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Background In France, two main diseases threaten Pacific oyster production. Since 2008, Crassostrea gigas spat have suffered massive losses due to the ostreid herpesvirus OsHV-1, and since 2012, significant mortalities in commercial-size adults have been related to infection by the bacterium Vibrio aestuarianus . The genetic basis for resistance to V. aestuarianus and OsHV-1 and the nature of the genetic correlation between these two traits were investigated by using 20 half-sib sire families, each containing two full-sib families. For each disease, controlled infectious challenges were conducted using naïve oysters that were 3 to 26 months old. In addition, siblings were tested under field, pond and raceway conditions to determine whether laboratory trials reflected mortality events that occur in the oyster industry. Results First, we estimated the genetic basis of resistance to V. aestuarianus in C. gigas . Susceptibility to the infection was low for oysters in spat stage but increased with later life stages. Second, we confirmed a strong genetic basis of resistance to OsHV-1 infection at early stages and demonstrated that it was also strong at later stages. Most families had increased resistance to OsHV-1 infection from the spat to adult stages, while others consistently showed low or high mortality rates related to OsHV-1 infection, regardless of the life stage. Our third main finding was the absence of genetic correlations between resistance to OsHV-1 infection and resistance to V. aestuarianus infection. Conclusions Selective breeding to enhance resistance to OsHV-1 infection could be achieved through selective breeding at early stages and would not affect resistance to V. aestuarianus infection. However, our results suggest that the potential to select for improved resistance to V. aestuarianus is lower. Selection for dual resistance to OsHV-1 and V. aestuarianus infection in C. gigas might reduce the impact of these two major diseases by selecting families that have the highest breeding values for resistance to both diseases.

A large number of Crassostrea oysters are found in Asia-Pacific. While analyses of interspecific variation have helped to establish historical relationships among these species, studies on intraspecific variation are necessary to understand their recent evolutionary history and current forces driving population biology. We resequenced 18 and analyzed 31 mitogenomes of five Crassostrea species from China: Crassostrea gigas, Crassostrea angulata, Crassostrea sikamea, Crassostrea ariakensis, and Crassostrea hongkongensis. Our analysis finds abundant insertions, deletions, and single-nucleotide polymorphisms in all species. Intraspecific variation varies greatly among species with polymorphic sites ranging from 54 to 293 and nucleotide diversity ranging from 0.00106 to 0.00683. In all measurements, C. hongkongensis that has the narrowest geographic distribution exhibits the least sequence diversity; C. ariakensis that has the widest distribution shows the highest diversity, and species with intermediate distribution show intermediate levels of diversity. Low sequence diversity in C. hongkongensis may reflect recent bottlenecks that are probably exacerbated by human transplantation. High diversity in C. ariakensis is likely due to divergence of northern and southern China populations that have been separated without gene flow. The significant differences in mitogenome diversity suggest that the five sister species of Crassostrea have experienced different evolutionary forces since their divergence. The recent divergence of two C. ariakensis populations and the C. gigas/angulata species complex provides evidence for continued diversification and speciation of Crassostrea species along China’s coast, which are shaped by unknown mechanisms in a north–south divide.

Infectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas , the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. Viral replication leads to the host entering an immune-compromised state, evolving towards subsequent bacteraemia by opportunistic bacteria. We propose the application of our integrative approach to decipher other multifactorial diseases that affect non-model species worldwide. Pacific oyster mortality syndrome is a poorly understood cause of mortality in commercially important oyster species. Here, the authors use multiple infection experiments to show that the syndrome is caused by sequential infection by herpesvirus and opportunistic bacteria.

As a benthic filter-feeder of estuaries, the eastern oyster, Crassostrea virginica , faces tremendous exposure to microbial pathogens. How eastern oysters without adaptive immunity survive in pathogen-rich environments is of fundamental interest, but studies on its immune system are hindered by the lack of genomic resources. We sequenced the transcriptome of an adult oyster with short Illumina reads and assembled 66,229 contigs with a N50 length of 1,503 bp. The assembly covered 89.4 % of published ESTs and 97.9 % of mitochondrial genes demonstrating its quality. A set of 39,978 contigs and unigenes (>300 bp) were identified and annotated by searching public databases. Analysis of the gene set yielded a diverse set of 657 genes related to innate immunity, including many pertaining to pattern recognition, effectors, signal transduction, cytokines, and apoptosis. Gene families encoding C1q domain containing proteins, CTLD, IAPs, Ig_I-set, and TRAFs expanded in C. virginica and Crassostrea gigas . Many key genes of the apoptosis system including IAP , BAX , BAC -2, caspase, FADD , and TNFR were identified, suggesting C. virginica posses advanced apoptosis and apoptosis-regulating systems. Our results show that short Illumina reads can produce transcriptomes of highly polymorphic genomes with coverage and integrity comparable to that from longer 454 reads. The expansion and high diversity in gene families related to innate immunity, point to a complex defense system in the lophotrochozoan C. virginica , probably in adaptation to a pathogen-rich environment.

Background Adrenergic receptors (ARs) specifically recognize and bind catecholamines via conserved seven-transmembrane G protein-coupled receptor (GPCR) domains, which are regarded as critical mediators of immune responses in molluscan species. Results In the present study, six ARs were identified in the Pacific oyster Crassostrea gigas , which exhibited conserved structural features of G protein-coupled receptors (GPCRs that were characterized by seven transmembrane helices (TM1–TM7) and a DR(Y) motif within the third intracellular loop. These receptors were classified into two subfamilies: α-type ( Cg α1A, Cg α2A, Cg α2C, Cg α2Da, and Cg α2Db-ARs) and β-type ( Cg β2-AR). Notably, evolutionary divergence between the Cg α2Da and Cg α2Db subtypes has led to the absence of their orthologs in most vertebrate species. Both subtypes ( Cg α2Da and Cg α2Db) are under relaxed purifying selection (Ka/Ks = 0.644 and 0.828, respectively). Transcriptomic profiling revealed distinct spatiotemporal expression patterns, with Cg α2A-AR, Cg α2C-AR, and Cg α2Da-AR predominantly expressed in hemocytes. Among them, Cg α2C-AR and Cg α2Da-AR were enriched in granulocytes, whereas Cg α2A-AR was preferentially expressed in agranulocytes. Moreover, transcripts of Cg α2A-AR, Cg α2C-AR, and Cg β2-AR in hemocytes increased significantly following the first Vibrio splendidus stimulation, with Cg α2A-AR exhibiting a significant increase again after the secondary stimulation. Conclusions Collectively, these results suggested that the retention of Cg α2Da/α2Db-AR subtypes in oysters under relaxed selection pressure reflects an evolutionary strategy for immune adaptability. Their lineage-restricted diversification drives differential expression (e.g., Cg α2Da-AR in granulocytes) and post-challenge resilience (e.g., Cg α2A-AR upregulation), balancing energy conservation and pathogen defense. These findings provided a foundation for further elucidation of their immunoregulatory roles in oysters and contribute to an improved understanding of AR evolution in invertebrates.

Background Primordial germ cells (PGCs) are the precursor cells of gametes and pivotal in understanding reproductive and developmental biology. Importantly, having a thorough understanding of PGC specification is leading to critical advances in sterility induction in aquaculture species. In shellfish, however, the ability to develop these approaches is hampered by the lack of information available regarding germ cell specification. The goal of this study was to identify genes uniquely expressed in these earliest germ cells of the economically and ecologically important bivalve mollusc, the Pacific oyster ( Crassostrea ( Magallana ) gigas ). Results To capture specification of the PGCs - which represent a rare cell type - during embryonic development, we analyzed single-cell transcriptomes during cleavage, blastula, and gastrulation stages of C. gigas development. We identified cells in gastrulae that likely represent developing, distinct larval tissue types and organs, including muscles and shell gland, as well as undifferentiated cells. Using expression of the germ cell marker gene vasa , we identified cells in blastulae that likely represent the developing germ cell lineage that had yet to fully differentiate and segregate from somatic cell types. However, by the gastrula stage, vasa expression was limited primarily to a single cluster of cells. Other genes uniquely expressed in these vasa -positive cells include those with functions in transcriptional repression, chromatin architecture, and DNA repair, suggesting these cells represent oyster PGCs. Interestingly, some genes with no known homologies are also uniquely expressed in this cluster, perhaps representing novel PGC-associated genes in bivalves. Conclusions We identified a suite of candidate genes that can be explored for their role in oyster PGC specification and advance efforts to develop methods to achieve reproductive sterility via germ cell disruption in cultured shellfish. In addition, this effort produced a transcriptional atlas of early developmental cell states in bivalve embryos, providing a wealth of information on genes contributing to other important developmental processes, such as tissue differentiation and shell production. These data represent the earliest developmental stages examined via single-cell RNA sequencing in a lophotrochozoan.

The evolution of TLR-mediated innate immunity is a fundamental question in immunology. Here, we report the characterization and functional analysis of four TLR members in the lophotrochozoans Crassostreagigas (CgTLRs). All CgTLRs bear a conserved domain organization and have a close relationship with TLRs in ancient non-vertebrate chordates. In HEK293 cells, every CgTLR could constitutively activate NF-κB responsive reporter, but none of the PAMPs tested could stimulate CgTLR-activated NF-κB induction. Subcellular localization showed that CgTLR members have similar and dual distribution on late endosomes and plasma membranes. Moreover, CgTLRs and CgMyD88 mRNA show a consistent response to multiple PAMP challenges in oyster hemocytes. As CgTLR-mediated NF-κB activation is dependent on CgMyD88, we designed a blocking peptide for CgTLR signaling that would inhibit CgTLR-CgMyD88 dependent NF-κB activation. This was used to demonstrate that a Vibrio parahaemolyticus infection-induced enhancement of degranulation and increase of cytokines TNF mRNA in hemocytes, could be inhibited by blocking CgTLR signaling. In summary, our study characterized the primitive TLRs in the lophotrocozoan C. gigas and demonstrated a fundamental role of TLR signaling in infection-induced hemocyte activation. This provides further evidence for an ancient origin of TLR-mediated innate immunity.

Background Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to CO 2 -acidified seawater to identify genes correlated with initial shell deposition. Results By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process. Conclusions Using an RNA-Seq approach with high temporal resolution allows us to identify a conceptual model for how oyster larval calcification is initiated. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.

Human activities have increased atmospheric concentrations of carbon dioxide by 36% during the past 200 years. One third of all anthropogenic CO(2) has been absorbed by the oceans, reducing pH by about 0.1 of a unit and significantly altering their carbonate chemistry. There is widespread concern that these changes are altering marine habitats severely, but little or no attention has been given to the biota of estuarine and coastal settings, ecosystems that are less pH buffered because of naturally reduced alkalinity. To address CO(2)-induced changes to estuarine calcification, veliger larvae of two oyster species, the Eastern oyster (Crassostrea virginica), and the Suminoe oyster (Crassostrea ariakensis) were grown in estuarine water under four pCO(2) regimes, 280, 380, 560 and 800 microatm, to simulate atmospheric conditions in the pre-industrial era, present, and projected future concentrations in 50 and 100 years respectively. CO(2) manipulations were made using an automated negative feedback control system that allowed continuous and precise control over the pCO(2) in experimental aquaria. Larval growth was measured using image analysis, and calcification was measured by chemical analysis of calcium in their shells. C. virginica experienced a 16% decrease in shell area and a 42% reduction in calcium content when pre-industrial and end of 21(st) century pCO(2) treatments were compared. C. ariakensis showed no change to either growth or calcification. Both species demonstrated net calcification and growth, even when aragonite was undersaturated, a result that runs counter to previous expectations for invertebrate larvae that produce aragonite shells. Our results suggest that temperate estuarine and coastal ecosystems are vulnerable to the expected changes in water chemistry due to elevated atmospheric CO(2) and that biological responses to acidification, especially calcifying biota, will be species-specific and therefore much more variable and complex than reported previously.

Molluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis. Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas. Larval SMPs are almost entirely different from those of adults in both species. RNA-seq data also confirm that gene expression profiles for larval and adult shell formation are nearly completely different. Therefore, bivalves have two repertoires of SMP genes to construct larval and adult shells. Despite considerable differences in larval and adult SMPs, some functional domains are shared by both SMP repertoires. Conserved domains include von Willebrand factor type A (VWA), chitin-binding (CB), carbonic anhydrase (CA), and acidic domains. These conserved domains are thought to play crucial roles in shell formation. Furthermore, a comprehensive survey of animal genomes revealed that the CA and VWA–CB domain-containing protein families expanded in molluscs after their separation from other Lophotrochozoan linages such as the Brachiopoda. After gene expansion, some family members were co-opted for molluscan SMPs that may have triggered to develop mineralized shells from ancestral, nonmineralized chitinous exoskeletons.