize gamete maturation stages and identify key genes and biological processes involved in the reproductive cycle. The identification of molecular markers aims to enhance reproductive management for aquaculture and population restoration.

Anthropogenic underwater noise is a growing environmental stressor in coastal ecosystems, yet its molecular effects on invertebrate early life stages remain poorly understood. Using a data-independent acquisition proteomic workflow, we characterized the proteome of blue mussel (Mytilus edulis) post-larvae and examined changes in protein abundance following exposure to realistic cargo-shipping noise. A total of 7249 proteins were identified, of which 902 showed significant abundance differences across low, medium, and high sound pressure levels (i.e., 121, 127, and 151 dB re 1 μPa, respectively). Functional enrichment and interaction analyses revealed coordinated, intensity-dependent changes in proteins involved in metabolic, cytoskeletal, and regulatory processes. Forty-nine proteins were consistently regulated across treatments, including candidates associated with developmental regulation, morphogenesis, and shell-related pathways, indicating a conserved molecular response to acoustic exposure. Those results provide a reference proteomic dataset for M. edulis post-larvae and highlight proteome-level plasticity associated with shipping-related acoustic disturbance during metamorphosis.

BACKGROUND:Understanding the genetic basis of resilience in marine organisms is critical for conservation and management, particularly in the face of escalating environmental stress and disease outbreaks. The bay scallop Argopecten irradians is a commercially and recreationally important shellfish species found in estuarine and coastal environments of the United States from New England to the Gulf of Mexico. In New York, adult bay scallop populations have been decimated every summer since 2019 leading to the collapse of their fishery. These mortality events were associated with annual outbreaks of an undescribed apicomplexan parasite recently named Bay Scallop Marosporida (BSM) that disrupts scallop kidneys. RESULTS:This study investigates host-pathogen interactions and assesses changes in population structure during BSM-associated mortality events. The research compared wild and aquacultured scallops used for stock enhancement in New York, revealing significant change in population structures throughout the mortality outbreak. The results underscore the selective pressures exerted by BSM infection and environmental stressors, as evidenced by shifts in genetic divergence and allele frequencies particularly in genes associated with kidney function, stress and infection response. Through a detailed genomic and population genetic approach, this research represents a unique case study highlighting the impact of disease on marine biodiversity and advances our understanding of the impact of summer mortality events on the scallop population in NY. CONCLUSIONS:This study highlights changes in the genomic structure of bay scallops during a BSM-associated mortality event. Identified mutations (such as the one in the nephrocystin-3-like gene) represent prime candidates for specific targeted investigations to link genotypes to phenotypes. By integrating genomic and epidemiological data, the research provides a basis for understanding the impact of disease on scallop biodiversity. These findings may help guide conservation strategies for sustainable fisheries in the face of environmental change and disease outbreaks.

Stocks of the European flat oyster, Ostrea edulis, have collapsed due to overfishing, habitat destruction, and pathogen outbreaks across most of their distribution range. Nonetheless, as a result of lower exploitation pressure and the absence of pathogens in the most northern part of the range, a large part of the remaining wild population can be found in relatively high densities in Scandinavia, a region in Northern Europe. However, despite recent studies focusing on flat oyster population structure along the European coast, little is known about the population structure of oysters in the Skagerrak marginal sea in Scandinavia, and how it is related to neighbouring regions. This study, therefore, aimed to investigate the population structure of flat oysters in Scandinavia, with a special emphasis on the Skagerrak. We gathered low-coverage whole-genome sequencing data from oysters in Sweden, Norway, and Denmark, the three countries that border the Skagerrak. Genetic diversity appeared to be homogeneously distributed over the sampled area in the Skagerrak, while samples collected from the east coast of Denmark and from a location with known historical farming activity on the Norwegian West Coast were genetically distinct from Skagerrak samples. A genetic barrier analysis indicated barriers to gene flow in the Baltic Sea transition zone and on the west coast of Norway. Overall, our results suggest that flat oysters from the Swedish Skagerrak coasts form a single panmictic population that is distinct from neighbouring seas, potentially allowing for regional management of stocks and restoration translocations in the area. However, the genetic composition of donor and recipient stocks should be assessed on a case-by-case basis, genetic diversity effects of hatchery practices should be monitored, and biosecurity measures need to be considered prior to any movement of stock.

The flat oyster Ostrea edulis is the native European oyster species, with a distribution extending from the Norwegian Sea in the north to Morocco in the south, and eastward through the Mediterranean to the Black Sea (OSPAR, 2009). Since the 19th century, the flat oyster industry has been in decline, primarily due to habitat destruction, over-exploitation, irregular recruitment, and the emergence of the parasites Marteilia refringens and Bonamia ostreae in the 1970s. O. edulis is a species of both economic and ecological significance, and efforts to protect and restore it have become extensive in response to the gradual decline of European populations. The ecosystem formed by flat oysters plays a crucial role in stabilizing substrates, maintaining water quality, and providing habitat for other species. In 2018, we launched a selective breeding program focused on traits such as hardiness (including survival, growth, and resistance to bonamiasis) with the main goal of producing a broad array of biparental oyster families. These oysters are intended for reintroduction in various locations, aiming to restore natural oyster beds and facilitate reef development. This natural reef reconstruction could, in turn, increase larval emissions, which could be collected for aquaculture purposes. Additionally, the development of new cultivation techniques, such as shore-based flat oyster farming, may help diversify aquaculture practices for industry professionals. At the same time, achieving a thorough understanding and control of the reproductive cycle in this species, based on experimentations and analyses relying on a complete reference genome1,2, opens the door to better-managed larval production in hatcheries, allowing the creation of strains that are well-suited for transfer to population restoration sites. This integrated approach—combining reproductive management, genetic selection, restoration of natural beds, and diversified cultivation practices—aims to revitalize the production of this species and support the restoration of marine ecosystems.1. Boutet et al. 2022. doi: 10.1111/eva.134622. Bean et al. 2022. doi: 10.1111/eva.13465

Bivalves of the family Lucinidae thrive in sulfidic sediments thanks to their chemoautotrophic bacterial symbionts. However, how different Lucinidae species respond to sulfide deprivation and associated symbiont loss remains poorly understood. Here, we investigated the responses of Lucinoma borealis and Loripes orbiculatus, two species that co-occur in temperate seagrass beds, exposed to prolonged sulfide starvation. Using metabolomics, ultrastructural TEM analyses and 16S rRNA-based metabarcoding, we monitored and compared responses in gills and visceral mass over a 4-month period. Both host species as well as their symbionts survived sulfide-free conditions. Hosts tissues displayed limited impact on ultrastructure and metabolites. Despite decrease in numbers and activity level, symbionts remained present throughout the experiment and no evidence for bacteremia or infection was detected. Our results also revealed differences, in particular in host apoptosis response, suggesting species-specific stress strategies. Altogether, both holobionts can survive extended low-sulfide periods without critical damage and without completely losing their symbionts. These could be adaptations to the extended low-sulfide periods that are associated with low primary production and the cold season in seagrass beds. Adaptations could involve a switch in the symbionts' physiological state to preserve a dormant symbiotic population. These findings highlight the importance of stress tolerance mechanisms in coastal Lucinidae, and raise questions about the nature of host–symbiont dependency in these periods.

The hard clam (Mercenaria mercenaria), a marine bivalve distributed along the U.S. eastern seaboard, supports a significant shellfish industry. Overharvest in the 1970s and 1980s led to a reduction in landings. While the transition of industry from wild harvest to aquaculture since that time has enhanced production, it has also exacerbated challenges such as disease outbreaks. In this study, we developed and validated a 66K SNP array designed to advance genetic studies and improve breeding programs in the hard clam, focusing particularly on the development of markers that could be useful in understanding disease resistance and environmental adaptability. Whole-genome resequencing of 84 individual clam samples and 277 pooled clam libraries yielded over 305 million SNPs, which were filtered down to a set of 370,456 SNPs that were used as input for the design of a 66K SNP array. This medium-density array features 66,543 probes targeting coding and non-coding regions, including 70 mitochondrial SNPs, to capture the extensive genetic diversity within the species. The SNPs were distributed evenly throughout the clam genome, with an average interval of 25,641 bp between SNPs. The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly QPX), enhancing its utility in disease management. Performance evaluation on 1,904 samples demonstrated a 72.7

Abalone pearl farming is an aquaculture activity with great potential for future growth and diversification of the global pearl sector, which has been dominated for decades by pearls of marine pearl oysters of the genus Pinctada. Despite this potential, there is a significant lack of knowledge regarding methods for nucleus (bead) seeding and the process of pearl formation in abalone, compared to the well-studied pearl oyster model. To address this problem, this review first compares the main anatomical differences and similarities between both groups of mollusks, particularly those associated with the structure and role of mantle tissue on the synthesis of CaCO3 compounds that integrate the inner nacreous layer. The iridescence (orient) and color properties of nacre in a cultured pearl is particularly related to the microstructure of aragonite crystals during biomineralization in each mollusk group. We then analyze the advantages and disadvantages of the adoption in abalone of methods originally developed for pearl oysters to produce bead-seeded pearls and half-pearls (or mabé pearls). For the red abalone Haliotis rufescens in particular, updated information on commercial production of both bead-seeded and mabé pearls is provided as a case of success for Latin America (Chile). Finally, the current status and future prospects for abalone pearl farming are discussed, assessing technology gaps and challenges to be addressed for the pearl sector to achieve its full potential, particularly for Latin America.

Zebra mussel (ZM), Dreissena polymorpha, commonly used as a sentinel species in freshwater biomonitoring, is now in competition for habitat with quagga mussel (QM), Dreissena rostriformis bugensis. This raises the question of the quagga mussel’s use in environmental survey. To better characterise QM response to stress compared with ZM, both species were exposed to cadmium (100 µg·L−1), a classic pollutant, for 7 days under controlled conditions. The gill proteomes were analysed using two-dimensional electrophoresis coupled with mass spectrometry. For ZM, 81 out of 88 proteoforms of variable abundance were identified using mass spectrometry, and for QM, 105 out of 134. Interestingly, the proteomic response amplitude varied drastically, with 5.6% of proteoforms of variable abundance (DAPs) in ZM versus 9.4% in QM. QM also exhibited greater cadmium accumulation. Only 12 common DAPs were observed. Several short proteoforms were detected, suggesting proteolysis. Functional analysis is consistent with the pleiotropic effects of the toxic metal ion cadmium, with alterations in sulphur and glutathione metabolisms, cellular calcium signalling, cytoskeletal dynamics, energy production, chaperone activation, and membrane events with numerous proteins involved in trafficking and endocytosis/exocytosis processes. Beyond common responses, the sister species display distinct reactions, with cellular response to stress being the main category involved in ZM as opposed to calcium and cytoskeleton alterations in QM. Moreover, QM exhibited greater evidence of proteolysis and cell death. Overall, these results suggest that QM has a weaker stress response capacity than ZM.

The structure and composition of mantle tissue from red abalone Haliotis rufescens were studied in relation to pearl farming. Histological (hematoxylin-eosin) and histochemical (PAS Alcian Blue, Sudan Black, Dahl's) tools were used to determine variations in the glycogen index, lipid index, and calcium coverage index of mantle tissue as a function of seasonality (cold and warm period) and body region (dorsal, central, ventral). Anatomically, only two well-developed and functional mantle folds (inner and outer) were observed across the marginal zone, together with a poorly developed, and presumably, rudimentary fold with the same cellular morphology as the inner fold. The inner mantle epithelium stored significantly higher concentrations of glycogen and mucins, triglycerides, and calcium than the outer epithelium. This pattern occurred significantly more during the cold season than during the warm season. Mucins from mantle tissue not only regulate crystal nucleation and orientation during biomineralization, but also give the inner nacreous layer its luster and color. High concentrations of lipids in mantle tissue could help compensate for the energy loss caused by the wound-healing processes associated with mantle tissue removal and seeding, which are stressful and energetically costly. The absorption of calcium ions from the environment to integrate a microlaminate of calcareous compounds gives the shell its structural properties of hardness and strength. An approach with molecular-ultrastructural tools is recommended to broaden the understanding of mantle tissue regionalization and its relationship to pearl sac formation, which may help increase pearl yield and quality in H. rufescens.

The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

Ostrea edulis, the European flat oyster, was once a widespread economically and ecologically important marine species, but has suffered dramatic declines over the past two centuries. Consequently, there has been a surge in European restoration efforts, many of which focus on restocking as a conservation measure. In this study, we used whole-genome sequencing (WGS) data to investigate the population structure, demographic history, and patterns of local adaptation of O. edulis across its natural distribution with increased sampling densities at Scandinavian localities. Results revealed seven distinct genetic clusters, including previously undescribed complex population structure in Norway, and evidence for introgression between genetic clusters in Scandinavia. We detected large structural variants (SVs) on three pseudo-chromosomes. These megabase long regions were characterised by strong linkage disequilibrium and clear geographical differentiation, suggestive of chromosomal inversions potentially associated with local adaptation. The results indicated that genomic traces of past translocations of non-native O. edulis were still present in some individuals, but overall, we found limited evidence of major impacts of translocations on the scale of contemporary population structure. Our findings highlight the importance of considering population structure and signatures of selection in the design of effective conservation strategies to preserve and restore wild native European flat oyster populations, and we provide direct knowledge safeguarding sustainable mitigation actions in this important species.

Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.

This volume of Evolutionary Applications sees the publication of two genomes for the European native flat oyster Ostrea edulis, a species of significant evolutionary, ecological and commercial value. Each is a highly contiguous chromosome-level assembly from individuals of different genetic backgrounds, which have been benchmarked against one another. This situation has resulted from the serendipitous discovery that two independent research groups were both deep into the process of building, annotating and investigating separately produced assemblies. Due to constraints with funder requirements and the need to recognize early career researchers for their work, alongside the technical challenge of integrating assemblies from two very different genomes, there was limited capacity to merge the sequences into one publication at the stage of discovery. This issue is likely to become very common over the next few years until the technologies for working with multiple genomes at once, for example, graph genomes, become commonplace in nonmodel species. Consequently, both of our teams have decided to collaborate rather than compete, recognizing the benefit to copublishing two separate genome resources for the research community, each with distinct scientific investigations, and working collaboratively to benchmark the assemblies.

The European flat oyster ( Ostrea edulis L.) is a bivalve naturally distributed across Europe that was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here we report a chromosome-level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing. A contig assembly (N50: 2.38Mb) was scaffolded into the expected karyotype of 10 pseudo-chromosomes. The final assembly is 935.13 Mb, with a scaffold-N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis . The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD-Seq technology, comprising 4,016 SNPs from four full-sib families (8 parents and 163 F1 offspring). Annotation of the genome integrating multi-tissue transcriptome data, comparative protein evidence and ab-initio gene prediction identified 35,699 protein-coding genes. Chromosome level synteny was demonstrated against multiple high-quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high-resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.