Early Development of the Japanese Spiny Oyster (Saccostrea kegaki): Characterization of Some Genetic Markers

Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

Pelagic larval stages are widespread across animals, yet it is unclear whether larvae were present in the last common ancestor of animals or whether they evolved multiple times due to common selective pressures. Many marine larvae are at least superficially similar; they are small, swim through the beating of bands of cilia, and sense the environment with an apical organ. To understand these similarities, we have generated single-cell atlases for marine larvae from two animal phyla and have compared their cell types. We found clear similarities among ciliary band cells and between neurons of the apical organ in the two larvae pointing to possible homology of these structures, suggesting a single origin of larvae within Spiralia. We also find several clade-specific innovations in each larva, including distinct myocytes and shell gland cells in the oyster larva. Oyster shell gland cells express many recently evolved genes that have made previous gene age estimates for the origin of trochophore larvae too young.

Identification and Expressional Analysis of Putative PRDI-BF1 and RIZ Homology Domain-Containing Transcription Factors in Mulinia lateralis

Mollusca represents one of the ancient bilaterian groups with high morphological diversity, while the formation mechanisms of the precursors of all germ cells, primordial germ cells (PGCs), have not yet been clarified in mollusks. PRDI-BF1 and RIZ homology domain-containing proteins (PRDMs) are a group of transcriptional repressors, and PRDM1 (also known as BLIMP1) and PRDM14 have been reported to be essential for the formation of PGCs. In the present study, we performed a genome-wide retrieval in Mulinia lateralis and identified 11 putative PRDMs, all of which possessed an N-terminal PR domain. Expressional profiles revealed that all these prdm genes showed specifically high expression levels in the given stages, implying that all PRDMs played important roles during early development stages. Specifically, Ml-prdm1 was highly expressed at the gastrula stage, the key period when PGCs arise, and was specifically localized in the cytoplasm of two or three cells of blastula, gastrula, or trochophore larvae, matching the typical characteristics of PGCs. These results suggested that Ml-prdm1-positive cells may be PGCs and that Ml-prdm1 could be a candidate marker for tracing the formation of PGCs in M. lateralis. In addition, the expression profiles of Ml-prdm14 hinted that it may not be associated with PGCs of M. lateralis. The present study provides insights into the evolution of the PRDM family in mollusks and offers a better understanding of the formation of PGCs in mollusks.

Molecular characterization of Vasa homolog in the pen shell Atrina pectinata: cDNA cloning and expression analysis during gonadal development

Vasa is an ATP-dependent RNA helicase of the DEAD (Asp-Glu-Ala-Asp) box family and a representative component of the germ plasm. In this study, we cloned the full-length vasa homolog in the bivalve Atrina pectinata (psvasa), and performed phylogenetic analysis, mRNA expression analysis for tissue-specific distributions, and immunostaining analysis to reveal its histological localization. The sequence of psvasa was 3587 bp in length and contained a 5' untranslated region of 150 bp, an open reading frame of 2214 bp, and a 3' untranslated region of 1223 bp. The deduced amino acid sequence of psvasa was 737 amino acids long and contained evolutionarily conserved sequences reported in other animals. The mRNA expression analysis showed the highest expression levels in the gonads. Expression was especially high in the ovaries, followed by the testes. The immunostaining analysis showed Vasa-positive cells in the developing gonads, suggesting the presence of putative germ stem cells contributing to the supply of germ cells. Furthermore, characteristic Vasa signals were observed in the basophilic nuclei of the oocytes, suggesting that psvasa plays an important role in the progression of meiosis in oocytes.

A mosaic of conserved and novel modes of gene expression and morphogenesis in mesoderm and muscle formation of a larval bivalve

The mesoderm gives rise to several key morphological features of bilaterian animals including endoskeletal elements and the musculature. A number of regulatory genes involved in mesoderm and/or muscle formation (e.g., Brachyury (Bra), even-skipped (eve), Mox, myosin II heavy chain (mhc)) have been identified chiefly from chordates and the ecdysozoans Drosophila and Caenorhabditis elegans, but data for non-model protostomes, especially those belonging to the ecdysozoan sister clade, Lophotrochozoa (e.g., flatworms, annelids, mollusks), are only beginning to emerge. Within the lophotrochozoans, Mollusca constitutes the most speciose and diverse phylum. Interestingly, however, information on the morphological and molecular underpinnings of key ontogenetic processes such as mesoderm formation and myogenesis remains scarce even for prominent molluscan sublineages such as the bivalves. Here, we investigated myogenesis and developmental expression of Bra, eve, Mox, and mhc in the quagga mussel Dreissena rostriformis, an invasive freshwater bivalve and an emerging model in invertebrate evodevo. We found that all four genes are expressed during mesoderm formation, but some show additional, individual sites of expression during ontogeny. While Mox and mhc are involved in early myogenesis, eve is also expressed in the embryonic shell field and Bra is additionally present in the foregut. Comparative analysis suggests that Mox has an ancestral role in mesoderm and possibly muscle formation in bilaterians, while Bra and eve are conserved regulators of mesoderm development of nephrozoans (protostomes and deuterostomes). The fully developed Dreissena veliger larva shows a highly complex muscular architecture, supporting a muscular ground pattern of autobranch bivalve larvae that includes at least a velum muscle ring, three or four pairs of velum retractors, one or two pairs of larval retractors, two pairs of foot retractors, a pedal plexus, possibly two pairs of mantle retractors, and the muscles of the pallial line, as well as an anterior and a posterior adductor. As is typical for their molluscan kin, remodelling and loss of prominent larval features such as the velum musculature and various retractor systems appear to be also common in bivalves.

Supplementary information

The online version contains supplementary material available at 10.1007/s13127-022-00569-5.

Comparative Single-Cell Transcriptomics Reveals Novel Genes Involved in Bivalve Embryonic Shell Formation and Questions Ontogenetic Homology of Molluscan Shell Types

Mollusks are known for their highly diverse repertoire of body plans that often includes external armor in form of mineralized hardparts. Representatives of the Conchifera, one of the two major lineages that comprises taxa which originated from a uni-shelled ancestor (Monoplacophora, Gastropoda, Cephalopoda, Scaphopoda, Bivalvia), are particularly relevant regarding the evolution of mollusk shells. Previous studies have found that the shell matrix of the adult shell (teleoconch) is rapidly evolving and that the gene set involved in shell formation is highly taxon-specific. However, detailed annotation of genes expressed in tissues involved in the formation of the embryonic shell (protoconch I) or the larval shell (protoconch II) are currently lacking. Here, we analyzed the genetic toolbox involved in embryonic and larval shell formation in the quagga mussel Dreissena rostriformis using single cell RNA sequencing. We found significant differences in genes expressed during embryonic and larval shell secretion, calling into question ontogenetic homology of these transitory bivalve shell types. Further ortholog comparisons throughout Metazoa indicates that a common genetic biomineralization toolbox, that was secondarily co-opted into molluscan shell formation, was already present in the last common metazoan ancestor. Genes included are engrailed, carbonic anhydrase, and tyrosinase homologs. However, we found that 25% of the genes expressed in the embryonic shell field of D. rostriformis lack an ortholog match with any other metazoan. This indicates that not only adult but also embryonic mollusk shells may be fast-evolving structures. We raise the question as to what degree, and on which taxonomic level, the gene complement involved in conchiferan protoconch formation may be lineage-specific or conserved across taxa.

Single-Cell RNA Sequencing Atlas From a Bivalve Larva Enhances Classical Cell Lineage Studies

Ciliated trochophore-type larvae are widespread among protostome animals with spiral cleavage. The respective phyla are often united into the superclade Spiralia or Lophotrochozoa that includes, for example, mollusks, annelids, and platyhelminths. Mollusks (bivalves, gastropods, cephalopods, polyplacophorans, and their kin) in particular are known for their morphological innovations and lineage-specific plasticity of homologous characters (e.g., radula, shell, foot, neuromuscular systems), raising questions concerning the cell types and the molecular toolkit that underlie this variation. Here, we report on the gene expression profile of individual cells of the trochophore larva of the invasive freshwater bivalve Dreissena rostriformis as inferred from single cell RNA sequencing. We generated transcriptomes of 632 individual cells and identified seven transcriptionally distinct cell populations. Developmental trajectory analyses identify cell populations that, for example, share an ectodermal origin such as the nervous system, the shell field, and the prototroch. To annotate these cell populations, we examined ontology terms from the gene sets that characterize each individual cluster. These were compared to gene expression data previously reported from other lophotrochozoans. Genes expected to be specific to certain tissues, such as Hox1 (in the shell field), Caveolin (in prototrochal cells), or FoxJ (in other cillia-bearing cells) provide evidence that the recovered cell populations contribute to various distinct tissues and organs known from morphological studies. This dataset provides the first molecular atlas of gene expression underlying bivalve organogenesis and generates an important framework for future comparative studies into cell and tissue type development in Mollusca and Metazoa as a whole.

Phalloidin fluorescence and confocal microscopy reveal the musculature development of clam Ruditapes philippinarum

Knowledge of early development in bivalves is of great importance to understand the function of animal organ systems and the evolution of phenotypic diversity. Manila clam (Ruditapes philippinarum) is an economically important bivalve living in marine intertidal zones. To determine the pattern of muscle development in the clams, we investigate the characteristics of musculature development utilizing phalloidin staining and confocal microscopy. Myofilaments first appear at the early trochophore stage, and gradually become orderly arranged during the transition from trochophore to veliger. For veliger, larval muscle system is mainly composed of dorsal velum retractors, medio-dorsal velum retractors, ventral velum retractors, ventral larval retractors and anterior and posterior adductor muscles. After metamorphosis, the muscle system of late veliger has been reconstructed, showing the irreversible shrink of velum retractor muscles, the rapid growth of wedge-shaped foot and mantle margins. One of the most striking changes in settled spats is the development of sophisticated architecture of foot musculature, which consists of transverse pedal muscles, anterior foot retractor and posterior foot retractor. These findings will not only provide the basis to understand the dynamic pattern of myogenesis in the burrowing bivalves, but also provide valuable information for comparative analysis of muscle development among bivalves.

A Potential Role of Bone Morphogenetic Protein 7 in Shell Formation and Growth in the Razor Clam Sinonovacula constricta

Bone morphogenetic proteins (BMPs) not only play essential roles in bone development but also are involved in embryonic growth, organogenesis cell proliferation and differentiation. However, the previous studies on the functions of shellfish BMPs genes are still very limited. To better understand its molecular structure and biological function, BMP7 of the razor clam Sinonovacula constricta (Sc-BMP7) was cloned and characterized in this study. The full length of Sc-BMP7 is 2252 bp, including an open reading frame (ORF) of 1257 bp encoding 418 amino acids. The protein sequence included a signal peptide (1–32 aa), a prodomain (38–270 aa) and a TGF-β domain (317–418 aa). The quantitative expression of eleven adult tissues showed that Sc-BMP7 was significantly higher expressed in the gill, foot, and mantle (P < 0.05), but lower in hemocytes and hepatopancreas. In the early development stages, low expression was detected in the stages of unfertilized mature eggs, fertilized eggs, 4-cell embryos, blastula, gastrulae, whereas it increased after the stage of trochophore and demonstrated the highest expression in umbo larvae (P < 0.01). In shell repair experiment, Sc-BMP7 showed increasing expression level after 12 h. The higher expression of Sc-BMP7 was detected while Ca²⁺ concentration was reduced in seawater. After inhibiting Sc-BMP7 expression using RNA interference (RNAi) technology, expression of Sc-BMP7 mRNA and protein were significantly down-regulated (P < 0.05) in the central zone of mantle (nacre formation related tissue) and the pallial zone of mantle (prismatic layer formation related tissue). Association analysis identified two shared SNPs in exon of Sc-BMP7 gene from 246 individuals of two groups. These results indicated that BMP7 might be involved in shell formation and growth. These results would contribute to clarify the role of Sc-BMP7 in the regulation of growth and shell formation, and provide growth-related markers for molecular marker assisted breeding of this species.

Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics

Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO₃ crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO₃ precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.

Establishment of the novel bivalve body plan through modification of early developmental events in mollusks

Mollusks have a wide variety of body plans, which develop through conserved early embryogenesis, namely spiral embryonic development and trochophore larvae. Although the comparative study of mollusks has attracted the interest of evolutionary developmental biology researchers, less attention has been paid to bivalves. In this review, we focused on the evolutionary process from single-shell ancestors to bivalves, which possess bilaterally separated shells. Our study tracing the lineage of shell field cells in bivalves did not support the old hypothesis that shell plate morphology is due to modification of the spiral cleavage pattern. Rather, we suggest that modification of the shell field induction process is the key to understanding the evolution of shell morphology. The novel body plan of bivalves cannot be established solely via separating shell plates, but rather requires the formation of additional organs, such as adductor muscles. The evolutionary biology of bivalves offers a unique view on how multiple organs evolve in a coordinated manner to establish a novel body plan.

Dual Gene Repertoires for Larval and Adult Shells Reveal Molecules Essential for Molluscan Shell Formation

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

The evolution of molluscs

Molluscs are extremely diverse invertebrate animals with a rich fossil record, highly divergent life cycles, and considerable economical and ecological importance. Key representatives include worm-like aplacophorans, armoured groups (e.g. polyplacophorans, gastropods, bivalves) and the highly complex cephalopods. Molluscan origins and evolution of their different phenotypes have largely remained unresolved, but significant progress has been made over recent years. Phylogenomic studies revealed a dichotomy of the phylum, resulting in Aculifera (shell-less aplacophorans and multi-shelled polyplacophorans) and Conchifera (all other, primarily uni-shelled groups). This challenged traditional hypotheses that proposed that molluscs gradually evolved complex phenotypes from simple, worm-like animals, a view that is corroborated by developmental studies that showed that aplacophorans are secondarily simplified. Gene expression data indicate that key regulators involved in anterior-posterior patterning (the homeobox-containing Hox genes) lost this function and were co-opted into the evolution of taxon-specific novelties in conchiferans. While the bone morphogenetic protein (BMP)/decapentaplegic (Dpp) signalling pathway, that mediates dorso-ventral axis formation, and molecular components that establish chirality appear to be more conserved between molluscs and other metazoans, variations from the common scheme occur within molluscan sublineages. The deviation of various molluscs from developmental pathways that otherwise appear widely conserved among metazoans provides novel hypotheses on molluscan evolution that can be tested with genome editing tools such as the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein9) system.

Oocyte maturation and origin of the germline as revealed by the expression of Nanos-like in the Pacific oyster Crassostrea gigas

Nanos gene plays an important role in germline development in animals. However, the molecular mechanisms involved in germline development in Mollusca, the second largest animal phylum, are still poorly understood. Here we identified the Nanos orthologue from the Pacific oyster Crassostrea gigas (Cg-Nanos-like), and investigated the expression patterns of Nanos during gametogenesis and embryogenesis in C. gigas. Tissue expression analysis showed that Cg-Nanos-like was specifically expressed in female gonads. During the reproductive cycle, the expression of Cg-Nanos-like mRNA increased matching the seasonal development of the ovarian tissues in diploids, while the expression levels were significantly lower in the ovaries of sterile triploids compared to diploids. High expression of Cg-Nanos-like transcripts were detected in early embryonic stages, while the expression significantly dropped at gastrulation and was barely detectable in veliger stages. In situ hybridization showed that Cg-Nanos-like was expressed at different stages of developing oocytes, whereas positive signals were detected only in spermatogonia during the spermatogenic cycle. These findings indicated that Cg-Nanos-like was involved in the development of germ cells, and maintenance of oocyte maturation. In early embryogenesis, the transcripts were broadly expressed; following gastrulation, the expression was restricted to two cell clumps, which might be the putative primordial germ cells (PGCs) or their precursors. Based on the results, the formation of the PGCs in C. gigas was consistent with the model of transition from epigenesis to preformation.

Molecular and functional analysis of PmCHST1b in nacre formation of Pinctada fucata martensii

Keratan sulfate possesses considerable amounts of negatively charged sulfonic acid groups and participates in biomineralization. In the present study, we investigated characteristics and functions of a CHST1 gene identified from the pearl oyster Pinctada fucata martensii (PmCHST1b) which participated in the synthesis of keratan sulfate. PmCHST1b amino acid sequence carried a typical sulfotransferase-3 domain (sulfotransfer-3 domain) and belonged to membrane-associated sulfotransferases. Homologous analysis of CHST1 from different species showed the conserved motif (5' PSB motif and 3' PB motif) which interacted with 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Structure analysis of sulfotransferase domain indicted that PmCHST1b showed the conserved catalytic structure character and the relationships presented in the phylogenetic tree conformed to that of traditional taxonomy. Expression pattern of PmCHST1b in different tissues and development stages showed that PmCHST1b widely expressed in all the detected tissues and development stages and showed the highest expression level in the central zone of mantle (MC). PmCHST1b expressed highly in the trochophore, D-stage larvae and spat which corresponded to prodissoconch and dissoconch shell formation, respectively. RNA interference (RNAi) successfully inhibited expression level of PmCHST1b in MC (P<0.05), and sulfate polymer content in the extrapallial fluid significantly reduced (P<0.05). Crystallization of shell nacre became irregular. Results above indicated that PmCHST1b may affect nacre formation by participating in synthesis of keratan sulfate in extrapallial fluid. This study provided fundamental materials for further research on the role of sulfotransferases and keratan sulfate in nacre formation.

Deviating from the Norm: Peculiarities of Aplysia cf. californica Early Cleavage Compared to Traditional Spiralian Models

Spiralia represents one of the main clades of bilaterally symmetrical metazoans (Bilateria). This group is of particular interest due to the remarkable conservation of its early developmental pattern despite of the high diversity of larval and adult body plans. Variations during embryogenesis are considered powerful tools to determine ancestral and derived characters under a phylogenetic framework. By direct observation of embryos cultured in vitro, we analyzed the early cleavage of the euopisthobranchs Aplysia cf. californica. We used tubulin immunocytochemistry to stain mitotic spindles during early cleavages, and followed each division with the aid of an autofluorescent compound inside yolk platelets, which differed from the characteristic pink-brownish pigment of the vegetal cytoplasm in zygotes and early embryos. We found that this species exhibits an unequal cleavage characterized by ooplasmic segregation, oblique inclination of mitotic spindles, and differences in size and positioning of the asters in relation to the cellular cortex. Furthermore, we detected asynchrony in cleavage timing between the two large macromeres C and D, which increases the number of cleavage rounds required to reach a particular cell stage in comparison to other spiralians. Here, we report the presence of a transient and previously undescribed U-shaped embryo in this species. The present detailed description of A. californica early development deviates considerably from stereotypical patterns described in other spiralians. Our observations demonstrate that early spiralian development can be more plastic than previously thought.

Dynamics of nuclear receptor gene expression during Pacific oyster development

BACKGROUND

Nuclear receptors are a highly conserved set of ligand binding transcription factors, with essential roles regulating aspects of vertebrate and invertebrate biology alike. Current understanding of nuclear receptor regulated gene expression in invertebrates remains sparse, limiting our ability to elucidate gene function and the conservation of developmental processes across phyla. Here, we studied nuclear receptor expression in the early life stages of the Pacific oyster, Crassostrea gigas, to identify at which specific key stages nuclear receptors are expressed RESULTS: We used quantitative RT-PCR to determine the expression profiles of 34 nuclear receptors, revealing three developmental key stages, during which nuclear receptor expression is dynamically regulated: embryogenesis, mid development from gastrulation to trochophore larva, and late larval development prior to metamorphosis. Clustering of nuclear receptor expression patterns demonstrated that transcriptional regulation was not directly related to gene phylogeny, suggesting closely related genes may have distinct functions. Expression of gene homologs of vertebrate retinoid receptors suggests participation in organogenesis and shell-formation, as they are highly expressed at the gastrulation and trochophore larval initial shell formation stages. The ecdysone receptor homolog showed high expression just before larval settlement, suggesting a potential role in metamorphosis.

CONCLUSION

Throughout early oyster development nuclear receptors exhibited highly dynamic expression profiles, which were not confined by gene phylogeny. These results provide fundamental information on the presence of nuclear receptors during key developmental stages, which aids elucidation of their function in the developmental process. This understanding is essential as ligand sensing nuclear receptors can be disrupted by xenobiotics, a mode of action through which anthropogenic environmental pollutants have been found to mediate effects.

Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2

Ocean acidification (OA) has been found to affect an array of normal physiological processes in mollusks, especially posing a significant threat to the fabrication process of mollusk shell. In the current study, the impact of exposure to elevated pCO2 condition was investigated in mantle tissue of Crassostrea gigas by an integrated metabolomic and proteomic approach. Analysis of metabolome and proteome revealed that elevated pCO2 could affect energy metabolism in oyster C. gigas, marked by differentially altered ATP, succinate, MDH, PEPCK and ALDH levels. Moreover, the up-regulated calponin-2, tropomyosins and myosin light chains indicated that elevated pCO2 probably caused disturbances in cytoskeleton structure in mantle tissue of oyster C. gigas. This work demonstrated that a combination of proteomics and metabolomics could provide important insights into the effects of OA at molecular levels.

Reproduction-related genes in the pearl oyster genome

Molluscan reproduction has been a target of biological research because of the various reproductive strategies that have evolved in this phylum. It has also been studied for the development of fisheries technologies, particularly aquaculture. Although fundamental processes of reproduction in other phyla, such as vertebrates and arthropods, have been well studied, information on the molecular mechanisms of molluscan reproduction remains limited. The recently released draft genome of the pearl oyster Pinctada fucata provides a novel and powerful platform for obtaining structural information on the genes and proteins involved in bivalve reproduction. In the present study, we analyzed the pearl oyster draft genome to screen reproduction-related genes. Analysis was mainly conducted for genes reported from other molluscs for encoding orthologs of reproduction-related proteins in other phyla. The gene search in the P. fucata gene models (version 1.1) and genome assembly (version 1.0) were performed using Genome Browser and BLAST software. The obtained gene models were then BLASTP searched against a public database to confirm the best-hit sequences. As a result, more than 40 gene models were identified with high accuracy to encode reproduction-related genes reported for P. fucata and other molluscs. These include vasa, nanos, doublesex- and mab-3-related transcription factor, 5-hydroxytryptamine (5-HT) receptors, vitellogenin, estrogen receptor, and others. The set of reproduction-related genes of P. fucata identified in the present study constitute a new tool for research on bivalve reproduction at the molecular level.

A genome-wide survey of genes encoding transcription factors in the Japanese pearl oyster, Pinctada fucata: I. homeobox genes

Homeobox genes are involved in various aspects of the development of multicellular animals, including anterior-posterior patterning of the body plan. We performed a genomic survey of homeobox genes in the Japanese pearl oyster, Pinctada fucata, and annotated 92 homeobox-containing genes and five homeobox-less Pax genes. This species possesses 10 or 11 Hox genes. We annotated another homeobox genes that cover 77 out of the 111 gene families identified in the amphioxus genome. Investigation of these repertoires of homeobox genes will shed new light on the comparatively less well-understood lophotrochozoan development.

A genome-wide survey of genes encoding transcription factors in Japanese pearl oyster Pinctada fucata: II. Tbx, Fox, Ets, HMG, NFκB, bZIP, and C2H2 zinc fingers

To gain a better understanding of molluscan development and its relation to the evolution of their unique body plan, we performed a genomic survey of genes encoding transcription factors, such as Tbx, Fox, Ets, HMG, NFκB, bZIP, and C2H2 zinc finger proteins in the Japanese pearl oyster, Pinctada fucata. We annotated 133 transcription factor genes. Together with the orthologs of known deuterostome genes, we found several orphan genes in each class of transcription factor. Some possessed clear orthologs in other species of lophotrochozoans, while no counterpart genes were found in the deuterostomes or ecdysozoans. These observations suggest that a number of transcription factor genes are unique to lophotrochozoans, and thus additional research frontiers remain to be explored with regard to such transcription factors.

DNA methylation is crucial for the early development in the Oyster C. gigas

In vertebrates, epigenetic modifications influence gene transcription, and an appropriate DNA methylation is critical in development. Indeed, a precise temporal and spatial pattern of early gene expression is mandatory for a normal embryogenesis. However, such a regulation and its underlying mechanisms remain poorly understood in more distant organisms such as Lophotrochozoa. Thus, despite DNA in the oyster genome being methylated, the role of DNA methylation in development is unknown. To clarify this point, oyster genomic DNA was examined during early embryogenesis and found differentially methylated. Reverse transcriptase quantitative polymerase chain reaction indicated stage-specific levels of transcripts encoding DNA-methyltransferase (DNMT) and methyl-binding domain proteins. In addition, as highlighted by electronic microscopy and immunohistochemistry, the DNMT inhibitor 5-aza-cytidine induced alterations in the quantity and the localisation of methylated DNA and severe dose-dependent development alterations and was lethal after zygotic genome reinitiation. Furthermore, methyl-DNA-immunoprecipitation-quantitative polymerase chain reaction revealed that the transcription level of most of the homeobox gene orthologues examined, but not of the other early genes investigated, was inversely correlated with their specific DNA methylation. Altogether, our results demonstrate that DNA methylation influences gene expression in Crassostrea gigas and is critical for oyster development, possibly by specifically controlling the transcription level of homeobox orthologues. These findings provide evidence for the importance of epigenetic regulation of development in Lophotrochozoans and bring new insights into the early life of C. gigas, one of the most important aquaculture resources worldwide.

Doubly uniparental inheritance of mitochondria as a model system for studying germ line formation

BACKGROUND

Doubly Uniparental Inheritance (DUI) of mitochondria occurs when both mothers and fathers are capable of transmitting mitochondria to their offspring, in contrast to the typical Strictly Maternal Inheritance (SMI). DUI was found in some bivalve molluscs, in which two mitochondrial genomes are inherited, one through eggs, the other through sperm. During male embryo development, spermatozoon mitochondria aggregate in proximity of the first cleavage furrow and end up in the primordial germ cells, while they are dispersed in female embryos.

METHODOLOGY/PRINCIPAL FINDINGS

We used MitoTracker, microtubule staining and transmission electron microscopy to examine the mechanisms of this unusual distribution of sperm mitochondria in the DUI species Ruditapes philippinarum. Our results suggest that in male embryos the midbody deriving from the mitotic spindle of the first division concurs in positioning the aggregate of sperm mitochondria. Furthermore, an immunocytochemical analysis showed that the germ line determinant Vasa segregates close to the first cleavage furrow.

CONCLUSIONS/SIGNIFICANCE

In DUI male embryos, spermatozoon mitochondria aggregate in a stable area on the animal-vegetal axis: in organisms with spiral segmentation this zone is not involved in cleavage, so the aggregation is maintained. Moreover, sperm mitochondria reach the same embryonic area in which also germ plasm is transferred. In 2-blastomere embryos, the segregation of sperm mitochondria in the same region with Vasa suggests their contribution in male germ line formation. In DUI male embryos, M-type mitochondria must be recognized by egg factors to be actively transferred in the germ line, where they become dominant replacing the Balbiani body mitochondria. The typical features of germ line assembly point to a common biological mechanism shared by DUI and SMI organisms. Although the molecular dynamics of the segregation of sperm mitochondria in DUI species are unknown, they could be a variation of the mechanism regulating the mitochondrial bottleneck in all metazoans.

Early development and cleavage pattern of the Japanese purple mussel, Septifer virgatus

Despite easy access to bivalves, few studies have examined the development of these animals, at least in part because most bivalve eggs are very small. In addition, annotating cells of the early bivalve embryo is difficult because few landmarks are present. We conducted detailed cell annotations of the Japanese purple mussel, Septifer virgatus, during early embryogenesis because of its relatively large eggs (ca. 130 microm in diameter). Septifer virgatus underwent the unique cell division profile reported for four other bivalve species, suggesting that the cleavage pattern itself is important for bivalve morphogenesis. The shell field invagination was led by 2d (X) lineage cells, supporting the hypothesis that lineage cells differentiate into cells excreting the shell matrix. The large egg size enabled us to trace cell movements in the early gastrulation phase, during which the invagination of the archenteron was initiated by 4d (M) lineage cells. These observations will serve as a basis for future analyses of S. virgatus embryogenesis and will contribute to understanding the evolution of the molluscan body plan, which is achieved by modification of early embryogenesis.

A novel role for dpp in the shaping of bivalve shells revealed in a conserved molluscan developmental program

During the molluscan evolution leading to the bivalves, the single dorsal shell was doubled. To elucidate the molecular developmental basis underlying this prominent morphological transition, we described the cell cleavage and expression patterns of three genes, brachyury, engrailed, and dpp in the Japanese spiny oyster Saccostrea kegaki, and examined the function of dpp in this species. The cleavage pattern of the S. kegaki embryo was nearly the same as the previously described pattern of other bivalve species, suggesting that the pattern itself is highly important for the establishment or the maintenance of the bivalve body plan. The expression pattern of a brachyury homolog in S. kegaki (SkBra) was similar to the pattern in gastopods even at the single cell level despite the deep divergence of gastropods and bivalves. Engrailed and dpp were previously found to be expressed around the shell anlagen in gastropods. Like that of gastropods, an engrailed homolog in S. kegaki (SkEn) was found to be expressed around the shell anlagen. However, the dpp homologin S. kegaki (SkDpp) was expressed only in the cells along the dorsal midline. ZfBMP4 treatment experiments revealed the importance of dpp in establishing the characteristic shape of the bivalve shell anlagen.