Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis

Physiological and transcriptomic analysis provides new insights into osmoregulation mechanism of Ruditapes philippinarum under low and high salinity stress

The Manila clam (Ruditapes philippinarum) is a commercially important marine bivalve, which inhabits the estuarine and mudflat areas. The osmoregulation is of great significance for molluscs adaptation to salinity fluctuations. In this study, we investigated the effects of low salinity (10 psu) and high salinity (40 psu) stress on survival and osmoregulation of the R. philippinarum. The results of physiological parameters showed that the ion (Na+, K+, Cl-) concentrations and Na+/K+-ATPase (NKA) activity of R. philippinarum decreased significantly under low salinity stress, but increased significantly under high salinity stress, indicating that there are differences in physiological adaptation of osmoregulation of R. philippinarum. In addition, we conducted the transcriptome analysis in the gills of R. philippinarum exposed to low (10 psu) and high (40 psu) salinity challenge for 48 h using RNA-seq technology. A total of 153 and 640 differentially expressed genes (DEGs) were identified in the low salinity (LS) group and high salinity (HS) group, respectively. The immune (IAP, TLR6, C1QL4, Ank3), ion transport (Slc34a2, SLC39A14), energy metabolism (PCK1, LDLRA, ACOX1) and DNA damage repair-related genes (Gadd45g, HSP70B2, GATA4) as well as FoxO, protein processing in endoplasmic reticulum and endocytosis pathways were involved in osmoregulation under low salinity stress of R. philippinarum. Conversely, the ion transport (SLC6A7, SLC6A9, SLC6A14, TRPM2), amino acid metabolism (GS, TauD, ABAT, ALDH4A1) and immune-related genes (MAP2K6, BIRC7A, CTSK, GVIN1), and amino acid metabolism pathways (beta-Alanine, Alanine, aspartate and glutamate, Glutathione) were involved in the process of osmoregulation under high salinity stress. The results obtained here revealed the difference of osmoregulation mechanism of R. philippinarum under low and high salinity stress through physiological and molecular levels. This study contributes to the assessment of salinity adaptation of bivalves in the context of climate change and provides useful information for marine resource conservation and aquaculture.

A common garden experiment supports a genetic component underlying the increased resilience of common cockle (Cerastoderma edule) to the parasite Marteilia cochillia

The common cockle is a valuable bivalve species inhabiting the Atlantic European coasts. The parasite Marteilia cochillia has devastated cockle beds in the southern Galician (NW Spain) rias since 2012. Previous data suggested that cockles from Ría de Arousa acquired some resilience to this parasite through natural selection after consecutive annual marteiliosis outbreaks and candidate markers associated with marteiliosis resilience were identified using population genomics and transcriptomics approaches. Here, a common garden experiment was performed using a naïve stock (from Ría de Muros-Noia) and an affected stock (from Ría de Arousa) to test this hypothesis. Breeders from both stocks were used to produce seed cohorts at hatchery, which were pre-grown in a raft (outdoor nursery stage) and deployed in two shellfish beds affected by marteiliosis in Ría de Arousa (growing-out stage). In both beds, the naïve stock showed high marteiliosis prevalence and was fully depleted in a short period, while the affected stock barely showed evidence of marteiliosis. A set of 45 SNPs putatively associated with marteiliosis resilience were fitted for MassARRAY genotyping to check their role in the differential resilience detected between both stocks. Though no significant differentiation was found between the naïve and the affected stocks with neutral markers, 28 SNPs showed significant divergence between them, suggesting that these SNPs were involved in directional selection during eight generations (to the most) of marteiliosis pressure (long-term selection). Furthermore, signals of selection were also detected in the naïve stock along the marteiliosis outbreak in the growing-out stage (short-term selection) and six SNPs, all shared with the long-term evaluation, showed consistent signals of differentiation according to the infection severity. Some of these SNPs were located within immune genes pertaining to families such as proteasome, ubiquitin, tumor necrosis factor, and glutathione S-transferase. These resilience-associated markers will be useful to recover cockle production in Galicia.

Host-microbiota interactions play a crucial role in oyster adaptation to rising seawater temperature in summer

Climate change, represented by rising and fluctuating temperature, induces systematic changes in marine organisms and in their bacterial symbionts. However, the role of host-microbiota interactions in the host's response to rising temperature and the underlying mechanisms are incompletely understood in marine organisms. Here, the symbiotic intestinal microbiota and transcriptional responses between diploid and triploid oysters that displayed susceptible and resistant performance under the stress of rising temperature during a summer mortality event were compared to investigate the host-microbiota interactions. The rising and fluctuating temperatures triggered an earlier onset and higher mortality in susceptible oysters (46.7%) than in resistant oysters (17.3%). Correlation analysis between microbial properties and environmental factors showed temperature was strongly correlated with indices of α-diversity and the abundance of top 10 phyla, indicating that temperature significantly shaped the intestinal microbiota of oysters. The microbiota structure of resistant oysters exhibited more rapid changes in composition and diversity compared to susceptible oysters before peak mortality, indicating that resistant oysters possessed a stronger ability to regulate their symbiotic microbiota. Meanwhile, linear discriminant analysis effect size (LefSe) analysis found that the probiotics Verrucomicrobiales and Clostridiales were highly enriched in resistant oysters, and that potential pathogens Betaproteobacteriales and Acidobacteriales were enriched in susceptible oysters. These results implied that the symbiotic microbiota played a significant role in the oysters' adaptation to rising temperature. Accompanying the decrease in unfavorable bacteria before peak mortality, genes related to phagocytosis and lysozymes were upregulated and the xenobiotics elimination pathway was exclusively expressed in resistant oysters, demonstrating the validity of these immunological functions in controlling proliferation of pathogens driven by rising temperature. Compromised immunological functions might lead to proliferation of pathogens in susceptible oysters. This study might uncover a conserved mechanism of adaptation to rising temperature in marine invertebrates from the perspective of interactions between host and symbiotic microbiota.

Transcriptomic identification of key genes in Pacific oysters Crassostrea gigas responding to major abiotic and biotic stressors

Oysters are commercially important intertidal filter-feeding species. Mass mortality events of oysters often occur due to environmental stresses, such as exposure to fluctuating temperatures, salinity, and air, as well as to metal pollution and pathogen infection. Here, RNA-seq data were used to identify shared and specific responsive genes by differential gene expression analysis and weighted gene co-expression network analysis. A total of 18 up-regulated and 10 down-regulated shared responsive genes were identified corresponding to five different stressors. Total 27 stressor-specific genes for temperature, 11 for salinity, 80 for air exposure, 51 for metal pollution, and 636 for Vibrio mediterranei pathogen stress were identified in oysters. Elongin-β was identified as a crucial gene for thermal stress response. Some HSP70s were determined to be shared responsive genes while others were specific to thermal tolerance. The proteins encoded by these stress-related genes should be further investigated to characterize their physiological functions. In addition, the uncharacterized proteins and ncRNAs that were identified may be involved in species-specific stress-response and regulatory mechanisms. This study identified specific genes related to stressors relevant to oyster cultivation. These findings provide useful information for new selective breeding strategies using a data driven method.

PacBio Full-Length and Illumina Transcriptomes of the Gill Reveal the Molecular Response of Corbicula fluminea under Aerial Exposure

Air exposure is a common stress for Corbicula fluminea, an economically important freshwater shellfish consumed in China, during aquaculture and transportation. However, little is known about its molecular responses to air exposure. Therefore, this study used a combination of PacBio full-length and Illumina transcriptomes to investigate its molecular responses to air exposure. A total of 36,772 transcripts were obtained using PacBio sequencing. Structural analysis identified 32,069 coding sequences, 1906 transcription factors, 8873 simple sequence repeats, and 17,815 long non-coding RNAs. Subcellular localization analysis showed that most transcripts were located in the cytoplasm and nucleus. After 96-h of air exposure, 210 differentially expressed genes (DEGs) in the gill were obtained via Illumina sequencing. Among these DEGs, most of the genes related to glycolysis, tricarboxylic acid cycle, lipid metabolism, and amino acid metabolism were upregulated. Additionally, many DEGs associated with immunity, cytoskeleton reorganization, autophagy, and ferroptosis were identified. These findings indicated that metabolic strategy change, immune response, cytoskeleton reconstruction, autophagy, and ferroptosis might be the important mechanisms that C. fluminea use to cope with air exposure. This study will enrich the gene resources of C. fluminea and provide valuable data for studying the molecular mechanisms coping with air exposure in C. fluminea and other freshwater mollusks.

Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification

Background

There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization.

Results

Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation.

Conclusions

Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08781-5.

Synergistic Interaction of Low Salinity Stress With Vibrio Infection Causes Mass Mortalities in the Oyster by Inducing Host Microflora Imbalance and Immune Dysregulation

A sudden drop in salinity following extreme precipitation events usually causes mass mortality of oysters exposed to pathogens in ocean environment. While how low salinity stress interacts with pathogens to cause mass mortality remains obscure. In this study, we performed an experiment by low salinity stress and pathogen infection with Vibrio alginolyticus to investigate their synergistic effect on the mortality of the Pacific oyster toward understanding of the interaction among environment, host, and pathogen. We showed that low salinity stress did not significantly affect proliferation and virulence of V. alginolyticus, but significantly altered microbial composition and immune response of infected oysters. Microbial community profiling by 16S rRNA amplicon sequencing revealed disrupted homeostasis of digestive bacterial microbiota with the abundance of several pathogenic bacteria being increased, which may affect the pathogenesis in infected oysters. Transcriptome profiling of infected oysters revealed that a large number of genes associated with apoptosis and inflammation were significantly upregulated under low salinity, suggesting that low salinity stress may have triggered immune dysregulation in infected oysters. Our results suggest that host-pathogen interactions are strongly affected by low salinity stress, which is of great significance for assessing future environmental risk of pathogenic diseases, decoding the interaction among environment, host genetics and commensal microbes, and disease surveillance in the oyster.

Transcriptome analysis of the mantle tissue of Pinctada fucata with red and black shells under salinity stress

To understand the molecular responses of Pinctada fucata with different shell colors to salinity stress, we used transcriptome sequencing on the mantle of P. fucata with a black shell and red shell color under the salinity of 20, 35, and 50. The 414 and 2371 differentially expressed genes (DEGs) in P. fucata with a black shell under low- or high-salt stress, while there were 588 and 3009 DEGs in P. fucata with a red shell. KEGG pathway enrichment analysis showed that, under low salt stress, the DEGs of P. fucata with the black shell were significantly enriched in pathways MAPK signaling pathway, protein processing in endoplasmic reticulum, vitamin B6 metabolism, longevity regulating pathway-multiple species, estrogen signaling pathway and antigen processing and presentation, the DEGs of P. fucata with a red shell were significantly enriched in pathways vitamin B6 metabolism. Under high salt stress, the DEGs of P. fucata with a red shell were significantly enriched in pathways arginine biosynthesis. 11 DEGs were randomly selected for quantitative real-time PCR, and the results were consistent with the RNA-seq. In addition, under high salt stress, DEGs were enriched into some pathways related to osmotic regulation and immune defense of P. fucata with black shell and red shell, such as Glycolysis / Gluconeogenesis, AMPK signaling pathway, Beta-Alanine metabolism, Glycine, serine and threonine metabolism, MAPK signaling pathway and Phagosome. The study showed that high salt stress had a greater influence on P. fucata with two shell colors, and P. fucata with a black shell made a positive immune defense response. Our results will improve to further understand the salt tolerance mechanism of P. fucata with different shell colors.

The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

Background

Apoptosis plays important roles in a variety of functions, including immunity and response to environmental stress. The Inhibitor of Apoptosis (IAP) gene family of apoptosis regulators is expanded in molluscs, including eastern, Crassostrea virginica, and Pacific, Crassostrea gigas, oysters. The functional importance of IAP expansion in apoptosis and immunity in oysters remains unknown.

Results

Phylogenetic analysis of IAP genes in 10 molluscs identified lineage specific gene expansion in bivalve species. Greater IAP gene family expansion was observed in C. virginica than C. gigas (69 vs. 40), resulting mainly from tandem duplications. Functional domain analysis of oyster IAP proteins revealed 3 novel Baculoviral IAP Repeat (BIR) domain types and 14 domain architecture types across gene clusters, 4 of which are not present in model organisms. Phylogenetic analysis of bivalve IAPs suggests a complex history of domain loss and gain. Most IAP genes in oysters (76% of C. virginica and 82% of C. gigas), representing all domain architecture types, were expressed in response to immune challenge (Ostreid Herpesvirus OsHV-1, bacterial probionts Phaeobacter inhibens and Bacillus pumilus, several Vibrio spp., pathogenic Aliiroseovarius crassostreae, and protozoan parasite Perkinsus marinus). Patterns of IAP and apoptosis-related differential gene expression differed between the two oyster species, where C. virginica, in general, differentially expressed a unique set of IAP genes in each challenge, while C. gigas differentially expressed an overlapping set of IAP genes across challenges. Apoptosis gene expression patterns clustered mainly by resistance/susceptibility of the oyster host to immune challenge. Weighted Gene Correlation Network Analysis (WGCNA) revealed unique combinations of transcripts for 1 to 12 IAP domain architecture types, including novel types, were significantly co-expressed in response to immune challenge with transcripts in apoptosis-related pathways.

Conclusions

Unprecedented diversity characterized by novel BIR domains and protein domain architectures was observed in oyster IAPs. Complex patterns of gene expression of novel and conserved IAPs in response to a variety of ecologically-relevant immune challenges, combined with evidence of direct co-expression of IAP genes with apoptosis-related transcripts, suggests IAP expansion facilitates complex and nuanced regulation of apoptosis and other immune responses in oysters.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08233-6.

Shotgun analysis to identify differences in protein expression between granulocytes and hyalinocytes of the European flat oyster Ostrea edulis

Recovery of wild populations of the European flat oyster Ostrea edulis is important for ecosystem health and conservation of this species, because native oyster populations have dramatically declined or disappeared in most European waters. Diseases have contributed to oyster decline and are important constrains for oyster recovery. Understanding oyster immune system should contribute to design effective strategies to fight oyster diseases. Haemocytes play a pivotal role in mollusc immune responses protecting from infection. Two main types of haemocytes, granulocytes and hyalinocytes, are distinguished in O. edulis. A study aiming to explore differential functions between both haemocyte types and, thus, to enrich the knowledge of Ostrea edulis immune system, was performed by comparing the proteome of the two haemolymph cell types, using a shotgun approach through liquid chromatography (LC) coupled to mass spectrometry (MS). Cells from oyster haemolymph were differentially separated by Percoll density gradient centrifugation. Shotgun LC-MS/MS performance allowed the identification of 145 proteins in hyalinocytes and 138 in the proteome of granulocytes. After a comparative analysis, 55 proteins with main roles in defence were identified, from which 28 were representative of granulocytes and 27 of hyalinocytes, plus 11 proteins shared by both cell types. Different proteins involved in signal transduction, apoptosis, oxidative response, processes related with the cytoskeleton and structure, recognition and wound healing were identified as representatives of each haemocyte type. Important signalling pathways in the immune response such as MAPK, Ras and NF-κβ seemed to be more relevant for granulocytes, while the Wnt signalling pathway, particularly relevant for wound healing, more relevant in hyalinocytes. The differences in proteins involved in recognition and in cytoskeleton and structure suggest differential specialisation in processes of phagocytosis and internalisation of pathogens between haemocyte types. Apoptosis seemed more active in granulocytes. The differences in proteins involved in oxidative response also suggest different redox processes in each cell type.

Atypical Salmonella Typhimurium persistence in the pacific oyster, Crassostrea gigas, and its effect on the variation of gene expression involved in the oyster's immune system

Salmonella is one of the most important pathogens involved in food intoxication outbreaks, and in many cases, the intoxication has been linked to shellfish which is typically consumed raw. While much is understood about the interactions between Salmonella and vertebrates, much less is known about its relationships with invertebrates, which could be an overlooked and important aspect to better understand the Salmonella interaction with its diversified hosts. The aim of this study was to investigate the effect of preadaptation in seawater microcosms during 12 months on Salmonella Typhimurium by determining its survival capacity within this mollusk over a period of 30 days. The results showed that the stressed bacteria are able to survive in this mollusk at a higher concentration even after thirty days of infection compared to bacteria in the normal state. In order to minimize the effect of an experimental device for one month on the survival of Salmonella, we carried out an in vitro study to determine the number of viable Salmonella in the hemocytes of oysters. Interestingly, we evaluated the effect of the antibacterial activity of different extracts of C. gigas using the solvents (Methanol, Ethanol and acetic acid) specifically against stressed and unstressed Salmonella. Furthermore, we compared the expression of three genes in the oyster Cg-big-def1, timp and sod in response to experimental infections of this mollusk with Vibrio splendidus kb133 and S. Typhimurium LT2DT104 in normal and stressed states. These findings are very important to contribute to explaining several questions about the persistence of S. Typhimurium for a long time in C. gigas and the host's immune response to this microorganism which is considered to be non-virulent for molluscs.

Differential Expression of Long Non-Coding RNA (lncRNA) in Mediterranean Mussel (Mytilus galloprovincialis) Hemocytes under Immune Stimuli

The Mediterranean mussel is one of the most economically relevant bivalve mollusk species in Europe and China. The absence of massive mortalities and their resistance to pathogens affecting other cultured bivalves has been under study in recent years. The transcriptome response of this species to different immune stimuli has been extensively studied, and even the complexity of its genome, which has recently been sequenced, has been suggested as one of the factors contributing to this resistance. However, studies concerning the non-coding RNA profiles remain practically unexplored-especially those corresponding to the lncRNAs. To the best of our knowledge, this is the second characterization and study of lncRNAs in this bivalve species. In this work, we identified the potential repertoire of lncRNAs expressed in mussel hemocytes, and using RNA-Seq we analyzed the lncRNA profile of mussel hemocytes stimulated in vitro with three different immune stimuli: LPS, poly I:C, and β-glucans. Compared to unstimulated hemocytes, LPS induced the highest modulation of lncRNAs, whereas poly I:C and β-glucans induced a similar discrete response. Based on the potential cis-regulatory activity of the lncRNAs, we identified the neighboring protein-coding genes of the regulated lncRNAs to estimate-at least partially-the processes in which they are implicated. After applying correlation analyses, it seems that-especially for LPS-the lncRNAs could participate in the regulation of gene expression, and substantially contribute to the immune response.

Effect of Different Species of Prorocentrum Genus on the Japanese Oyster Crassostrea gigas Proteomic Profile

This paper assesses the effects of exposure to toxic concentrations (1200 to 6000 cells/mL) of the dinoflagellates Prorocentrum lima, Prorocentrum minimum, and Prorocentrum rhathymum and several concentrations of aqueous and organic extracts obtained from the same species (0 to 20 parts per thousand) on the Crassostrea gigas (5-7 mm) proteomic profile. Through comparative proteomic map analyses, several protein spots were detected with different expression levels, of which eight were selected to be identified by liquid chromatography-mass spectrometry (LC-MS/MS) analyses. The proteomic response suggests that, after 72 h of exposure to whole cells, the biological functions of C. gigas affected proteins in the immune system, stress response, contractile systems and cytoskeletal activities. The exposure to organic and aqueous extracts mainly showed effects on protein expressions in muscle contraction and cytoskeleton morphology. These results enrich the knowledge on early bivalve developmental stages. Therefore, they may be considered a solid base for new bioassays and/or generation of specific analytical tools that allow for some of the main effects of algal proliferation phenomena on bivalve mollusk development to be monitored, characterized and elucidated.

Dynamic Immune Response to Vibriosis in Pacific Oyster Crassostrea gigas Larvae during the Infection Process as Supported by Accurate Positioning of GFP-Tagged Vibrio Strains

As the immune system is not fully developed during the larval stage, hatchery culture of bivalve larvae is characterized by frequent mass mortality caused by bacterial pathogens, especially Vibrio spp. However, the knowledge is limited to the pathogenesis of vibriosis in oyster larvae, while the immune response to pathogenic microorganisms in this early life stage is still far from being fully elucidated. In this study, we combined green fluorescent protein (GFP)-tagging, histological and transcriptomic analyses to clarify the pathogenesis of experimental vibriosis and the mechanisms used by the host Pacific oyster Crassostrea gigas larvae to resist infection. The Vibrio strains first colonized the digestive system and rapidly proliferated, while only the transcription level of IκB kinase (IKK) and nuclear factor κB (NF-κB) associated with signaling transduction were up-regulated in oyster at 18 h post challenge (hpc). The mRNA levels for integrin β-1, peroxinectin, and heat shock protein 70 (HSP70), which are associated with phagocytosis, cell adhesion, and cytoprotection, were not upregulated until 30 hpc when the necrosis already happened in the larval digestive system. This suggested that the immunity in the early stages of C. gigas is not strong enough to prevent vibriosis and future research may focus on the strengthening of the gastrointestinal immune ability to defend vibriosis in bivalve larvae.

Transcriptomics Analysis and Re-sequencing Reveal the Mechanism Underlying the Thermotolerance of an Artificial Selection Population of the Pacific Oyster

The Pacific oyster is a globally important aquaculture species inhabiting the intertidal environment, which experiences great temperature variation. Mass deaths in the summer pose a major challenge for the oyster industry. We initiated an artificial selection breeding program in 2017 using acute heat shock treatments of the parents to select for thermotolerance in oysters. In this study, we compared the respiration rate, summer survival rate, gene expression, and gene structure of F₂ selected oysters and non-selected wild oysters. A transcriptional analysis revealed global divergence between the selected and control groups at the larval stage, including 4764 differentially expressed genes, among which 79 genes were heat-responsive genes. Five heat shock proteins were enriched, and four of the six genes (five heat stock genes in the enriched GO terms and KEGG pathways and BAG4) were differentially expressed in 1-year-old oysters. Integration of the transcriptomic and re-sequencing data of the selected and the control groups revealed 1090 genes that differentiated in both gene structure and expression. Two SNPs (single nucleotide polymorphism) that may mediate the expression of CGI_10022585 and CGI_10024709 were validated. In addition, the respiration rate of 1-year-old oysters varied significantly between the selected group and the control group at room temperature (20°C). And the summer survival rate of the selected population was significantly improved. This study not only shows that artificial selection has a significant effect on the gene structure and expression of oysters, but it also helps reveal the mechanism underlying their tolerance of high temperature as well as the ability of oysters to adapt to climate change.

Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca-The Blue Mussel (Mytilus edulis), Soft Shell Clam (Mya arenaria), Eastern Oyster (Crassostrea virginica) and Atlantic Jacknife Clam (Ensis leei)

Simple Summary

Oysters and clams form an important component of the food chain and food security and are of considerable commercial value worldwide. They are affected by pollution and climate change, as well as a range of infections, some of which are opportunistic. For aquaculture purposes they are furthermore of great commercial value and changes in their immune responses can also serve as indicators of changes in ocean environments. Therefore, studies into understanding new factors in their immune systems may aid new biomarker discovery and are of considerable value. This study assessed new biomarkers relating to changes in protein function in four economically important marine molluscs, the blue mussel, soft shell clam, Eastern oyster, and Atlantic jacknife clam. These findings indicate novel regulatory mechanisms of important metabolic and immunology related pathways in these mollusks. The findings provide new understanding to how these pathways function in diverse ways in different animal species as well as aiding new biomarker discovery for Mollusca aquaculture.

Abstract

Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.

Vibrio-bivalve interactions in health and disease

In the marine environment, bivalve mollusks constitute habitats for bacteria of the Vibrionaceae family. Vibrios belong to the microbiota of healthy oysters and mussels, which have the ability to concentrate bacteria in their tissues and body fluids, including the hemolymph. Remarkably, these important aquaculture species respond differently to infectious diseases. While oysters are the subject of recurrent mass mortalities at different life stages, mussels appear rather resistant to infections. Thus, Vibrio species are associated with the main diseases affecting the worldwide oyster production. Here, we review the current knowledge on Vibrio-bivalve interaction in oysters (Crassostrea sp.) and mussels (Mytilus sp.). We discuss the transient versus stable associations of vibrios with their bivalve hosts as well as technical issues limiting the monitoring of these bacteria in bivalve health and disease. Based on the current knowledge of oyster/mussel immunity and their interactions with Vibrio species pathogenic for oyster, we discuss how differences in immune effectors could contribute to the higher resistance of mussels to infections. Finally, we review the multiple strategies evolved by pathogenic vibrios to circumvent the potent immune defences of bivalves and how key virulence mechanisms could have been positively or negatively selected in the marine environment through interactions with predators.

Opsonic character of the plasma proteins in phagocytosis-dependent host response to bacterial infection in a marine invertebrate, Crassostrea gigas

Phagocytosis is an evolutionarily conserved immune response, whose efficiency is fundamentally coupled with opsonization of extracellular microbes. How marine mollusks cells recognize and selectively capture pathogens during phagocytosis to clear them is not completely understood. In this study, we observed that plasma is extremely effective for oyster hemocyte phagocytosis, so we investigated candidate proteins among plasma proteins with binding affinity for Vibrio parahaemolyticus in Pacific oyster (Crassostrea gigas) by subjecting them to mass spectroscopy analysis for protein identification and characterization, and address the complex regulatory network to engulf invaders. There were 620 identified proteins potentially associated with bacteria binding and phagocytosis which could be quantified. Our results showed that C1q and lectins identified in Pacific oyster plasma held binding ability to bacteria, clearly suggesting their potent to be opsonins. The dominant expressed plasma protein p1-CgC1q (Complement component 1q)-like protein was identified and its opsonic role was confirmed in this study. The cell surface receptor Cgintegrin interacts directly with p1-CgC1q to mediate phagocytosis. We further confirmed that the interaction between C1q and integrin not rely on the typical recognition site RGD but on the RGE. Evidence exist revealed that p1-CgC1q could coat bacteria via the endotoxin LPS (lipopolysaccharide) and subsequently bind the receptor integrin to significantly enhance hemocytic phagocytosis and bacteria clearance. This study has thus furnished clear evidence for the importance of plasma proteins in mollusk, shedding light on the humoral immunity and an underappreciated strategy in marine host-pathogen interactions.

Identification of immune-related proteins of Dreissena polymorpha hemocytes and plasma involved in host-microbe interactions by differential proteomics

Biological responses of zebra mussel Dreissena polymorpha are investigated to assess the impact of contaminants on aquatic organisms and ecosystems. In addition to concentrate chemical contaminants in their tissues, zebra mussels accumulate several microorganisms such as viruses, protozoa and bacteria. In order to understand the molecular mechanisms involved in the defence against microorganisms this study aims at identifying immune proteins from D. polymorpha hemolymph involved in defence against protozoa and viruses. For this purpose, hemolymph were exposed ex vivo to Cryptosporidium parvum and RNA poly I:C. Differential proteomics on both hemocytes and plasma revealed immune proteins modulated under exposures. Different patterns of response were observed after C. parvum and RNA poly I:C exposures. The number of modulated proteins per hemolymphatic compartments suggest that C. parvum is managed in cells while RNA poly I:C is managed in plasma after 4 h exposure. BLAST annotation and GO terms enrichment analysis revealed further characteristics of immune mechanisms. Results showed that many proteins involved in the recognition and destruction of microorganisms were modulated in both exposure conditions, while proteins related to phagocytosis and apoptosis were exclusively modulated by C. parvum. This differential proteomic analysis highlights in zebra mussels modulated proteins involved in the response to microorganisms, which reflect a broad range of immune mechanisms such as recognition, internalization and destruction of microorganisms. This study paves the way for the identification of new markers of immune processes that can be used to assess the impact of both chemical and biological contaminations on the health status of aquatic organisms.

Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as other viral respiratory infections. The aim of this study was to acquire a better understanding of the PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of 80 pigs following infection by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 dpi) to make 16 libraries—analyses are by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as uncovered genes related to intersecting and unique host immune responses to the three viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in the development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.

Interaction of a Densovirus with Glycans of the Peritrophic Matrix Mediates Oral Infection of the Lepidopteran Pest Spodoptera frugiperda

The success of oral infection by viruses depends on their capacity to overcome the gut epithelial barrier of their host to crossing over apical, mucous extracellular matrices. As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitinous peritrophic matrix, that lines and protects the midgut epithelium; how capsids stick to and cross these barriers to reach their final cell destination where replication goes has been poorly studied in insects. Here, we analyzed the early interaction of the Junonia coenia densovirus (JcDV) with the midgut barriers of caterpillars from the pest Spodoptera frugiperda. Using combination of imaging, biochemical, proteomic and transcriptomic analyses, we examined in vitro, ex vivo and in vivo the early interaction of the capsids with the peritrophic matrix and the consequence of early oral infection on the overall gut function. We show that the JcDV particle rapidly adheres to the peritrophic matrix through interaction with different glycans including chitin and glycoproteins, and that these interactions are necessary for oral infection. Proteomic analyses of JcDV binding proteins of the peritrophic matrix revealed mucins and non-mucins proteins including enzymes already known to act as receptors for several insect pathogens. In addition, we show that JcDV early infection results in an arrest of N-Acetylglucosamine secretion and a disruption in the integrity of the peritrophic matrix, which may help viral particles to pass through. Finally, JcDV early infection induces changes in midgut genes expression favoring an increased metabolism including an increased translational activity. These dysregulations probably participate to the overall dysfunction of the gut barrier in the early steps of viral pathogenesis. A better understanding of early steps of densovirus infection process is crucial to build biocontrol strategies against major insect pests.

The transcriptional response of the Pacific oyster Crassostrea gigas under simultaneous bacterial and heat stresses

Bacterial infection and heat stress are considered as two major environmental threats for the aquaculture industry of oyster Crassostrea gigas. In the present study, the expression profiles of mRNA transcripts in the hemocytes of oysters under bacterial challenge and heat stress were examined by next-generation sequencing. There were 21,095, 21,957 and 21,141 transcripts identified in the hemocytes of oysters from three groups, respectively, including control group (designated as Con group), Vibrio splendidus challenge group (Bac group), and bacterial and heat stress combined treatment group (BacHeat group). There were 4610, 5093 and 5149 differentially expressed transcripts (DTs) in the three pairwise comparisons Con/Bac, Con/BacHeat and Bac/BacHeat, respectively. The main enriched GO terms in biological process category of the DTs included the metabolic processes, cellular process, response to stimulus and immune system process. The expression patterns of DTs involved in pattern recognition, immune signal transduction and energy metabolic indicated that the immune response to bacterial challenge was disturbed under acute heat stress, which was also confirmed by quantitative real-time PCR. The neuroendocrine immunomodulation, especially the catecholaminergic regulation, played indispensable roles in stress response. The total energy reserves as well as cellular energy allocation (CEA) in hepatopancreas of oysters decreased remarkably especially in BacHeat group, while the energy consumption generally increased, suggesting that the immune defense against the simultaneous stimulation of pathogen and heat stress imposed greater costs on oyster's energy expenditure than a single stressor. These results above indicated that, the heat stress disturbed the normal expression of genes involved in immune response and energy metabolism, accelerated energy consumption and broke the metabolic balance, leading to a decline in resilience to infection and mass mortality of oyster in summer.

Transcriptome analysis and discovery of genes involved in immune pathways in Solen strictus (Gould, 1861) under Vibrio anguillarum

The Solen strictus (Gould, 1861) has been recognized as an important marine economic bivalve in Eastern and Southeast Asia. To gain a better understanding of the S. strictus immune system and its related genes in response to bacterial infections, we performed a comparative gene transcription analysis from S. strictus with Vibrio anguillarum through RNA-Seq technology, meanwhile the differentially expressed genes (DEGs) were investigated. After assembly, a total of 195,774 transcripts with an average length of 996 bp were obtained. Total 153,038 unigenes were annotated in the nr, Swiss-Prot, KEGG, COG, KOG, GO and Pfam databases, and 56,597 unigenes (36.98%) were annotated in at least one database. After bacterial challenge, there were 1588 significant differentially expressed genes (DEGs) between the challenged and control groups, including 999 up-regulated and 589 down-regulated genes. All the DEGs were classified into three gene ontology categories, and allocated to 225 KEGG pathways. Immune-related genes were detected from immune system pathways among the top 20 enriched pathways, such as Toll-like receptor signaling, RIG-I-like receptor signaling and NOD-like receptor signaling pathway. In addition, 56,079 potential simple sequence repeats (SSRs) and 1,031,521 candidate single nucleotide polymorphisms (SNPs) were detected and identified in the S. strictus transcriptome. Results of the present study will provide valuable theoretical resources for future genetic and genomic research on S. strictus. The research results will be helpful for improving the efficiency and quality of artificial breeding, establishing genetic linkage map, and enhancing health management for this species.

Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event

Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.

Anti-Inflammatory Activity of β-thymosin Peptide Derived from Pacific Oyster (Crassostrea gigas) on NO and PGE₂ Production by Down-Regulating NF-κB in LPS-Induced RAW264.7 Macrophage Cells

β-thymosin is known for having 43 amino acids, being water-soluble, having a light molecular weight and ubiquitous polypeptide. The biological activities of β-thymosin are diverse and include the promotion of wound healing, reduction of inflammation, differentiation of T cells and inhibition of apoptosis. Our previous studies showed that oyster β-thymosin originated from the mantle of the Pacific oyster, Crassostrea gigas and had antimicrobial activity. In this study, we investigated the anti-inflammatory effects of oyster β-thymosin in lipopolysaccharide (LPS)-induced RAW264.7 macrophage cells using human β-thymosin as a control. Oyster β-thymosin inhibited the nitric oxide (NO) production as much as human β-thymosin in LPS-induced RAW264.7 cells. It also showed that oyster β-thymosin suppressed the expression of prostaglandin E₂ (PGE₂), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, oyster β-thymosin reduced inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6). Oyster β-thymosin also suppressed the nuclear translocation of phosphorylated nuclear factor-κB (NF-κB) and degradation of inhibitory κB (IκB) in LPS-induced RAW264.7 cells. These results suggest that oyster β-thymosin, which is derived from the mantle of the Pacific oyster, has as much anti-inflammatory effects as human β-thymosin. Additionally, oyster β-thymosin suppressed NO production, PGE₂ production and inflammatory cytokines expression via NF-κB in LPS-induced RAW264.7 cells.

Ralstonia eutropha, containing high poly-β-hydroxybutyrate levels, regulates the immune response in mussel larvae challenged with Vibrio coralliilyticus

Marine invertebrates rely mainly on innate immune mechanisms that include both humoral and cellular responses. Antimicrobial peptides (AMPs), lysozyme and phenoloxidase activity, are important components of the innate immune defense system in marine invertebrates. They provide an immediate and rapid response to invading microorganisms. The impact of amorphous poly-β-hydroxybutyrate (PHB-A) (1 mg PHB-A L^-1) on gene expression of the AMPs mytimycin, mytilinB, defensin and the hydrolytic enzyme lysozyme in infected blue mussel larvae was investigated during "in vivo" challenge tests with Vibrio coralliilyticus (10⁵ CFU mL^-1). RNAs were isolated from mussel larvae tissue, and AMPs were quantified by q-PCR using the 18srRNA gene as a housekeeping gene. Our data demonstrated that AMPs genes had a tendency to be upregulated in challenged mussel larvae, and the strongest expression was observed from 24 h post-exposure onwards. The presence of both PHB-A and the pathogen stimulated the APMs gene expression, however no significant differences were noticed between treatments or between exposure time to the pathogen V. coralliilyticus. Looking at the phenoloxidase activity in the infected mussels, it was observed that the addition of PHB-A significantly increased the activity.

Seawater Acidification Reduced the Resistance of Crassostrea gigas to Vibrio splendidus Challenge: An Energy Metabolism Perspective

Negative physiological impacts induced by exposure to acidified seawater might sensitize marine organisms to future environmental stressors, such as disease outbreak. The goal of this study was to evaluate if ocean acidification (OA) could reduce the resistance capability of the Pacific oyster (Crassostrea gigas) to Vibrio splendidus challenge from an energy metabolism perspective. In this study, the Pacific oyster was exposed to OA (pH 7.6) for 28 days and then challenged by V. splendidus for another 72 h. Antioxidative responses, lipid peroxidation, metabolic (energy sensors, aerobic metabolism, and anaerobic metabolism) gene expression, glycolytic enzyme activity, and the content of energy reserves (glycogen and protein) were investigated to evaluate the environmental risk of pathogen infection under the condition of OA. Our results demonstrated that following the exposure to seawater acidification, oysters exhibited an energy modulation with slight inhibition of aerobic energy metabolism, stimulation of anaerobic metabolism, and increased glycolytic enzyme activity. However, the energy modulation ability and antioxidative regulation of oysters exposed to seawater acidification may be overwhelmed by a subsequent pathogen challenge, resulting in increased oxidative damage, decreased aerobic metabolism, stimulated anaerobic metabolism, and decreased energy reserves. Overall, although anaerobic metabolism was initiated to partially compensate for inhibited aerobic energy metabolism, increased oxidative damage combined with depleted energy reserves suggested that oysters were in an unsustainable bioenergetic state and were thereby incapable of supporting long-term population viability under conditions of seawater acidification and a pathogen challenge from V. splendidus.

Transcriptomic and Quantitative Proteomic Analyses Provide Insights Into the Phagocytic Killing of Hemocytes in the Oyster Crassostrea gigas

As invertebrates lack an adaptive immune system, they depend to a large extent on their innate immune system to recognize and clear invading pathogens. Although phagocytes play pivotal roles in invertebrate innate immunity, the molecular mechanisms underlying this killing remain unclear. Cells of this type from the Pacific oyster Crassostrea gigas were classified efficiently in this study via fluorescence-activated cell sorting (FACS) based on their phagocytosis of FITC-labeled latex beads. Transcriptomic and quantitative proteomic analyses revealed a series of differentially expressed genes (DEGs) and proteins present in phagocytes; of the 352 significantly high expressed proteins identified here within the phagocyte proteome, 262 corresponding genes were similarly high expressed in the transcriptome, while 140 of 205 significantly low expressed proteins within the proteome were transcriptionally low expressed. A pathway crosstalk network analysis of these significantly high expressed proteins revealed that phagocytes were highly activated in a number of antimicrobial-related biological processes, including oxidation–reduction and lysosomal proteolysis processes. A number of DEGs, including oxidase, lysosomal protease, and immune receptors, were also validated in this study using quantitative PCR, while seven lysosomal cysteine proteases, referred to as cathepsin Ls, were significantly high expressed in phagocytes. Results show that the expression level of cathepsin L protein in phagocytes [mean fluorescence intensity (MFI): 327 ± 51] was significantly higher (p < 0.01) than that in non-phagocytic hemocytes (MFI: 83 ± 26), while the cathepsin L protein was colocalized with the phagocytosed Vibrio splendidus in oyster hemocytes during this process. The results of this study collectively suggest that oyster phagocytes possess both potent oxidative killing and microbial disintegration capacities; these findings provide important insights into hemocyte phagocytic killing as a component of C. gigas innate immunity.

Inefficient immune response is associated with microbial permissiveness in juvenile oysters affected by mass mortalities on field

Since 2008, juvenile Crassostrea gigas oysters have suffered from massive mortalities in European farming areas. This disease of complex etiology is still incompletely understood. Triggered by an elevated seawater temperature, it has been associated to infections by a herpes virus named OsHV-1 as well as pathogenic vibrios of the Splendidus clade. Ruling out the complexity of the disease, most of our current knowledge has been acquired in controlled experiments. Among the many unsolved questions, it is still ignored what role immunity plays in the capacity oysters have to survive an infectious episode. Here we show that juvenile oysters susceptible to the disease mount an inefficient immune response associated with microbial permissiveness and death. We found that, in contrast to resistant adult oysters having survived an earlier episode of mortality, susceptible juvenile oysters never exposed to infectious episodes died by more than 90% in a field experiment. Susceptible oysters were heavily colonized by OsHV-1 herpes virus as well as bacteria including vibrios potentially pathogenic for oysters, which proliferated in oyster flesh and body fluids during the mortality event. Nonetheless, susceptible oysters were found to sense microbes as indicated by an overexpression of immune receptors and immune signaling pathways. However, they did not express important immune effectors involved in antimicrobial immunity and apoptosis and showed repressed expression of genes involved in ROS and metal homeostasis. This contrasted with resistant oysters, which expressed those important effectors, controlled bacterial and viral colonization and showed 100% survival to the mortality event. Altogether, our results demonstrate that the immune response mounted by susceptible oysters lacks some important immune functions and fails in controlling microbial proliferation. This study opens the way to more holistic studies on the "mass mortality syndrome", which are now required to decipher the sequence of events leading to oyster mortalities and determine the relative weight of pathogens, oyster genetics and oyster-associated microbiota in the disease.

Autophagic processes in Mytilus galloprovincialis hemocytes: Effects of Vibrio tapetis

Autophagy is a highly conserved and regulated catabolic process involved in maintaining cell homeostasis in response to different stressors. The autophagic machinery is also used as an innate immune mechanism against microbial infection. In invertebrates, that lack acquired immunity, autophagy may thus play a key role in the protection against potential pathogens. In aquatic molluscs, evidence has been provided for induction of autophagy by starvation and different environmental stressors; however, no information is available on autophagic pathways in the immune cells, the hemocytes. In this work, the autophagic processes were investigated in the hemocytes of the marine bivalve, the mussel Mytilus galloprovincialis. The effects of classical inducers/inhibitors of mammalian autophagy were first tested. Rapamycin induced a decrease in lysosomal membrane stability-LMS that was prevented by the autophagy inhibitor Wortmannin. Increased MDC fluorescence and expression of LC3-II were also observed. Moreover, responses to in vitro challenge with the bivalve pathogen Vibrio tapetis were evaluated. Mussel hemocytes were unable to activate the immune response towards V. tapetis; however, bacterial challenge induced a moderate decrease in LMS, corresponding to lysosomal activation but no cytotoxicity; the effect was prevented by Wortmannin. TEM observations showed that V. tapetis resulted in rapid formation of autophagosomes and autolysosomes. Accordingly, increased LC3-II expression, decreased levels of phosphorylated mTor and of p62 were observed. The results represent the first evidence for autophagic processes in bivalve hemocytes in response to bacterial challenge, and underline the protective role of autophagy towards potential pathogenic vibrios.

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress

Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ♀ × Crassostrea angulata♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress.

The B-cell translocation gene 1 (CgBTG1) identified in oyster Crassostrea gigas exhibit multiple functions in immune response

B-cell translocation gene 1 (BTG1) is a member of the anti-proliferative gene family, which plays important roles in regulation of cell cycle. In the present study, a B-cell translocation gene 1 molecule homologue (designed CgBTG1) are identified and characterized in oyster Crassostrea gigas. CgBTG1 contains a conserved BTG domain with Box A and Box B motifs, and it shares high similarities with both BTG1 and BTG2 proteins in vertebrates. CgBTG1 mRNA is predominantly expressed in hemocytes, and its expression level in hemocytes is significantly up-regulated at 6 h (5.40-fold, p < 0.01) post Vibrio splendidus stimulation. The apoptosis rate of oyster hemocytes is significantly decreased (p < 0.05) after CgBTG1 interfered by dsRNA (dsCgBTG1). This is indicated that CgBTG1 participated in the regulation of oyster hemocytes apoptosis. Furthermore, CgBTG1 could also induce the apoptosis of cancer cells (HeLa, A549 and BEL7402) in vitro. Compared with normal oysters, both vessel-like structures and muscle fibers in CgBTG1 interfered oysters are severely damaged after V. splendidus challenge in paraffin section, considering that CgBTG1 possessed an analogous feature of angiogenesis for maintenance of vessel-like structures in adductor muscle of oyster. The results suggests that CgBTG1 is a multi-functional molecule involved in the immune response of C. gigas against pathogen infection, which provides more clues for intensive studies of BTG family proteins in invertebrates.

Long dsRNAs promote an anti-viral response in Pacific oyster hampering ostreid herpesvirus 1 replication

Double stranded RNA-mediated genetic interference (RNAi) is a widely used reverse genetic tool for determining the loss-of-function phenotype of a gene. Here, the possible induction of an immune response by long dsRNA was tested in a marine bivalve, i.e. Crassostrea gigas, as well as the specific role of the subunit 2 of the nuclear factor κB inhibitor (IκB2). This gene is a candidate of particular interest for functional investigations in the context of massive mortality oyster events as Cg-IκB2 mRNA levels exhibited significant variation depending on the amount of ostreid herpesvirus 1 (OsHV-1) DNA detected. In the present study, dsRNAs targeting Cg-IκB2 and Green Fluorescence Protein genes were injected in vivo into oysters before being challenged by OsHV-1. Survival appeared close to 100% in both dsRNA injected conditions associated with a low detection of viral DNA and a low expression of a panel of 39 OsHV-1 genes as compared to infected control. Long dsRNA molecules, both Cg-IκB2- and GFP-dsRNA, may have induced an anti-viral state controlling the OsHV-1 replication and precluding the understanding of the Cg-IκB2 specific role. Immune-related genes including Cg-IκB1, Cg-Rel1, Cg-IFI44, Cg-PKR, and Cg-IAP appeared activated in dsRNA-injected condition potentially hampering viral replication and thus conferring a better resistance to OsHV-1 infection. We revealed that long dsRNA-mediated genetic interference triggered an anti-viral state in the oyster, emphasizing the need of new reverse genetics tools for assessing immune gene function and avoiding off-target effects in bivalves.

Effect of 4-nonylphenol on the immune response of the Pacific oyster Crassostrea gigas following bacterial infection with Vibrio campbellii

The xenoestrogen 4-nonylphenol (NP) is a ubiquitous aquatic pollutant and has been shown to impair reproduction, development, growth and, more recently, immune function in marine invertebrates. We investigated the effects of short-term (7 d) exposure to low (2 μg l^-1) and high (100 μg l^-1) levels of NP on cellular and humoral elements of the innate immune response of Crassostrea gigas to a bacterial challenge. To this end, we measured 1) total hemocyte counts (THC), 2) relative transcript abundance of ten immune-related genes (defh1, defh2, bigdef1, bigdef2, bpi, lysozyme-1, galectin, C-type lectin 2, timp, and transglutaminase) in the hemocytes, gill and mantle, and 3) hemolymph plasma lysozyme activity, following experimental Vibrio campbellii infection. Both low and high levels of NP were found to repress a bacteria-induced increase in THC observed in the control oysters. While several genes were differentially expressed following bacterial introduction (bigdef2, bpi, lysozyme-1, timp, transglutaminase), only two genes (bpi in the hemocytes, transglutaminase in the mantle) exhibited a different bacteria-induced expression profile following NP exposure, relative to the control oysters. Independently of infection-status, exposure to NP also altered mRNA transcript abundance of several genes (bpi, galectin, C-type lectin 2) in naïve, saline-injected oysters. Finally, plasma lysozyme activity levels were significantly higher in low dose NP-treated oysters (both naïve and bacteria challenged) relative to control oysters. Combined, these results suggest that exposure to ecologically-relevant (low) and extreme (high) levels of NP can alter both cellular and humoral elements of the innate immune response in C. gigas, an aquaculture species of global economic importance.

Caspase-3 serves as an intracellular immune receptor specific for lipopolysaccharide in oyster Crassostrea gigas

Apoptosis is a form of programmed cell death process controlled by a family of cysteine proteases called caspases, which plays a crucial role in the immune system homeostasis. The apoptosis and the detailed regulation mechanism have been well studied in vertebrate, but the information in lower animals, especially invertebrates, is still very limited. In the present study, Caspase-3 in the Pacific oyster Crassostrea gigas (designated CgCaspase-3) was enriched by lipopolysaccharide (LPS) affinity chromatography and further identified by MALDI-TOF/TOF-mass spectrometry. The binding activity of CgCaspase-3 to LPS was confirmed by enzyme-linked immunosorbent assay, and surface plasmon resonance analysis revealed its high binding specificity and moderate binding affinity (KD = 1.08 × 10(-6) M) to LPS. The recombinant CgCaspase-3 exhibited high proteolytic activity to substrate Ac-DEVD-pNA and relatively weak activity to substrate Ac-DMQD-pNA and Ac-VDQQD-pNA. The binding of CgCaspase-3 to LPS significantly inhibited its proteolytic activity toward AC-DEVD-pNA in vitro. The over-expression of CgCaspase-3 leaded to the phosphatidylserine exposure on the external plasma membrane and the cleavage of poly (ADP-ribose) polymerase, which reduced cell viability, and finally induced cell apoptosis. But the cell apoptosis mediated by CgCaspase-3 in vivo was significantly inhibited by the treatment of LPS. These results collectively indicated that CgCaspase-3 could serve as an intracellular LPS receptor, and the interaction of LPS with CgCaspase-3 specifically inhibited the cell apoptosis induced by CgCaspase-3.

First characterization of three cyclophilin family proteins in the oyster, Crassostrea ariakensis Gould

Cyclophilins (CyPs) are a family of proteins that bind the immunosuppressive agent cyclosporin A (CsA) with high-affinity and belong to one of the three superfamilies of peptidyl-prolyl cis-trans isomerases (PPIase). In this report, three cyclophilin genes (Ca-CyPs), including Ca-CyPA, Ca-CyPB and Ca-PPIL3, were identified from oyster, Crassostrea ariakensis Gould in which Ca-CyPA encodes a protein with 165 amino acid sequences, Ca-CyPB encodes a protein with 217 amino acid sequences and Ca-PPIL3 encodes a protein with 162 amino acid sequences. All of the three Ca-CyPs genes contain a typical CyP-PPIase domain with its signature sequences and Ca-CyPB contains an N-signal peptide sequences. Tissue distribution study revealed that Ca-CyPs were ubiquitously expressed in all examined tissues and the highest levels were observed in hemocytes. RLO incubation upregulated the mRNA expression levels of Ca-CyPs, indicating that three Ca-CyPs might be involved in oyster immune response against RLO infection.

Distinct immune responses of juvenile and adult oysters (Crassostrea gigas) to viral and bacterial infections

Since 2008, massive mortality events of Pacific oysters (Crassostrea gigas) have been reported worldwide and these disease events are often associated with Ostreid herpesvirus type 1 (OsHV-1). Epidemiological field studies have also reported oyster age and other pathogens of the Vibrio genus are contributing factors to this syndrome. We undertook a controlled laboratory experiment to simultaneously investigate survival and immunological response of juvenile and adult C. gigas at different time-points post-infection with OsHV-1, Vibrio tasmaniensis LGP32 and V. aestuarianus. Our data corroborates epidemiological studies that juveniles are more susceptible to OsHV-1, whereas adults are more susceptible to Vibrio. We measured the expression of 102 immune-genes by high-throughput RT-qPCR, which revealed oysters have different transcriptional responses to OsHV-1 and Vibrio. The transcriptional response in the early stages of OsHV-1 infection involved genes related to apoptosis and the interferon-pathway. Transcriptional response to Vibrio infection involved antimicrobial peptides, heat shock proteins and galectins. Interestingly, oysters in the later stages of OsHV-1 infection had a transcriptional response that resembled an antibacterial response, which is suggestive of the oyster’s microbiome causing secondary infections (dysbiosis-driven pathology). This study provides molecular evidence that oysters can mount distinct immune response to viral and bacterial pathogens and these responses differ depending on the age of the host.

Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling

During the life cycle of shellfish, larval development, especially metamorphosis, has a vital influence on the dynamics, distribution, and recruitment of natural populations, as well as seed breeding. Rapana venosa, a carnivorous gastropod, is an important commercial shellfish in China, and is an ecological invader in the United States, Argentina, and France. However, information about the mechanism of its early development is still limited, because research in this area has long suffered from a lack of genomic resources. In this study, 15 digital gene expression (DGE) libraries from five developmental stages of R. venosa were constructed and sequenced on the IIIumina Hi-Sequation 2500 platform. Bioinformaticsanalysis identified numerous differentially and specifically expressed genes, which revealed that genes associated with growth, nervous system, digestive system, immune system, and apoptosis participate in important developmental processes. The functional analysis of differentially expressed genes was further implemented by gene ontology, and Kyoto encyclopedia of genes and genomes enrichment. DGE profiling provided a general picture of the transcriptomic activities during the early development of R. venosa, which may provide interesting hints for further study. Our data represent the first comparative transcriptomic information available for the early development of R. venosa, which is a prerequisite for a better understanding of the physiological traits controlling development.

A novel ubiquitin-protein ligase E3 functions as a modulator of immune response against lipopolysaccharide in Pacific oyster, Crassostrea gigas

Ubiquitination is an important post-translational protein modification and plays a crucial role in various processes such as cell cycle, signal transduction, and transcriptional regulation. In the present study, a novel ubiquitin (Ub)-protein ligase E3 (designed as CgE3Rv1) was identified from Crassostrea gigas, and its ubiquitination regulation in the immune response against lipopolysaccharide (LPS) stimulation was investigated. The open reading frame of CgE3Rv1 gene was of 1455 bp encoding a polypeptide of 484 amino acids with the predicted molecular mass of 54.89 kDa. There were two transmembrane regions and a RING-variant (RINGv) domain identified in CgE3Rv1. CgE3Rv1 shared similar C4HC3 zinc-finger-like motif with those RINGv domain Ub-protein ligases E3s identified from vertebrates and invertebrates, and it was closely clustered with the membrane-associated RING-CH2 (MARCH2) Ub-protein ligases E3s in the phylogenetic tree. The mRNA transcript of CgE3Rv1 was highest expressed in gonads and hemolymph (p < 0.05), and its mRNA expression level in hemocytes was significantly increased at 6 h (p < 0.01) after the stimulation of LPS, while the up-regulated mRNA expression was significantly decreased (p < 0.01) after acetylcholine stimulation. No significant changes of CgE3Rv1 expression were observed after peptidoglycan or mannan stimulation. Immunohistochemistry and in situ hybridization assays revealed that CgE3Rv1 protein and mRNA were dominantly distributed in the gonad. In the hemocytes, CgE3Rv1 was mainly located around the nucleus, and slightly distributed in the cytoplasm and on the cell membrane. Recombinant CgE3Rv1 RINGv domain protein (rCgE3Rv1-RINGv) was confirmed to activate the Ub reaction system in vitro with the aid of Ub-activating enzyme E1 and Ub-conjugating enzyme E2. These results demonstrated that CgE3Rv1 was an Ub-protein ligase E3, which was involved in the immune response against LPS and the interaction with cell surface signal molecules of neuroendocrine-immune system in oysters.

Multi-species protein similarity clustering reveals novel expanded immune gene families in the eastern oyster Crassostrea virginica

Comparative genomics research in non-model species has highlighted how invertebrate hosts possess complex diversified repertoires of immune molecules. The levels of diversification in particular immune gene families appear to differ between invertebrate lineages and even between species within lineages, reflecting differences not only in evolutionary histories, but also in life histories, environmental niches, and pathogen exposures. The goal of this research was to identify immune-related gene families experiencing high levels of diversification in eastern oysters, Crassostrea virginica. Families containing 1) transcripts differentially expressed in eastern oysters in response to bacterial challenge and 2) a larger number of transcripts compared to other species included those coding for the C1q and C-type lectin domain containing proteins (C1qDC and CTLDC), GTPase of the immune-associated proteins (GIMAP), scavenger receptors (SR), fibrinogen-C domain containing proteins (also known as FREPs), dopamine beta-hydrolase (DBH), interferon-inducible 44 (IFI44), serine protease inhibitors, apextrin, and dermatopontin. Phylogenetic analysis of two of the families significantly expanded in bivalves, IFI44 and GIMAP, showed a patchy distribution within both protostomes and deuterostomes, suggesting multiple independent losses and lineage-specific expansions. Increased availability of genomic information for a broader range of non-model species broadly distributed through vertebrate and invertebrate phyla will likely lead to improved knowledge on mechanisms of immune-gene diversification.

The immunological capacity in the larvae of Pacific oyster Crassostrea gigas

As the immune system has not fully developed during early developmental stages, bivalve larvae are more susceptible for pathogens, which frequently leads to the significant mortality in hatcheries. In the present study, the development of immune system and its response against bacteria challenge were investigated in order to characterize the repertoire of immunological capacity of Pacific oyster Crassostrea gigas during the ontogenesis. The phagocytosis was firstly observed in the early D-veliger larvae (17 hpf), especially in their velum site, which indicated the appearance of functional hemocytes during early D-veliger larvae stage. The whole-mount immunofluorescence assay of three pattern recognition receptors (integrin β-1, caspase-3 and C-type lectin 3) and one immune effector gene (IL17-5) was performed in blastula, early D-veliger and umbo larvae, suggested that velum and digestive gland were the potential sites of immune system in the larvae. The lowest activities of antioxidant enzymes (superoxide dismutase and catalase) and hydrolytic enzyme (lysozyme), as well as descended expression levels of 12 immune genes at the transition between embryogenesis and planktonic, indicated that the larvae at hatching (9 hpf) were in hypo-immunity. While the ascending activities of enzymes and expression levels of seven immune genes during the trochophore stage (15 hpf) suggested the initiation of immune system. The steadily increasing trend of all the 12 candidate genes at the early umbo larvae (120 h) hinted that the immune system was well developed at this stage. After bacterial challenge, some immune recognition (TLR4) and immune effector (IL17-5 and defh2) genes were activated in blastula stage (4 hpf), and other immune genes were up regulated in D-veliger larvae, indicating that the zygotic immune system could respond earlier against the bacterial challenge during its development. These results indicated that the cellular and humoral immune components appeared at trochophore stage, and the cellular immune system was activated with its occurrence, while the humoral immune system executed until the early umbo larval stage. The immune system emerged earlier to aid larvae in defending bacterial challenge during the early stages of oyster development.

Can selection for resistance to OsHV-1 infection modify susceptibility to Vibrio aestuarianus infection in Crassostrea gigas? First insights from experimental challenges using primary and successive exposures

Since 2008, the emergent virus OsHV-1µvar has provoked massive mortality events in Crassostrea gigas spat and juveniles in France. Since 2012, mortality driven by the pathogenic bacteria Vibrio aestuarianus has stricken market-sized adults. A hypothesis to explain the sudden increase in mortality observed in France since 2012 is that selective pressure due to recurrent viral infections could have led to a higher susceptibility of adults to Vibrio infection. In our study, two OsHV-1-resistant lines (AS and BS) and their respective controls (AC and BC) were experimentally challenged in the laboratory to determine their level of susceptibility to V. aestuarianus infection. At the juvenile stage, the selected lines exhibited lower mortality (14 and 33%) than the control lines (71 and 80%), suggesting dual-resistance to OsHV-1 and V. aestuarianus in C. gigas. Interestingly, this pattern was not observed at the adult stage, where higher mortality was detected for AS (68%) and BC (62%) than AC (39%) and BS (49%). These results were confirmed by the analysis of the expression of 31 immune-related genes in unchallenged oysters. Differential gene expression discriminated oysters according to their susceptibility to infection at both the juvenile and adult stages, suggesting that resistance to V. aestuarianus infection resulted in complex interactions between the genotype, stage of development and immunity status. Finally, survivors of the V. aestuarianus challenge at the juvenile stage still exhibited significant mortality at the adult stage during a second and third V. aestuarianus challenge, indicating that these survivors were not genetically resistant.

OsHV-1 countermeasures to the Pacific oyster's anti-viral response

The host-pathogen interactions between the Pacific oyster (Crassostrea gigas) and Ostreid herpesvirus type 1 (OsHV-1) are poorly characterised. Herpesviruses are a group of large, DNA viruses that are known to encode gene products that subvert their host's antiviral response. It is likely that OsHV-1 has also evolved similar strategies as its genome encodes genes with high homology to C. gigas inhibitors of apoptosis (IAPs) and an interferon-stimulated gene (termed CH25H). The first objective of this study was to simultaneously investigate the expression of C. gigas and OsHV-1 genes that share high sequence homology during an acute infection. Comparison of apoptosis-related genes revealed that components of the extrinsic apoptosis pathway (TNF) were induced in response to OsHV-1 infection, but we failed to observe evidence of apoptosis using a combination of biochemical and molecular assays. IAPs encoded by OsHV-1 were highly expressed during the acute stage of infection and may explain why we didn't observe evidence of apoptosis. However, C. gigas must have an alternative mechanism to apoptosis for clearing OsHV-1 from infected gill cells as we observed a reduction in viral DNA between 27 and 54 h post-infection. The reduction of viral DNA in C. gigas gill cells occurred after the up-regulation of interferon-stimulated genes (viperin, PKR, ADAR). In a second objective, we manipulated the host's anti-viral response by injecting C. gigas with a small dose of poly I:C at the time of OsHV-1 infection. This small dose of poly I:C was unable to induce transcription of known antiviral effectors (ISGs), but these oysters were still capable of inhibiting OsHV-1 replication. This result suggests dsRNA induces an anti-viral response that is additional to the IFN-like pathway.

Immune and stress responses in oysters with insights on adaptation

Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster's immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster's immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster's adaptation to highly stressful and widely changing environments.

The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view

Oysters are sessile filter feeders that live in close association with abundant and diverse communities of microorganisms that form the oyster microbiota. In such an association, cellular and molecular mechanisms have evolved to maintain oyster homeostasis upon stressful conditions including infection and changing environments. We give here cellular and molecular insights into the Crassostrea gigas antimicrobial defense system with focus on antimicrobial peptides and proteins (AMPs). This review highlights the central role of the hemocytes in the modulation and control of oyster antimicrobial response. As vehicles for AMPs and other antimicrobial effectors, including reactive oxygen species (ROS), and together with epithelia, hemocytes provide the oyster with local defense reactions instead of systemic humoral ones. These reactions are largely based on phagocytosis but also, as recently described, on the extracellular release of antimicrobial histones (ETosis) which is triggered by ROS. Thus, ROS can signal danger and activate cellular responses in the oyster. From the current literature, AMP production/release could serve similar functions. We provide also new lights on the oyster genetic background that underlies a great diversity of AMP sequences but also an extraordinary individual polymorphism of AMP gene expression. We discuss here how this polymorphism could generate new immune functions, new pathogen resistances or support individual adaptation to environmental stresses.

The genome-wide identification of mitogen-activated protein kinase kinase (MKK) genes in Yesso scallop Patinopecten yessoensis and their expression responses to bacteria challenges

Mitogen-activated protein kinase kinases (MKK) are the essential components of the evolutionarily conserved MAPK signaling cascade, which regulates a variety of cellular activities and innate immune responses. Although MKK genes have been extensively studied in various vertebrate and invertebrate species, they have not been systematically characterized in bivalves. In this study, we identified and characterized five MKK genes (PyMKK1/2, PyMKK4, PyMKK5, PyMKK3/6 and PyMKK7) in the Yesso scallop (Patinopecten yessoensis). Phylogenetic and protein structural analyses were conducted to determine their identities and evolutionary relationships. To gain insights into the possible roles of MKK genes during scallop innate immune responses, quantitative real-time PCR (qRT-PCR) was used to investigate their expression profiles during different developmental stages in samples taken from healthy adult tissues and hemocytes after Micrococcus luteus and Vibrio anguillarum bacterial infections. The Yesso scallop MKKs (PyMKKs) were found to have highly conserved structural features compared to the MKK genes from other invertebrate species. Using qRT-PCR analysis, three distinct expression patterns were detected among the PyMKKs over the course of ten different developmental stages. In adult scallops, the majority of the PyMKKs were highly expressed in mantle, gill, muscle and hemocytes. The differential expression patterns of the five PyMKKs after M. luteus (Gram-positive) and V. anguillarum (Gram-negative) bacterial infections suggested their possible involvement in the innate immune response and provide the foundation and resource for the further study on innate immune response of MAPK signal pathway in mollusk.

Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila

The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we used the Solexa/Illumina technology to analyze the transcriptomic profile after artificial bacterial infection. Two nonnormalized cDNA libraries were synthesized from tissues collected from control blunt snout bream or those injected with A. hydrophila. After assembly, 155,052 unigenes (average length 692.8 bp) were isolated. All unigenes were annotated using BLASTX relative to several public databases: the National Center for Biotechnology Information nonreduntant (Nr) database, SwissProt, Eukaryotic Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). The sequence similarity (86%) of the assembled unigenes was to zebrafish based on the Nr database. A number of unigenes (n = 30,482) were assigned to three GO categories: biological processes (25,242 unigenes), molecular functions (26,096 unigenes), and cellular components (22,778 unigenes). 20,909 unigenes were classified into 25 KOG categories and 28,744 unigenes were assigned into 315 specific signaling pathways. In total, 238 significantly differentially expressed unigenes (mapped to 125 genes) were identified: 101 upregulated genes and 24 downregulated genes. Another 303 unigenes were mapped to unknown or novel genes. Among the known expressed genes identified, 53 were immune-related genes and were distributed in 71 signaling pathways. The expression patterns of selected up- and downregulated genes from the control and injected groups were determined with reverse transcription-quantitative PCR (RT-qPCR). Microsatellites (n = 10,877), including di-to pentanucleotide repeat motifs, were also identified in the blunt snout bream transcriptome profiles. This study extends our understanding of the immune defense mechanisms of the blunt snout bream against A. hydrophila and provides useful data for further studies of the immunogenetics of this species.

The use of -omic tools in the study of disease processes in marine bivalve mollusks

Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in the bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show that epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress -omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.