Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera

BACKGROUND

In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes.

RESULTS

We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene.

CONCLUSIONS

Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.

Transcriptomic Analysis Provides Insights into Candidate Genes and Molecular Pathways Involved in Growth of Mytilus coruscus Larvae

Growth is a fundamental aspect of aquaculture breeding programs, pivotal for successful cultivation. Understanding the mechanisms that govern growth and development differences across various stages can significantly boost seedling production of economically valuable species, thereby enhancing aquaculture efficiency and advancing the aquaculture industry. Mytilus coruscus, a commercially vital marine bivalve, underscores this importance. To decipher the intricate molecular mechanisms dictating growth and developmental disparities in marine shellfish, we conducted transcriptome sequencing and meticulously analyzed gene expression variations and molecular pathways linked to growth traits in M. coruscus. This study delved into the molecular and gene expression variations across five larval development stages, with a specific focus on scrutinizing the differential expression patterns of growth-associated genes using RNA sequencing and quantitative real-time PCR analysis. A substantial number of genes-36,044 differentially expressed genes (DEGs)-exhibited significant differential expression between consecutive developmental stages. These DEGs were then categorized into multiple pathways (Q value < 0.05), including crucial pathways such as the spliceosome, vascular smooth muscle contraction, DNA replication, and apoptosis, among others. In addition, we identified two pivotal signaling pathways-the Hedgehog (Hh) signaling pathway and the TGF-beta (TGF-β) signaling pathway-associated with the growth and development of M. coruscus larvae. Ten key growth-related genes were pinpointed, each playing crucial roles in molecular function and the regulation of growth traits in M. coruscus. These genes and pathways associated with growth provide deep insights into the molecular basis of physiological adaptation, metabolic processes, and growth variability in marine bivalves.

Ioxynil and diethylstilbestrol impair cardiac performance and shell growth in the mussel Mytilus coruscus

The herbicide ioxynil (IOX) and the synthetic estrogen diethylstilbestrol (DES) are environmentally relevant contaminants that act as endocrine disruptors (EDCs) and have recently been shown to be cardiovascular disruptors in vertebrates. Mussels, Mytilus coruscus, were exposed to low doses of IOX (0.37, 0.037 and 0.0037 mg/L) and DES (0.27, 0.027 and 0.0027 mg/L) via the water and the effect monitored by generating whole animal transcriptomes and measuring cardiac performance and shell growth. One day after IOX (0.37 and 0.037 mg/L) and DES (0.27 and 0.027 mg/L) exposure heart rate frequency was decreased in both groups and 0.27 mg/L DES significantly reduced heart rate frequency with increasing time of exposure (P < 0.05) and no acclimatization occurred. The functional effects were coupled to significant differential expression of genes of the serotonergic synapse pathway and cardiac-related genes at 0.027 mg/L DES, which suggests that impaired heart function may be due to interference with neuroendocrine regulation and direct cardiac effect genes. Multiple genes related to detoxifying xenobiotic substances were up regulated and genes related to immune function were down regulated in the DES group (vs. control), indicating that detoxification processes were enhanced, and the immune response was depressed. In contrast, IOX had a minor disrupting effect at a molecular level. Of note was a significant suppression (P < 0.05) by DES of shell growth in juveniles and lower doses (< 0.0027 mg/L) had a more severe effect. The shell growth depression in 0.0027 mg/L DES-treated juveniles was not accompanied by abundant differential gene expression, suggesting that the effect of 0.0027 mg/L DES on shell growth may be direct. The results obtained in the present study reveal for the first time that IOX and DES may act as neuroendocrine disrupters with a broad spectrum of effects on cardiac performance and shell growth, and that DES exposure had a much more pronounced effect than IOX in a marine bivalve.

Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams

The grooved carpet shell (Ruditapes decussatus) is a clam species with high economic and social importance in several European and Mediterranean countries. Production of this species suffered a decline caused by biotic (parasite infection) and abiotic factors (environmental factors, stress, poor management methods and intensive culture of the introduced species Ruditapes philippinarum). The protozoan parasite Perkinsus olseni is also responsible for the decline of production, being nowadays one of the major issues for clam culture. Molecular biomarkers that might represent tolerance of R. decussatus to P. olseni have already been uncovered, shedding light in a possible production improvement by selecting those clams with a strongest immune response. In the present study, new tolerance biomarkers to P. olseni infection in R. decussatus were identified. The haemolymph proteomic profiles of naturally non/low-infected (tolerant) and highly-infected (susceptible) clams by the parasite across several heavy affected areas of Europe were characterized through a shotgun proteomics approach. Also, the mechanisms that might be involved in the responses against the disease in chronic infections were explored. Proteins related to energy restoration and balance, metabolic regulation, energy accumulation, ROS production, lysosomal activity, amino acid synthesis, proteolytic activity, iron regulation, iron withholding, and immune response modulation were significantly regulated in susceptible clams. In the tolerant group, proteins related to phagocytosis regulation, control of cell growth and proliferation, gonadal maturation, regulation of apoptosis, growth modulation, response to oxidative stress, iron regulation, shell development and metabolic regulation were significantly expressed. In summary, the protein expression profile of tolerant individuals suggests that an efficient pathogen elimination mechanism coupled to a better metabolic regulation leads to a tolerance to the parasite infection by limiting the spread through the tissues.

Metabolic size scaling reflects growth performance effects on age-size relationships in mussels (Mytilus galloprovincialis)

Body-size scaling of metabolic rate in animals is typically allometric, with mass exponents that vary to reflect differences in the physiological status of organisms of both endogenous and environmental origin. Regarding the intraspecific analysis of this relationship in bivalve molluscs, one important source of metabolic variation comes from the large inter-individual differences in growth performance characteristic of this group. In the present study, we aimed to address the association of growth rate differences recorded among individual mussels (Mytilus galloprovincialis) with variable levels of the standard metabolic rate (SMR) resulting in growth-dependent shift in size scaling relationships. SMR was measured in mussels of different sizes and allometric functions fitting SMR vs. body-mass relationships were compared both inter- and intra-individually. The results revealed a metabolic component (the overhead of growth) attributable to the differential costs of maintenance of feeding and digestion structures between fast and slow growers; these costs were estimated to amount to a 3% increase in SMR per unit of increment in the weight specific growth rate. Scaling exponents computed for intraindividual SMR vs body-mass relationships had a common value b = 0.79 (~ ¾); however, when metabolic effects caused by differential growth were discounted, this value declined to 0.67 (= ⅔), characteristic of surface dependent processes. This last value of the scaling exponent was also recorded for the interindividual relationships of both standard and routine metabolic rates (SMR and RMR) after long-lasting maintenance of mussels under optimal uniform conditions in the laboratory. The above results were interpreted based on the metabolic level boundaries (MLB) hypothesis.

Integrated application of transcriptomics and metabolomics provides insights into condition index difference mechanisms in the Pacific oyster (Crassostrea gigas)

The condition index (CI) is an economically important tool for assessing the quality of oysters, such as the Pacific oyster Crassostrea gigas. However, little is known about the mechanisms that underlie differences in CI between different C. gigas populations. In this study, we integrated transcriptomic and metabolomic profiling to investigate the mechanisms that underlie the differences between high- and low-CI groups in one- and two-year-old populations of C. gigas. The results indicate that differences in CI were associated with the regulation of growth-related genes, the FoxO signaling pathway, and the complex regulation of carbohydrate, lipid, amino acid, and energy metabolism. Moreover, the mechanisms underlying these differences differed between the populations. This study is the first to elucidate the molecular and chemical mechanisms associated with CI, and the results will be helpful for breeding higher quality oysters.

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.

Nature more than nurture affects the growth rate of mussels

We tested the hypothesis that environmental trophic conditions prominent during the growing period (nurture conditions) can modify the differing physiological profiles between fast (F)- and slow (S)-growing juveniles of the mussel Mytilus galloprovincialis. Approximately 200 individuals were fed a high organic content diet dosed below the pseudofaeces threshold (BP), whereas another 200 were fed a low organic content diet dosed above the pseudofaeces threshold (AP), forcing them to maintain a continuous production of pseudofaeces. After 3 months, F and S individuals in each rearing condition were selected and used in feeding experiments. We measured the physiological parameters of the energy balance of selected F and S mussels fed on 4 different diets and tested the effects of the rearing condition (BP vs AP) and growth condition (F vs S) upon the physiological variables. Irrespective of the rearing condition, F-mussels attained higher values of scope for growth with the four experimental diets due to their capacity to display higher clearance rates and preingestive selection efficiencies. F-individuals also had higher gill-surface areas than S individuals. We discussed the role of the gills in determining inter-individual growth rate differences in the mussel.

Mytilus galloprovincialis fast growing phenotypes under different restrictive feeding conditions: Fast feeders and energy savers

The present study aims to test if the environmental conditions prevailing during the growing period can determine the physiological profiles of specimens differentiated as fast (F) or slow (S) growers in the mussel Mytilus galloprovincialis. We reared mussel spats in the laboratory under two different conditions. In Treatment I (continuous feeding during discontinuous immersion), two mussel groups were submitted to a daily air exposure of 8 h and fed continuously during immersion-time, with either high-quality food dosed below the pseudofaeces threshold (BP group) or low organic content food dosed above the pseudofaeces threshold (AP group). In Treatment II (discontinuous feeding during continuous immersion), mussels were continuously immersed but fed only 1 day per week (RC group). Mussels were reared for 7 and 11 months (time required for size-differentiation) in Treatments I and II, respectively, and the smallest and largest individuals from each group were selected as S and F specimens. A series of feeding experiments (with different food quality, food ration and under continuous food supply) were performed to analyse the physiological performance of selected F and S mussels. In Treatment I, no significant differences were found in the metabolic rates between F and S mussels, and the faster growth rate of F-mussels resulted from their capacity to display higher clearance-ingestion rates and pre-ingestive selections. The physiological basis of growth rate differences between F and S mussels were found to be the same in mussels reared with diets below or above a pseudofaeces threshold (F_BP, F_AP, S_BP and S_AP). In contrast, the mussels from Treatment II had no significant differences in the feeding rates between F_RC and S_RC mussels. However, F individuals were found to have a 33% lower standard metabolic rate, indicating that fast growth under severe feeding restriction stemmed from a higher capacity of F-mussels to save energy during long periods of starvation. Despite the differences in the physiological basis explaining fast growth between the two treatments, F-mussels were found to possess significantly higher gill-surface area in both cases. It is thus concluded that endogenous factors affecting the gill-surface area play a major role in determining inter-individual growth rate differences in the mussel, Mytilus galloprovincialis.

Biochemical bases of growth variation during development: a study of protein turnover in pedigreed families of bivalve larvae (Crassostrea gigas)

Animal size is a highly variable trait regulated by complex interactions between biological and environmental processes. Despite the importance of understanding the mechanistic bases of growth, predicting size variation in early stages of development remains challenging. Pedigreed lines of the Pacific oyster (Crassostrea gigas) were crossed to produce contrasting growth phenotypes to analyze the metabolic bases of growth variation in larval stages. Under controlled environmental conditions, substantial growth variation of up to 430% in shell length occurred among 12 larval families. Protein was the major biochemical constituent in larvae, with an average protein-to-lipid content ratio of 2.8. On average, 86% of protein synthesized was turned over (i.e. only 14% retained as protein accreted), with a regulatory shift in depositional efficiency resulting in increased protein accretion during later larval growth. Variation in protein depositional efficiency among families did not explain the range in larval growth rates. Instead, changes in protein synthesis rates predicted 72% of growth variation. High rates of protein synthesis to support faster growth, in turn, necessitated greater allocation of the total ATP pool to protein synthesis. An ATP allocation model is presented for larvae of C. gigas that includes the major components (82%) of energy demand: protein synthesis (45%), ion pump activity (20%), shell formation (14%) and protein degradation (3%). The metabolic trade-offs between faster growth and the need for higher ATP allocation to protein synthesis could be a major determinant of fitness for larvae of different genotypes responding to the stress of environmental change.

Sensitivity to ocean acidification differs between populations of the Sydney rock oyster: Role of filtration and ion-regulatory capacities

Understanding mechanisms of intraspecific variation in resilience to environmental drivers is key to predict species' adaptive potential. Recent studies show a higher CO₂ resilience of Sydney rock oysters selectively bred for increased growth and disease resistance ('selected oysters') compared to the wild population. We tested whether the higher resilience of selected oysters correlates with an increased ability to compensate for CO₂-induced acid-base disturbances. After 7 weeks of exposure to elevated seawater PCO₂ (1100 μatm), wild oysters had a lower extracellular pH (pH_e = 7.54 ± 0.02 (control) vs. 7.40 ± 0.03 (elevated PCO₂)) and increased hemolymph PCO₂ whereas extracellular acid-base status of selected oysters remained unaffected. However, differing pH_e values between oyster types were not linked to altered metabolic costs of major ion regulators (Na⁺/K⁺-ATPase, H⁺-ATPase and Na⁺/H⁺-exchanger) in gill and mantle tissues. Our findings suggest that selected oysters possess an increased systemic capacity to eliminate metabolic CO₂, possibly through higher and energetically more efficient filtration rates and associated gas exchange. Thus, effective filtration and CO₂ resilience might be positively correlated traits in oysters.

A Microarray Study of Carpet-Shell Clam (Ruditapes decussatus) Shows Common and Organ-Specific Growth-Related Gene Expression Differences in Gills and Digestive Gland

Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i.e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/Ras/Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in the microarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO term enrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.

Oyster reproduction is compromised by acidification experienced seasonally in coastal regions

Atmospheric carbon dioxide concentrations have been rising during the past century, leading to ocean acidification (OA). Coastal and estuarine habitats experience annual pH variability that vastly exceeds the magnitude of long-term projections in open ocean regions. Eastern oyster (Crassostrea virginica) reproduction season coincides with periods of low pH occurrence in estuaries, thus we investigated effects of moderate (pH 7.5, pCO₂ 2260 µatm) and severe OA (pH 7.1, pCO₂ 5584 µatm; and 6.7, pCO₂ 18480 µatm) on oyster gametogenesis, fertilization, and early larval development successes. Exposure at severe OA during gametogenesis caused disruption in oyster reproduction. Oogenesis appeared to be more sensitive compared to spermatogenesis. However, Eastern oyster reproduction was resilient to moderate OA projected for the near-future. In the context of projected climate change exacerbating seasonal acidification, OA of coastal habitats could represent a significant bottleneck for oyster reproduction which may have profound negative implications for coastal ecosystems reliant on this keystone species.

Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway

Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (p < 0.0001), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq. Pathways differentially expressed included structural gene pathways. Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. NOD2 pathway members that were upregulated included a subset of isoforms of RIPK2 (mean 3.3-fold increase in expression), ERK/MAPK14 (3.8-fold), JNK/MAPK8 (4.1-fold), and NFκB (4.08-fold). These transcriptomes will be useful resources for both the aquaculture community and researchers with an interest in mollusks and growth heterosis.

Metabolic Cost of Protein Synthesis in Larvae of the Pacific Oyster (Crassostrea gigas) Is Fixed Across Genotype, Phenotype, and Environmental Temperature

The energy made available through catabolism of specific biochemical reserves is constant using standard thermodynamic conversion equivalents (e.g., 24.0 J mg protein(-1)). In contrast, measurements reported for the energy cost of synthesis of specific biochemical constituents are highly variable. In this study, we measured the metabolic cost of protein synthesis and determined whether this cost was influenced by genotype, phenotype, or environment. We focused on larval stages of the Pacific oyster Crassostrea gigas, a species that offers several experimental advantages: availability of genetically pedigreed lines, manipulation of ploidy, and tractability of larval forms for in vivo studies of physiological processes. The cost of protein synthesis was measured in larvae of C. gigas for 1) multiple genotypes, 2) phenotypes with different growth rates, and 3) different environmental temperatures. For all treatments, the cost of protein synthesis was within a narrow range--near the theoretical minimum--with a fixed cost (mean ± one standard error, n = 21) of 2.1 ± 0.2 J (mg protein synthesized)(-1) We conclude that there is no genetic variation in the metabolic cost of protein synthesis, thereby simplifying bioenergetic models. Protein synthesis is a major component of larval metabolism in C. gigas, accounting for more than half the metabolic rate in diploid (59%) and triploid larvae (54%). These results provide measurements of metabolic cost of protein synthesis in larvae of C. gigas, an indicator species for impacts of ocean change, and provide a quantitative basis for evaluating the cost of resilience.

Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation

Transcriptomics has emerged as a powerful approach for exploring physiological responses to the environment. However, like any other experimental approach, transcriptomics has its limitations. Transcriptomics has been criticized as an inappropriate method to identify genes with large impacts on adaptive responses to the environment because: (1) genes with large impacts on fitness are rare; (2) a large change in gene expression does not necessarily equate to a large effect on fitness; and (3) protein activity is most relevant to fitness, and mRNA abundance is an unreliable indicator of protein activity. In this review, these criticisms are re-evaluated in the context of recent systems-level experiments that provide new insight into the relationship between gene expression and fitness during environmental stress. In general, these criticisms remain valid today, and indicate that exclusively using transcriptomics to screen for genes that underlie environmental adaptation will overlook constitutively expressed regulatory genes that play major roles in setting tolerance limits. Standard practices in transcriptomic data analysis pipelines may also be limiting insight by prioritizing highly differentially expressed and conserved genes over those genes that undergo moderate fold-changes and cannot be annotated. While these data certainly do not undermine the continued and widespread use of transcriptomics within environmental physiology, they do highlight the types of research questions for which transcriptomics is best suited and the need for more gene functional analyses. Such information is pertinent at a time when transcriptomics has become increasingly tractable and many researchers may be contemplating integrating transcriptomics into their research programs.

Adaptation to abiotic stress in the oyster Crassostrea angulata relays on genetic polymorphisms

Here we describe the whole genome re-sequencing of the Portuguese oyster Crassostrea angulata, an edible cupped oyster of major commercial importance with an important role as biosensor of coastal water pollution. We sequenced the genome of the C. angulata to 29.3-fold coverage using ABI SOLID system. Comparisons of the sequences with the reference assembly of the Pacific oyster (Crassostrea gigas), yielded 129 million SNPs, 151,620 from which were located in 20,908 genes from the C. gigas database. The analysis of Gene Ontology (GO) terms associated with gene regions containing SNPs, revealed that significant GO terms showing differences between the two oyster species, were related to activities of response to stress caused both by drying and by metal contamination. In the Biological Process domain, the GO terms ion transport, phosphorylation and proteolysis processes, among others, showed many polymorphic genes in C. angulata. These processes are related to combating genotoxic and hypo-osmotic stress in the oyster. It is noteworthy that more than 200 polymorphic genes were associated with DNA repair processes. These results reveal that most of the gene polymorphisms observed in C. angulata are associated with processes related to genome adaptation to abiotic stress in estuarine regions and support that genetic polymorphisms may be the base to the observed ability of C. angulata to retain the phenomenally high concentrations of toxic heavy metals. Our results also provide the framework for future investigations to establish the molecular basis of phenotypic variation of adaptive traits and should contribute to the management of the species' genetic resources.

Intrinsic variability in shell and soft tissue growth of the freshwater mussel Lampsilis siliquoidea

Freshwater mussels are ecologically and economically important members of many aquatic ecosystems, but are globally among the most imperiled taxa. Propagation techniques for mussels have been developed and used to boost declining and restore extirpated populations. Here we use a cohort of propagated mussels to estimate the intrinsic variability in size and growth rate of Lampsilis siliquoidea (a commonly propagated species). Understanding the magnitude and pattern of variation in data is critical to determining whether effects observed in nature or experimental treatments are likely to be important. The coefficient of variation (CV) of L. siliquoidea soft tissues (6.0%) was less than the CV of linear shell dimensions (25.1-66.9%). Size-weight relationships were best when mussel width (the maximum left-right dimension with both valves appressed) was used as a predictor, but 95% credible intervals on these predictions for soft tissues were ∼145 mg wide (about 50% of the mean soft tissue mass). Mussels in this study were treated identically, raised from a single cohort and yet variation in soft tissue mass at a particular size class (as determined by shell dimensions) was still high. High variability in mussel size is often acknowledged, but seldom discussed in the context of mussel conservation. High variability will influence the survival of stocked juvenile cohorts, may affect the ability to experimentally detect sublethal stressors and may lead to incongruities between the effects that mussels have on structure (via hard shells) and biogeochemical cycles (via soft tissue metabolism). Given their imperiled status and longevity, there is often reluctance to destructively sample unionid mussel soft tissues even in metabolic studies (e.g., studies of nutrient cycling). High intrinsic variability suggests that using shell dimensions (particularly shell length) as a response variable in studies of sublethal stressors or metabolic processes will make confident identifications of smaller effect sizes difficult.

Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas

The economic and ecological importance of the oyster necessitates further research on the molecular mechanisms, which both regulate the commercially important traits of the oyster and help it to survive in the variable marine environment. Single nucleotide polymorphisms (SNPs) have been widely used to assess genetic variation and identify genes underlying target traits. In addition, high-resolution melting (HRM) analysis is a potentially powerful method for validating candidate SNPs. In this study, we adopted a rapid and efficient pipeline for the screening and validation of SNPs in the genic region of Crassostrea gigas based on transcriptome sequencing and HRM analysis. Transcriptomes of three wild oyster populations were sequenced using Illumina sequencing technology. In total, 50-60 million short reads, corresponding to 4.5-5.4 Gbp, from each population were aligned to the oyster genome, and 5.8 × 10(5) SNPs were putatively identified, resulting in a predicted SNP every 47 nucleotides on average. The putative SNPs were unevenly distributed in the genome and high-density (≥2%), nonsynonymous coding SNPs were enriched in genes related to apoptosis and responses to biotic stimuli. Subsequently, 1,671 loci were detected by HRM analysis, accounting for 64.7% of the total selected candidate primers, and finally, 1,301 polymorphic SNP markers were developed based on HRM analysis. All of the validated SNPs were distributed into 897 genes and located in 672 scaffolds, and 275 of these genes were stress inducible under unfavourable salinity, temperature, and exposure to air and heavy metals. The validated SNPs in this study provide valuable molecular markers for genetic mapping and characterization of important traits in oysters.

Physiological response and resilience of early life-stage Eastern oysters (Crassostrea virginica) to past, present and future ocean acidification

The Eastern oyster, Crassostrea virginica (Gmelin, 1791), is the second most valuable bivalve fishery in the USA and is sensitive to high levels of partial pressure of CO2 (pCO2). Here we present experiments that comprehensively examined how the ocean's past, present and projected (21st and 22nd centuries) CO2 concentrations impact the growth and physiology of larval stages of C. virginica. Crassostrea virginica larvae grown in present-day pCO2 concentrations (380 μatm) displayed higher growth and survival than individuals grown at both lower (250 μatm) and higher pCO2 levels (750 and 1500 μatm). Crassostrea virginica larvae manifested calcification rates, sizes, shell thicknesses, metamorphosis, RNA:DNA ratios and lipid contents that paralleled trends in survival, with maximal values for larvae grown at 380 μatm pCO2 and reduced performance in higher and lower pCO2 levels. While some physiological differences among oysters could be attributed to CO2-induced changes in size or calcification rates, the RNA:DNA ratios at ambient pCO2 levels were elevated, independent of these factors. Likewise, the lipid contents of individuals exposed to high pCO2 levels were depressed even when differences in calcification rates were considered. These findings reveal the cascading, interdependent impact that high CO2 can have on oyster physiology. Crassostrea virginica larvae are significantly more resistant to elevated pCO2 than other North Atlantic bivalves, such as Mercenaria mercenaria and Argopecten irradians, a finding that may be related to the biogeography and/or evolutionary history of these species and may have important implications for future bivalve restoration and aquaculture efforts.

High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc

Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method-2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.

Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome sequencing

Background

The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait.

Results

Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated.

Conclusion

De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.

Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanisms

Because of the tremendous advances in functional genomics and the current availability of a large number of superior hybrids, rice is an excellent model crop system for heterosis research. Genetic dissection of yield and yield component traits of an elite rice hybrid using an ultra-high density linkage map identified overdominance as the principal genetic basis of heterosis in this hybrid. This is not an expected finding based on the reported effects of single genes. Here we propose a gene expression and protein quality control hypothesis as one possible explanation for the overdominance in hybrids bred for yield. Future studies will be directed toward the identification of the genetic and biochemical mechanisms underlying the biology of hybrid vigor.

Transcriptomic analysis of the clam Meretrix meretrix on different larval stages

The clam Meretrix meretrix (Mollusca: Bivalvia) is an important commercial species in China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its complex and unique developmental processes. To improve this situation, in this study, a large-scale RNA sequencing was conducted on M. meretrix on larval stages. In particular, mRNAs of trochophore, D-veliger, pediveliger, and postlarva were purified, reverse transcribed, and sequenced through 454 sequencing technology. A total of 704,671 reads were obtained and assembled into 124,737 unique sequences (35,205 contigs and 89,532 singletons). Further analysis showed that 118,075 (94.66%) of these sequences were low-expression-level transcripts. Fifteen thousand two hundred fifteen (12.20%) of the unique sequences were annotated by searching against Uniprot Protein Knowledgebase, while the others (109,522, 87.80%) were left as novel sequences. Gene ontology analysis of the annotated sequences showed that most of them were assigned to certain gene ontology terms. By analyzing the depth of each unique sequence, a preliminary quantification analysis was conducted. An amount of sequences that showed a dramatic transcript discrepancy among the four larval stages were screened, which were related to development, growth, shell formation, and immune responses etc. As the first attempt on large-scale RNA sequencing of marine bivalve larvae, this work would enrich the knowledge of larval development of marine bivalves and provide fundamental support for further researches.

A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding

Hybrids between genetically diverse varieties display enhanced growth, and increased total biomass, stress resistance and grain yield. Gene expression and metabolic studies in maize, rice and other species suggest that protein metabolism plays a role in the growth differences between hybrids and inbreds. Single trait heterosis can be explained by the existing theories of dominance, overdominance and epistasis. General multigenic heterosis is observed in a wide variety of different species and is likely to share a common underlying biological mechanism. This review presents a model to explain differences in growth and yield caused by general multigenic heterosis. The model describes multigenic heterosis in terms of energy-use efficiency and faster cell cycle progression where hybrids have more efficient growth than inbreds because of differences in protein metabolism. The proposed model is consistent with the observed variation of gene expression in different pairs of inbred lines and hybrid offspring as well as growth differences in polyploids and aneuploids. It also suggests an approach to enhance yield gains in both hybrid and inbred crops via the creation of an appropriate computational analysis pipeline coupled to an efficient molecular breeding program.