Transcriptomic analysis of the clam Meretrix meretrix on different larval stages

Transcriptome Analysis and Identification of Cadmium-Induced Oxidative Stress Response Genes in Different Meretrix meretrix Developmental Stages

Cadmium (Cd) is one of the major pollutants in the aquatic environment, and it can easily accumulate in aquatic animals and result in toxic effects by changing the metabolism of the body, causing a serious impact on the immune system, reproductive system, and the development of offspring. The clam Meretrix meretrix is one of the commercially important species that is cultivated in large-scale aquaculture in China. To elucidate the underlying molecular mechanisms of Cd2+ in the developmental processes, fertilized eggs and larvae of M. meretrix at different developmental stages were exposed to Cd2+ (27.2 mg L-1 in natural seawater) or just natural seawater without Cd2+ (control), and high-throughput transcriptome sequencing and immunohistochemistry techniques were used to analyze the toxic effects of Cd on larvae at different early developmental stages. The results revealed 31,914 genes were differentially expressed in the different stages of M. meretrix development upon treatment with Cd2+. Ten of these genes were differentially expressed in all stages of development examined, but they comprised only six unigenes (CCO, Ndh, HPX, A2M, STF, and pro-C3), all of which were related to the oxidative stress response. Under Cd exposure, the expression levels of CCO and Ndh were significantly upregulated in D-shaped and pediveliger larvae, while pro-C3 expression was significantly upregulated in the fertilized egg, D-shaped larva, and pediveliger. Moreover, HPX, A2M, and STF expression levels in the fertilized egg and pediveliger larvae were also significantly upregulated. In contrast, CCO, Ndh, HPX, A2M, STF, and pro-C3 expression levels in the postlarva were all downregulated under Cd exposure. Besides the genes with changes in expression identified by the transcriptome, the expression of two other oxidative stress-related genes (MT and Nfr2) was also found to change significantly in the different developmental stages of M. meretrix upon Cd exposure, confirming their roles in combating oxidative stress. Overall, the findings of this study indicated that Cd would interfere with cellular respiration, ion transport, and immune response through inducing oxidative stress, and changes in the expression of oxidative stress-related genes might be an important step for M. meretrix to deal with the adverse effects of Cd at different stages of its development.

Transcriptome Profiling Based at Different Time Points after Hatching Deepened Our Understanding on Larval Growth and Development of Amphioctopus fangsiao

As the quality of life improves, there is an increasing demand for nutrition-rich marine organisms like fish, shellfish, and cephalopods. To address this, artificial cultivation of these organisms is being explored along with ongoing research on their growth and development. A case in point is Amphioctopus fangsiao, a highly valued cephalopod known for its tasty meat, nutrient richness, and rapid growth rate. Despite its significance, there is a dearth of studies on the A. fangsiao growth mechanism, particularly of its larvae. In this study, we collected A. fangsiao larvae at 0, 4, 12, and 24 h post-hatching and conducted transcriptome profiling. Our analysis identified 4467, 5099, and 4181 differentially expressed genes (DEGs) at respective intervals, compared to the 0 h sample. We further analyzed the expression trends of these DEGs, noting a predominant trend of continuous upregulation. Functional exploration of this trend entailed GO and KEGG functional enrichment along with protein-protein interaction network analyses. We identified GLDC, DUSP14, DPF2, GNAI1, and ZNF271 as core genes, based on their high upregulation rate, implicated in larval growth and development. Similarly, CLTC, MEF2A, PPP1CB, PPP1R12A, and TJP1, marked by high protein interaction numbers, were identified as hub genes and the gene expression levels identified via RNA-seq analysis were validated through qRT-PCR. By analyzing the functions of key and core genes, we found that the ability of A. fangsiao larvae to metabolize carbohydrates, lipids, and other energy substances during early growth may significantly improve with the growth of the larvae. At the same time, muscle related cells in A. fangsiao larvae may develop rapidly, promoting the growth and development of larvae. Our findings provide preliminary insights into the growth and developmental mechanism of A. fangsiao, setting the stage for more comprehensive understanding and broader research into cephalopod growth and development mechanisms.

The Inhibitory Effects of RNA-Interference-Mediated Guanylate Cyclase Knockdown on Larval Metamorphosis and Early Progeny Growth of Razor Clam

Guanylate cyclase (GC, cGMPase) is a key enzyme in organisms, catalyzing the synthesis of cGMP from GTP, thus making cGMP work. cGMP plays a vital role in the regulation of cell and biological growth as a second messenger in signaling pathways. In this study, we screened and identified cGMPase from the razor clam Sinonovacula constricta, which encoded 1257 amino acids and was widely expressed in different tissues, especially the gill and liver. We also screened one double-stranded RNA (dsRNA), cGMPase, which was used to knockdown cGMPase at three larval metamorphosis development stages: trochophores-veliger larve, veliger larve-umbo larve, and umbo larve-creeping larvae. We showed that interference at these stages significantly inhibited larval metamorphosis and survival rates. cGMPase knockdown resulted in an average metamorphosis rate of 60% and an average mortality rate of 50% when compared with control clams. After 50 days, shell length and body weight were inhibited to 53% and 66%, respectively. Thus, cGMPase appeared to regulate metamorphosis development and growth in S. constricta. By examining the role of the key gene in the metamorphosis development of S. constricta larvae and the growth and development period, we can provide some data reference for studying the growth and development mechanism of shellfish, and the results provided basic information for the breeding of S. constricta.

Comparative transcriptomic analysis revealed dynamic changes of distinct classes of genes during development of the Manila clam (Ruditapes philippinarum)

Background

The Manila clam Ruditapesphilippinarum is one of the most economically important marine shellfish. However, the molecular mechanisms of early development in Manila clams are largely unknown. In this study, we collected samples from 13 stages of early development in Manila clam and compared the mRNA expression pattern between samples by RNA-seq techniques.

Results

We applied RNA-seq technology to 13 embryonic and larval stages of the Manila clam to identify critical genes and pathways involved in their development and biological characteristics. Important genes associated with different morphologies during the early fertilized egg, cell division, cell differentiation, hatching, and metamorphosis stages were identified. We detected the highest number of differentially expressed genes in the comparison of the pediveliger and single pipe juvenile stages, which is a time when biological characteristics greatly change during metamorphosis. Gene Ontology (GO) enrichment analysis showed that expression levels of microtubule protein-related molecules and Rho genes were upregulated and that GO terms such as ribosome, translation, and organelle were enriched in the early development stages of the Manila clam. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the foxo, wnt, and transforming growth factor-beta pathways were significantly enriched during early development. These results provide insights into the molecular mechanisms at work during different periods of early development of Manila clams.

Conclusion

These transcriptomic data provide clues to the molecular mechanisms underlying the development of Manila clam larvae. These results will help to improve Manila clam reproduction and development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08813-0.

Transcriptome Dynamics of an Oyster Larval Response to a Conspecific Cue-Mediated Settlement Induction in the Pacific Oyster Crassostrea gigas

The molecular mechanisms underlying the conspecific cue-mediated larval settlement in Crassostrea gigas is not yet fully understood. In this study, we described and compared the transcriptomes of competent pediveligers (Pedi) and conspecific cue-induced postlarvae (PL). A total of 2383 candidate transcripts were identified: 740 upregulated and 1643 downregulated transcripts, after settlement. Gene Ontology analysis revealed active chitin binding, calcium ion binding, and extracellular region processes in both stages. Results showed that the differential expression trend of six candidate transcripts were consistent between the quantitative real-time PCR and transcriptome data. The differential transcript expression related to shell formation showed closely linked dynamics with a gene regulatory network that may involve the interplay of various hormone receptors, neurotransmitters, and neuropeptide receptors working together in a concerted way in the Pedi and PL stages. Our results highlight the transcriptome dynamics underlying the settlement of oysters on conspecific adult shells and demonstrate the potential use of this cue as an attractant for wild and hatchery-grown oyster larval attachment on artificial substrates. It also suggests the possible involvement of an ecdysone signal pathway that may be linked to a neuroendocrine-biomineralization crosstalk in C. gigas settlement.

Temporally balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring

Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favour of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity, while also inherently sheltering genetic load within oyster populations.

Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks

The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~400 µatm) and high (~1600 µatm) pCO2 conditions, both in domesticated and naturalized "wild" oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early "D-stage" larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~26% fewer loci with changing allele frequencies across developmental stages and <50% as many loci affected by acidified culture conditions, compared to larvae from wild broodstock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.

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.

Single-molecule long-read (SMRT) transcriptome sequencing of Mercenaria mercenaria reveals a powerful anti-apoptotic system critical for air exposure endurance

Mercenaria mercenaria is an economically important clam species and exhibits an outstanding resistance to multiple environmental stressors. However, our understanding of their stress adaptability is limited due to a lack of genomic information, such as transcriptome resources. In this study, single-molecule long-read (SMRT) mRNA sequencing was performed to obtain the full-length gill transcriptome reference sequences of M. mercenaria under air exposure stress. In all, 14.5 G subreads were obtained and assembled into 64,603 unigenes, among which 50,613 were successfully annotated. Additionally, 56,295 SSRs, 1457 transcription factors, and 5924 lncRNAs were identified in M. mercenaria transcriptome. Furthermore, numerous apoptosis-related transcripts were identified according to Swiss-Prot annotation and their numbers were counted. We also found that most apoptosis-related transcripts exhibited typical domains of a certain protein family through conserved domain prediction. Additionally, eight typical sequences related to apoptosis pathway were detected by RT-PCR, with the aim to show the sequential variation of gene expression levels under air exposure. These results implied that the complicated apoptosis system, especially the powerful anti-apoptotic system was critical for M. mercenaria to endure air exposure.

Integrated mRNA and Small RNA Sequencing Reveals Regulatory Expression of Larval Metamorphosis of the Razor Clam

The razor clam, Sinonovacula constricta, is an important economic marine shellfish, and its larval development involves obvious morphological and physiological changes. MicroRNA plays a key role in the physiological changes of the organism through regulating targeted mRNA. This study performed miRNA-mRNA sequencing for eight different developmental stages of S. constricta using Illumina sequencing. A total of 2156 miRNAs were obtained, including 2069 known miRNAs and 87 novel miRNAs. In addition, target genes were predicted for key miRNAs differentially expressed between adjacent development samples by integrating the mRNA transcriptome. Further analysis revealed that the differentially expressed genes were enriched in complement activation, alternative pathways, translation, and negative regulation of monocyte molecular protein-1 production. KEGG pathway annotation showed significant enrichment in the regulation of the ribosome, phagosome, tuberculosis and fluid shear stress, and atherosclerosis. Ten mRNAs and ten miRNAs that are related to larval metamorphosis were identified using real-time PCR. Furthermore, the double luciferase experiment validated the negative regulatory relationship between miR-133 and peroxisome proliferator-activated receptor-γ (PPAR-γ). These results indicated that the target genes regulated by these differentially expressed miRNAs may play an important regulatory role in the metamorphosis development of S. constricta.

De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes

In the present study, we identified salt stress tolerant genes from the marine bacterium Staphylococcus sp. strain P-TSB-70 through transcriptome sequencing. In favour of whole-genome transcriptome profiling of Staphylococcus sp. strain P-TSB-70 (GenBank Accn. No. KP117091) which tolerated upto 20% NaCl stress, the strain was cultured in the laboratory condition with 20% NaCl stress. Transcriptome analyses were performed by SOLiD4.0 sequencing technology from which 10280 and 9612 transcripts for control and treated, respectively, were obtained. The coverage per base (CPB) statistics were analyzed for both the samples. Gene ontology (GO) analysis has been categorized at varied graph levels based on three primary ontology studies viz. cellular components, biological processes, and molecular functions. The KEGG analysis of the assembled transcripts using KAAS showed presumed components of metabolic pathways which perhaps implicated in diverse metabolic pathways responsible for salt tolerance viz. glycolysis/gluconeogenesis, oxidative phosphorylation, glutathione metabolism, etc. further involving in salt tolerance. Overall, 90 salt stress tolerant genes were identified as of 186 salt-related transcripts. Several genes have been found executing normally in the TCA cycle pathway, integral membrane proteins, generation of the osmoprotectants, enzymatic pathway associated with salt tolerance. Recognized genes fit diverse groups of salt stress genes viz. abc transporter, betaine, sodium antiporter, sodium symporter, trehalose, ectoine, and choline, that belong to different families of genes involved in the pathway of salt stress. The control sample of the bacterium showed elevated high proportion of transcript contigs (29%) while upto 20% salt stress treated sample of the bacterium showed a higher percentage of transcript contigs (31.28%). A total of 1,288 and 1,133 transcript contigs were measured entirely as novel transcript contigs in both control and treated samples, respectively. The structure and function of 10 significant salt stress tolerant genes of Staphylococcus sp. have been analyzed in this study. The information acquired in the present study possibly used to recognize and clone the salt stress tolerant genes and support in developing the salt stress-tolerant plant varieties to expand the agricultural productivity in the saline system.

Effects of a Sudden Drop in Salinity on Immune Response Mechanisms of Anadara kagoshimensis

In this experiment, the effects of a sudden drop of salinity on the immune response mechanisms of the ark shell Anadara kagoshimensis were examined by simulating the sudden drop of salinity that occurs in seawater after a rainstorm. Additionally, the differentially expressed genes (DEGs) were identified using transcriptome sequencing. When the salinity dropped from 30‱ (S30) to 14‱ (S14), the phagocytic activity of blood lymphocytes, the O₂^- levels produced from respiratory burst, the content of reactive oxygen species, and the activities of lysozymes and acid phosphatases increased significantly, whereas the total count of blood lymphocytes did not increase. Total count of blood lymphocytes in 22‱ salinity (S22) was significantly higher than that in any other group. The raw data obtained from sequencing were processed with Trimmomatic (Version 0.36). The expression levels of unigenes were calculated using transcripts per million (TPM) based on the effects of sequencing depth, gene length, and sample on reads. Differential expression analysis was performed using DESeq (Version 1.12.4). Transcriptome sequencing revealed 269 (101 up-regulated, 168 down-regulated), 326 (246 up-regulated, 80 down-regulated), and 185 (132 up-regulated, 53 down-regulated) significant DEGs from comparison of the S14 vs. S22, S22 vs. S30, and S14 vs. S30 groups, respectively. Gene Ontology enrichment analysis of the DEGs in these salinity comparison groups revealed that the cellular amino acid metabolic process, the regulation of protein processing, the regulation of response to stress, and other terms were significantly enriched. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that nucleotide-binding, oligomerization domain (NOD)-like receptor signaling pathway (ko04621), apoptosis-multiple species (ko04215), Toll and Imd signaling pathway (ko04624), NF-κB signaling pathway (ko04064), apoptosis (ko04210), and focal adhesion (ko04510) were significantly enriched in all salinity comparison groups. qRT-PCR verification of 12 DEGs in the above six pathways was conducted, and the results were consistent with the transcriptome sequencing results in terms of up-regulation and down-regulation, which illustrates that the transcriptome sequencing data are credible. These results were used to preliminarily explore the effects of a sudden drop of salinity on blood physiological and biochemical indexes and immunoregulatory mechanisms of A. kagoshimensis. They also provide a theoretical basis for the selection of bottom areas optimal for release and proliferation of A. kagoshimensis required to restore the declining populations of this species.

Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

Ruditapes philippinarum is an economically important bivalve with remarkable diversity in its shell coloration patterns. In this study, we sequenced the whole genome of the Manila clam and investigated the molecular basis of its adaptation to hypoxia, acidification, and parasite stress with transcriptome sequencing and an RNA sequence analysis of different tissues and developmental stages to clarify these major issues. A number of immune-related gene families are expanded in the R. philippinarum genome, such as TEP, C3, C1qDC, Hsp70, SABL, and lysozyme, which are potentially important for its stress resistance and adaptation to a coastal benthic life. The transcriptome analyses demonstrated the dynamic and orchestrated specific expression of numerous innate immune-related genes in response to experimental challenge with pathogens. These findings suggest that the expansion of immune- and stress-related genes may play vital roles in resistance to adverse environments and has a profound effect on the clam's adaptation to benthic life.

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We present a new genome assembly of the Manila clam Ruditapes philippinarum

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Analysis of gene family expansions and transcriptome characterization were conducted

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Tyr and mitf genes were potentially involved in shell color patterns of Manila clam

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Expansion of GPCRs and immune-related genes were found in R. philippinarum

FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation

Along with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/. This new web-based annotator will shed light on field studies involving organisms without a reference genome.

Transcriptomic analysis of oyster Crassostrea gigas larvae illustrates the response patterns regulated by catecholaminergic system upon acute heat and bacterial stress

Bacterial infection and heat stress, as two major environmental threats of marine molluscs, could affect larval development and dramatically promote mortality of oysters. In the present study, next-generation sequencing, together with determinations of mRNA expression and measurements of enzyme activities, were employed to understand the response patterns of oyster larvae under acute heat and bacterial stress. After RNA-seq, a total of 9472 differentially expressed genes including 4895 significantly up-regulated ones and 4577 significantly down-regulated ones were obtained from 12 transcriptome libraries. GO overrepresentation analysis of the up-regulated genes revealed that the neuroendocrine immunomodulation pathway was activated after acute heat and bacterial stimulation, in which the catecholaminergic regulation played an important role. GO overrepresentation analysis of the down-regulated genes suggested that the immune capacity of Crassostrea gigas larvae was suppressed under stress, which was further validated since superoxide dismutase (SOD) and phenoloxidase (PO) activities in the total protein extract of larvae decreased dramatically after stress. Moreover, the shell formation of trochophore was inhibited and severe mortality was caused after acute heat and bacterial stress. These results collectively indicated that acute heat and bacterial stress could significantly inhibit larval development and suppress immune response of oyster C. gigas larvae. And the neuroendocrine immunomodulation, especially the catecholaminergic regulation, played an indispensable role in the stress response of molluscan larvae.

Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster, Pinctada fucata, Based on Transcriptome Analysis

P. fucata experiences a series of transformations in appearance, from swimming larvae to sessile juveniles, during which significant changes in gene expression likely occur. Thus, P. fucata could be an ideal model in which to study the molecular mechanisms of larval metamorphosis during development in invertebrates. To study the molecular driving force behind metamorphic development in larvae of P. fucata, transcriptomes of five larval stages (trochophore, D-shape, umbonal, eyespots, and spats) were sequenced using an Illumina HiSeq™ 2000 system and assembled and characterized with the transcripts of six tissues. As a result, a total of 174,126 unique transcripts were assembled and 60,999 were annotated. The number of unigenes varied among the five larval stages. Expression profiles were distinctly different between trochophore, D-shape, umbonal, eyespots, and spats larvae. As a result, 29 expression trends were sorted, of which eight were significant. Among others, 80 development-related, differentially expressed unigenes (DEGs) were identified, of which the majority were homeobox-containing genes. Most DEGs occurred among trochophore, D-shaped, and UES (umbonal, eyespots, and spats) larvae as verified by qPCR. Principal component analysis (PCA) also revealed significant differences in expression among trochophore, D-shaped, and UES larvae with ten transcripts identified but no matching annotations.

Developmental piRNA profiles of the invasive vector mosquito Aedes albopictus

Background

In eukaryotic organisms, Piwi-interacting RNAs (piRNAs) control the activities of mobile genetic elements and ensure genome maintenance. Recent evidence indicates that piRNAs are involved in multiple biological pathways, including transcriptional regulation of protein-coding genes, sex determination and even interactions between host and pathogens. Aedes albopictus is a major invasive species that transmits a number of viral diseases in humans. Ae. albopictus has the largest genome and the highest abundance of repetitive sequences when compared with members that belong to Culicidae with a published genome. Analysis of piRNA profiles will provide a developmental and evolutionary perspective on piRNAs in Ae. albopictus.

Methods

piRNAs were identified and characterized during the development of Ae. albopictus, and piRNA expression patterns in adult males and females as well as sugar-fed females and blood-fed females were compared.

Results

Our results reveal that, despite the large genome size of Ae. albopictus, the piRNA pool of Ae. albopictus (1.2 × 10⁷) is smaller than those of Aedes aegypti (1.7 × 10⁷) and Drosophila melanogaster (1.6 × 10⁷). In Ae. albopictus, piRNAs displayed the highest abundance at the embryo stage and the lowest abundance at the pupal stage. Approximately 50 % of the piRNAs mapped to intergenic regions with no known functions. Approximately 30 % of the piRNAs mapped to repetitive elements, and 77.69 % of these repeat-derived piRNAs mapped to Class I TEs; 45.42 % of the observed piRNA reads originated from piRNA clusters, and most of the top 10 highest expressed piRNA clusters and 100 highest expressed piRNAs from each stage displayed biased expression patterns across the developmental stages. All anti-sense-derived piRNAs displayed a preference for uridine at the 5′ end; however, the sense-derived piRNAs showed adenine bias at the tenth nucleotide position and a typical ping-pong signature, suggesting that the biogenesis of piRNAs was conserved throughout development. Our results also show that 962 piRNAs displayed sex-biased expression, and 522 piRNAs showed higher expression in the blood-fed females than in the sugar-fed females.

Conclusions

Our results suggest that piRNAs, aside from silencing transposable elements in Ae. albopictus, may have a role in other biological pathways.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1815-8) contains supplementary material, which is available to authorized users.

Combined exposure to pyrene and fluoranthene and their molecular effects on the Sydney rock oyster, Saccostrea glomerata

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitously detected in the water column, associated with particulate matter or in the tissue of marine organisms such as molluscs. PAH exposure and their resultant bioaccumulation in molluscs can cause a range of serious physiological effects in the affected animals. To examine the molecular response of these xenobiotics in bivalves, Sydney rock oysters (Saccostrea glomerata) were exposed to pyrene and fluoranthene for seven days. Chemical analysis of the soft-tissue of PAH stressed S. glomerata confirmed that pyrene and fluoranthene could be bioaccumulated by these oysters. RNA-Seq analysis of PAH-exposed S. glomerata showed a total of 765 transcripts differentially expressed between control and PAH-stressed oysters. Closer examination of the transcripts revealed a range genes encoding enzymes involved in PAH detoxification (e.g. cytochrome P450), innate immune responses (e.g. pathogen recognition, phagocytosis) and protein synthesis. Overall, pyrene and fluoranthene exposure appears to have resulted in a suppression of pathogen recognition and some protein synthesis processes, whereas transcripts of genes encoding proteins involved in clearance of cell debris and some transcripts of genes involved in PAH detoxification were induced in response to the stressors. Pyrene and fluoranthene exposure thus invoked a complex molecular response in S. glomerata, with results suggesting that oysters focus on removing the stressors from their system and dealing with the downstream effects of PAH exposure, potentially at the exclusion of other, less immediate concerns (e.g. protection from infection).

Seasonal proliferation rates and the capacity to express genes involved in cell cycling and maintenance in response to seasonal and experimental food shortage in Laternula elliptica from King George Island

Melting of coastal glaciers at the West Antarctic Peninsula (WAP) causes shorter winter sea ice duration, intensified ice scouring, sediment erosion and surface freshening in summer, which alters coastal productivity and feeding conditions for the benthos. The soft shell clam Laternula elliptica is a fast growing and abundant filter feeder in coastal Antarctica and a key element for bentho-pelagic carbon recycling. Our aim was to assess the cellular growth and maintenance capacity of small and large clams during natural winter food shortage (seasonal sampling) and in response to experimental starvation exposure. We measured tissue specific proliferation rates, the expression of cell cycling genes, and the iron binding protein Le-ferritin in freshly collected specimens in spring (Nov 2008) and at the end of summer (March 2009). For the experimental approach, we focused on 14 cell cycling and metabolic genes using the same animal size groups. Mantle tissue of young bivalves was the only tissue showing accelerated proliferation in summer (1.7% of cells dividing per day in March) compared to 0.4% dividing cells in animals collected in November. In mantle, siphon and adductor muscle proliferation rates were higher in younger compared to older individuals. At transcript level, Le-cyclin D was upregulated in digestive gland of older animals collected in spring (Nov) compared to March indicating initiation of cell proliferation. Likewise, during experimental starvation Le-cyclin D expression increased in large clam digestive gland, whereas Le-cyclin D and the autophagic factor beclin1 decreased in digestive gland of smaller starved clams. The paper corroborates earlier findings of size and age dependent differences in the metabolic response and gene expression patterns in L. elliptica under energetic deprivation. Age structure of shallow water populations can potentially change due to differences in cellular response between young and old animals as environmental stress levels increase.

Transcriptome Analysis of the Sydney Rock Oyster, Saccostrea glomerata: Insights into Molluscan Immunity

BACKGROUND

Oysters have important ecological functions in their natural environment, acting as global carbon sinks and improving water quality by removing excess nutrients from the water column. During their life-time oysters are exposed to a variety of pathogens that can cause severe mortality in a range of oyster species. Environmental stressors encountered in their habitat can increase the susceptibility of oysters to these pathogens and in general have been shown to impact on oyster immunity, making immune parameters expressed in these marine animals an important research topic.

RESULTS

Paired-end Illumina high throughput sequencing of six S. glomerata tissues exposed to different environmental stressors resulted in a total of 484,121,702 paired-end reads. When reads and assembled transcripts were compared to the C. gigas genome, an overall low level of similarity at the nucleotide level, but a relatively high similarity at the protein level was observed. Examination of the tissue expression pattern showed that some transcripts coding for cathepsins, heat shock proteins and antioxidant proteins were exclusively expressed in the haemolymph of S. glomerata, suggesting a role in innate immunity. Furthermore, analysis of the S. glomerata ORFs showed a wide range of genes potentially involved in innate immunity, from pattern recognition receptors, components of the Toll-like signalling and apoptosis pathways to a complex antioxidant defence mechanism.

CONCLUSIONS

This is the first large scale RNA-Seq study carried out in S. glomerata, showing the complex network of innate immune components that exist in this species. The results confirmed that many of the innate immune system components observed in mammals are also conserved in oysters; however, some, such as the TLR adaptors MAL, TRIF and TRAM are either missing or have been modified significantly. The components identified in this study could help explain the oysters' natural resilience against pathogenic microorganisms encountered in their natural environment.

Developmental Transcriptome Analysis and Identification of Genes Involved in Larval Metamorphosis of the Razor Clam, Sinonovacula constricta

The razor clam Sinonovacula constricta is an important commercial species. The deficiency of developmental transcriptomic data is becoming the bottleneck of further researches on the mechanisms underlying settlement and metamorphosis in early development. In this study, de novo transcriptome sequencing was performed for S. constricta at different early developmental stages by using Illumina HiSeq 2000 paired-end (PE) sequencing technology. A total of 112,209,077 PE clean reads were generated. De novo assembly generated 249,795 contigs with an average length of 585 bp. Gene annotation resulted in the identification of 22,870 unigene hits against the NCBI database. Eight unique sequences related to metamorphosis were identified and analyzed using real-time PCR. The razor clam reference transcriptome would provide useful information on early developmental and metamorphosis mechanisms and could be used in the genetic breeding of shellfish.

De novo transcriptome sequencing and analysis of Rapana venosa from six different developmental stages using Hi-seq 2500

The carnivorous whelk Rapana venosa is regarded as a biological invader with strong ecological fitness in the United States, Argentina, France and other countries. R. venosa may seriously damage bivalve resources. Nonetheless, in China, R. venosa is an important commercial species. Larval development, especially metamorphosis, influences the natural population and industrial breeding. However, there are few studies on the early development of R. venosa, and our understanding is further limited by a lack of genomic information. In this study, de novo sequencing was performed to obtain a comprehensive transcriptome profile during early development. A Hi-seq 2500 sequencing run produced 148,737,902 raw reads that were assembled into 1,137,556 unigenes (average length of 619 nucleotides, of which 49,673 could be annotated). The unigenes were assigned to biological processes and functions after annotation in Gene Ontology, eukaryotic Ortholog Groups and Kyoto Encyclopedia of Genes and Genomes. We also identified 93,196 simple sequence repeats among the unigenes. Six unique sequences associated with neuroendocrine function were analyzed by quantitative real-time PCR. Our data represent the first comprehensive transcriptomic resource for R. venosa. Functional annotation of the unigenes involved in various biological processes could stimulate research on the mechanisms of early development in this species. Understanding the mechanism of early development and metamorphosis would benefit antifouling research and aquaculture of R. venosa.

De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile

Paphia textile is an important, aquaculture bivalve clam species distributed mainly in China, Philippines, and Malaysia. Recent studies of P. textile have focused mainly on artificial breeding and nutrition analysis, and the transcriptome and genome of P. textile have rarely been reported. In this work, the transcriptome of P. textile foot tissue was sequenced on an Illumina HiSeq™ 2000 platform. A total of 20,219,795 reads were generated, resulting in 4.08 Gb of raw data. The raw reads were cleaned and assembled into 54,852 unigenes with an N50 length of 829 bp. Of these unigenes, 38.92% were successfully annotated based on their matches to sequences in seven public databases. Among the annotated unigenes, 14,571 were assigned Gene Ontology terms, 5448 were classified to Clusters of Orthologous Groups categories, and 6738 were mapped to 228 pathways in the Kyoto Encyclopedia of Genes and Genomes database. For functional marker development, 5605 candidate simple sequence repeats were identified in the transcriptome and 80 primer pairs were selected randomly and amplified in a wild population of P. textile. A total of 36 loci that exhibited obvious repeat length polymorphisms were detected. The transcriptomic data and microsatellite markers will provide valuable resources for future functional gene analyses, genetic map construction, and quantitative trait loci mapping in P. textile.

De novo transcriptome sequencing to identify the sex-determination genes in Hyriopsis schlegelii

This study presents the first analysis of expressed transcripts in the spermary and ovary of Hyriopsis schlegelii (H. schlegelii). A total of 132,055 unigenes were obtained and 31,781 of these genes were annotated. In addition, 19,511 upregulated and 25,911 downregulated unigenes were identified in the spermary. Ten sex-determination genes were selected and further analyzed by real-time PCR. In addition, mammalian genes reported to govern sex-determination pathways, including Sry, Dmrt1, Dmrt2, Sox9, GATA4, and WT1 in males and Wnt4, Rspo1, Foxl2, and β-catenin in females, were also identified in H. schlegelii. These results suggest that H. schlegelii and mammals use similar gene regulatory mechanisms to control sex determination. Moreover, genes associated with dosage compensation mechanisms, such as Msl1, Msl2, and Msl3, and hermaphrodite phenotypes, such as Tra-1, Tra-2α, Tra-2β, Fem1A, Fem1B, and Fem1C, were also identified in H. schlegelii. The identification of these genes indicates that diverse regulatory mechanisms regulate sexual polymorphism in H. schlegelii.

Characterization of a long-chain fatty acid-CoA ligase 1 gene and association between its SNPs and growth traits in the clam Meretrix meretrix

Long-chain fatty acid-CoA ligases (ACSLs) play crucial roles in fatty acid (FA) metabolism. They convert free long-chain FA into acyl-CoAs, which are key intermediates in both anabolic and catabolic pathways. A long-chain fatty acid-CoA ligase gene was cloned in the clam Meretrix meretrix (MmeACSL1), with a full-length cDNA of 1865 bp encoding 475 amino acids. Its expression was only detected in hepatopancreas by semi-quantitative reverse transcription PCR. Expression level of MmeACSL1 exhibited a significant increase in a starvation experiment (P<0.05). This indicates that MmeACSL1 plays an important role in normal metabolism of M. meretrix and may be involved in energy supply and storage. Two exon SNPs and six intron SNPs were developed in this gene by direct sequencing. A marker-trait association analysis showed that five of these SNPs were significantly associated with growth traits (P<0.05). Also, haplotypes comprised of the five SNPs were revealed to be significantly growth-related (P<0.05), which further corroborates the relationship of this gene to growth traits of M. meretrix.

Identification of a Serum amyloid A gene and the association of SNPs with Vibrio-resistance and growth traits in the clam Meretrix meretrix

Serum amyloid A (SAA), an acute response protein as well as an apolipoprotein, is considered to play crucial roles in both innate immunity and lipid metabolism. In this study, a SAA gene (MmSAA) was identified in the clam Meretrix meretrix. The full length DNA of MmSAA was 1407bp, consisting of three exons and two introns. The distribution of MmSAA in clam tissues was examined with the highest expression in hepatopancreas. In response to the Vibrio parahaemolyticus challenge, MmSAA mRNA showed significantly higher expression at 24 h post-challenge in experimental clams (P < 0.05). Forty-eight single nucleotide polymorphisms (SNPs) in the DNA partial sequence of MmSAA were discovered and examined for their association with Vibrio-resistance and growth traits, respectively. The single SNP association analysis indicated that five single SNPs (g.42, g.72, g.82, g.147 and g.165) were significantly associated with Vibrio-resistance (P < 0.05). Haplotype analysis produced additional support for association with the Chi-square values 6.393 (P = 0.012). Among the five selected SNPs, the effect of a missense mutation (g.82, A → G) was detected by site-directed mutagenesis with fusion expression of protein assay, and the result showed that the recombinant plasmids containing wild-type pET30a-MmSAA had more inhibition effect than the mutant ones on the growth rate of the host bacteria. In addition, four growth traits of the clams in 09G3SPSB population were recorded and the SNP g.176 was found to be significantly associated with the growth traits with the Global score value 0.790 (P = 0.015). Our findings suggested that common genetic variation in MmSAA might contribute to the risk of susceptibility to Vibrio infection and might be associated with the growth traits in the clams M. meretrix, and more works are still needed to validate these SNPs as potential markers for actual selective breeding.

Development of Vibrio spp. infection resistance related SNP markers using multiplex SNaPshot genotyping method in the clam Meretrix meretrix

The clam Meretrix meretrix is a commercially important mollusc species in the coastal areas of South and Southeast Asia. In the present study, large-scale SNPs were genotyped by the Multiplex SNaPshot genotyping method among the stocks of M. meretrix with different Vibrio spp. infection resistance profile. Firstly, the AUTOSNP software was applied to mine SNPs from M. meretrix transcriptome, and 323 SNP loci (including 120 indels) located on 64 contigs were selected based on Uniprot-GO associations. Then, 38 polymorphic SNP loci located on 15 contigs were genotyped successfully in the clam stocks with different resistance to Vibrio parahaemolyticus infection (11-R and 11-S groups). Pearson's Chi-square test was applied to compare the allele and genotype frequency distributions of the SNPs between the different stocks, and seven SNP markers located on three contigs were found to be associated with V. parahaemolyticus infection resistance trait. Haplotype-association analysis showed that six haplotypes had significantly different frequency distributions in 11-S and 11-R (P < 0.05). With selective genotyping between 09-R and 09-C populations, which had different resistance to Vibrio harveyi infection, four out of the seven selected SNPs had significantly different distributions (P < 0.05) and therefore they were considered to be associated with Vibrio spp. infection resistance. Sequence alignments and annotations indicated that the contigs containing the associated SNPs had high similarity to the immune related genes. All these results would be useful for the future marker-assisted selection of M. meretrix strains with high Vibrio spp. infection resistance.

Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling

Heterosis is a concern to all breeders, but the mechanism of heterosis remains unknown. In F1 organisms, genetic material is inherited from the two parents and theoretically, heterosis might be caused by differences in gene expression or modification. Differential gene expression was analyzed in hybrids and parents in Bombyx mori. The results showed that there were significant changes in gene expression in the fat body involving biological regulation, cellular and metabolic processes. Consistent trends in expression patterns covering different hybrid combinations were seen in 74 genes. Moreover, these differential gene expression patterns included overdominance, dominance, and additive effects. By correlating these patterns with economic traits, a potential relationship was found. Differential gene expression was seen in different cross combinations and in different sexes. In addition, a regulatory mechanism involving metabolism and ErbB signaling pathways was also found, suggesting that such a network might also be related to heterosis in Bombyx mori. Together, our data provide a comprehensive overview and useful resource for transcriptional analysis of heterosis of Bombyx mori.

The role of Cu/Zn-SOD and Mn-SOD in the immune response to oxidative stress and pathogen challenge in the clam Meretrix meretrix

The copper/zinc superoxide dismutase (Cu/Zn-SOD) and manganese superoxide dismutase (Mn-SOD) could effectively eliminate reactive oxygen species (ROS) and maintain the redox balance of immune system. In the present study, the potential synergy of Cu/Zn-SOD and Mn-SOD in immune system was investigated in the clam Meretrix meretrix. The expression of Cu/Zn-SOD mainly distributed in hepatopancreas and that of Mn-SOD was higher in gill of M. meretrix, and their mRNA and protein activity paralleled with each other. In response to H2O2 challenge, Cu/Zn-SOD mRNA showed significantly higher level at 24 h post-challenge and Mn-SOD mRNA was significantly higher at 12 and 24 h post-challenge in the experimental clams than in the control clams (P<0.05). After injection with Vibrio-parahaemolyticus-related bacterium (MM21), the Cu/Zn-SOD mRNA was significantly up-regulated at 24 h and 48 h post-injection and Mn-SOD mRNA was significantly higher at 24 h post-injection in MM21-injected clams than in control clams (P<0.05), suggesting that both of them might involve in the immune defense to Vibrio challenge. The mRNA expression of Cu/Zn-SOD and Mn-SOD was examined in a Vibrio-resistant population and a control population after MM21 immersion challenge. The increased transcription of Cu/Zn-SOD and Mn-SOD in the resistant population suggested both of them could benefit the immune system to defend against pathogen infection. As expression of Mn-SOD mRNA depended on stimuli and was more easily inducible, its response to H2O2 and Vibrio challenge was earlier than Cu/Zn-SOD. Our study suggested the redox balance might play an important role in M. meretrix to resist pathogen infection.

Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions

Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.

The involvement of cysteine-rich intestinal protein in early development and innate immunity of Asiatic hard clam, Meretrix meretrix

Cysteine-rich intestinal protein (CRIP), a Zn(2+)-binding protein, contains a single copy of the highly conserved double-zinc-finger structure known as the LIM (lin-11-isl-1-mec-3) motif. In this paper, a cDNA encoding MmCRIP was isolated from the Asiatic hard clam Meretrix meretrix. The full-length cDNA of MmCRIP consists of a 237-bp open reading frame that encodes a polypeptide of 78 amino acids with a predicted molecular weight (MW) of 8635.8 Da and theoretical isoelectric point (pI) of 9.01. Bioinformatics analysis showed that it belonged to a new member of the CRIP subfamily. Relationship analysis revealed that MmCRIP has high-levels of sequence similarity to many CRIPs reported in other animals, particularly in invertebrates. Real-time PCR analysis showed that the highest level of MmCRIP expression was in hemocyte tissue and at pediveligers stage. To investigate immune function, mature clams were challenged with Aeromonas hydrophila. During A. hydrophila infection, up-regulation of MmCRIP transcript in clam's hemocyte, gill and hepatopancreas was detected. DsRNAi (double-strand RNA interference) approach was employed to study the function of MmCRIP and the data showed that inactivation of the MmCRIP gene blocked larvae development and caused mass mortalities. The probable roles of MmCRIP in clam early development and innate immunity are presented for the first time.

Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, annotation and marker discovery

The ridgetail white prawn Exopalaemon carinicauda is one of major economic mariculture species in eastern China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its good traits. In the present study, 454 pyrosequencing was undertaken to investigate the transcriptome profiles of E. carinicauda. A collection of 1,028,710 sequence reads (459.59 Mb) obtained from cDNA prepared from eyestalk and hemocytes was assembled into 162,056 expressed sequence tags (ESTs). Of these, 29.88 % of 48,428 contigs and 70.12 % of 113,628 singlets possessed high similarities to sequences in the GenBank non-redundant database, with most significant (E value <1e(-10)) unigenes matches occurring with crustacean and insect sequences. KEGG analysis of unigenes identified putative members of biological pathways related to growth and immunity. In addition, we obtained a total of putative 125,112 SNPs and 13,467 microsatellites. These results will contribute to the understanding of the genome makeup and provide useful information for future functional genomic research in E. carinicauda.

De novo transcriptomic profile in the gonadal tissues of the intertidal whelk Reishia clavigera

The intertidal whelk Reishia clavigera (formerly named as Thais clavigera) is one of the most sensitive species to organotin-associated imposex. However, the limited information on mRNA transcriptome of the species has restricted the molecular investigation on such endocrine disruption. By means of Illumina sequencing, we obtained a global de novo transcriptome from the gonadal tissues of both male and female R. clavigera, with 197,324 assembled transcripts and 151,684 condensed non-redundant transcripts. Blast hit results from the NCBI's non-redundant molluscan database showed that 28,948 transcripts were successfully annotated with significant matches at an e-value of ⩽1e(-6). Among them, 1108 transcripts were assigned a well-defined gene ontology term. As the first transcriptomic study on the gonadal tissues of R. clavigera, this study has enhanced the information of mRNA transcriptome on this species and will thus facilitate mechanistic studies of chemical contaminants (e.g., organotins) on this common biomonitor species.

Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica

BACKGROUND

The eastern oyster, Crassostrea virginica, is a euryhaline species that can thrive across a wide range of salinities (5-35). As with all estuarine species, individual oysters must be able to regulate their osmotic balance in response to constant temporal variation in salinity. At the population level, recurrent viability selection may be an additional mechanism shaping adaptive osmoregulatory phenotypes at the margins of oyster salinity tolerance. To identify candidate genes for osmoregulation, we sequenced, assembled, and annotated the transcriptome of wild juvenile eastern oysters from 'high' and 'low' salinity regimes. Annotations and candidates were mostly based on the Pacific oyster (Crassostrea gigas) genome sequence so osmoregulatory relevance in C. virginica was explored by testing functional enrichment of genes showing spatially discrete patterns of expression and by quantifying coding sequence divergence.

RESULTS

The assembly of sequence reads and permissive clustering of potentially oversplit alleles resulted in 98,729 reftigs (contigs and singletons). Of these, 50,736 were annotated with 9,307 belonging to a set of candidate osmoregulatory genes identified from the C. gigas genome. A total of 218,777 SNPs (0.0185 SNPs/bp) were identified in annotated reftigs of C. virginica. Amino acid divergence between translations of C. virginica annotated reftigs and C. gigas coding sequence averaged 23.2 % with an average dN/dS ratio of 0.074, suggesting purifying selection on protein sequences. The high and low salinity source oysters each expressed a subset of genes unique to that group, and the functions for these annotated genes were consistent with known molecular mechanisms for osmotic regulation in molluscs.

CONCLUSIONS

Most of the osmoregulatory gene candidates experimentally identified in C. gigas are present in this C. virginica transcriptome. In general these congeners show coding sequence divergence too high to make the C. gigas genome a useful reference for C. virginica bioinformatics. However, strong purifying selection is characteristic of the osmoregulatory candidates so functional annotations are likely to correspond. An initial examination of C. virginica presence/absence expression patterns across the salinity gradient in a single estuary suggests that many of these candidates have expression patterns that co-vary with salinity, consistent with osmoregulatory function in C. virginica.

Deep sequencing of the mantle transcriptome of the great scallop Pecten maximus

RNA-Seq transcriptome data were generated from mantle tissue of the great scallop, Pecten maximus. The consensus data were produced from a time course series of animals subjected to a 56-day thermal challenge at 3 different temperatures. A total of 26,064 contigs were assembled de novo, providing a useful resource for both the aquaculture community and researchers with an interest in mollusc shell production.

Analysis of the skin transcriptome in two oujiang color varieties of common carp

Background

Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding.

Methodology/Principal Findings

In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW.

Conclusions

The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.

Transcriptome analysis reveals a rich gene set related to innate immunity in the Eastern oyster (Crassostrea virginica)

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

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.

Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds

The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.

Identification of reference genes for qRT-PCR analysis in Yesso scallop Patinopecten yessoensis

BACKGROUND

Bivalves comprise around 30,000 extant species and have received much attention for their importance in ecosystems, aquaculture and evolutionary studies. Despite the increasing application of real-time quantitative reverse transcription PCR (qRT-PCR) in gene expression studies on bivalve species, little research has been conducted on reference gene selection which is critical for reliable and accurate qRT-PCR analysis. For scallops, systematic evaluation of reference genes that can be used among tissues or embryo/larva stages is lacking, and β-actin (ACT) is most frequently used as qRT-PCR reference gene without validation.

RESULTS

In this study, 12 commonly used candidate reference genes were selected from the transcriptome data of Yesso scallop (Patinopectenyessoensis) for suitable qRT-PCR reference genes identification. The expression of these genes in 36 tissue samples and 15 embryo/larva samples under normal physiological conditions was examined by qRT-PCR, and their expression stabilities were evaluated using three statistic algorithms, geNorm, NormFinder, and comparative ∆Ct method. Similar results were obtained by the three approaches for the most and the least stably expressed genes. Final comprehensive ranking for the 12 genes combing the results from the three programs showed that, for different tissues, DEAD-box RNA helicase (HELI), ubiquitin (UBQ), and 60S ribosomal protein L16 (RPL16) were the optimal reference genes combination, while for different embryo/larva stages, gene set containing Cytochrome B (CB), Cytochrome C (CC), Histone H3.3 (His3.3), and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were recommended for qRT-PCR normalization. ACT was among the least stable genes for both adult tissues and embryos/larvae.

CONCLUSIONS

This work constitutes the first systematic analysis on reference genes selection for qRT-PCR normalization in scallop under normal conditions. The suitable reference genes we recommended will be useful for the identification of genes related to biological processes in Yesso scallop, and also in the reference gene selection for other scallop or bivalve species.

Expression patterns of an i-type lysozyme in the clam Meretrix meretrix along with larval development

An i-type lysozyme (MmeLys) has been proved to function in immunity of the clam Meretrix meretrix in our previous studies. In this study, the expression patterns of MmeLys mRNA and protein at four chief developmental stages of M. meretrix were analyzed, which was able to provide information about how ontogeny of immunity and, in particular, antibacterial ability occured in the bivalve. The results of real-time PCR and western blot showed that MmeLys expressions were activated in D-veligers and dramatically increased to the highest level in pediveligers. It is proposed that the expression changes at these two stages might be due to the visceral organs changes, which were related to the archenteron formation in D-veligers and the organ-restructuring in pediveligers during metamorphosis. In addition, new methods of whole mount in situ hybridization and whole mount immunofluorescence were applied to identify the MmeLys expression tissues, and these tissues (i.e. hepatopancreas, gill, mantle, mouth, velum and foot) may be involved in the immune function during development of clams. Our study is valuable to a certain extent for exploring the origin of immune functions in clams and provides new methodology for future studies on the immune ontogeny of bivalves.

Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix

The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P < 0.01), which suggested that the clams carrying these two alleles have stronger resistance against vibrio. Clam individuals of 11-S were divided into three subgroups based on the survival time post-challenge, and the multi-dimensional scaling (MDS) analysis showed that clusters generated by genetic similarity revealed by the three SSR markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding.

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.

Mollusk shell structures and their formation mechanism

In nature, mollusk shells have a role in protecting the soft body of the mollusk from predators and from the external environment, and the shells consist mainly of calcium carbonate and small amounts of organic matrices. Organic matrices in mollusk shells are thought to play key roles in shell formation. However, enough information has not been accumulated so far. High toughness and stiffness have been focused on as being adaptable to the development of organic–inorganic hybrid materials. Because mollusks can produce elaborate microstructures containing organic matrices under ambient conditions, the investigation of shell formation is expected to lead to the development of new inorganic–organic hybrid materials for various applications. In this review paper, we summarize the structures of mollusk shells and their process of formation, together with the analysis of various organic matrices related to shell calcification.

Gigabase-scale transcriptome analysis on four species of pearl oysters

Pearl oysters have been found to secrete nacre and form pearls with good quality and significant commercial interest. However, the transcriptomic and genomic resources for pearl oysters are still limited. To improve this situation, transcriptome sequencing was conducted from four species of pearl oysters with Illumina HiSeq™ 2000. There were four gigabase-scale transcriptomes for four species of pearl oysters, ∼26.3 million reads with ∼2.37 gigabase base pairs (Gbp) in Pinctada fucata, ∼26.5 million reads with ∼2.39 Gbp in Pinctada margaritifera, ∼27.0 million reads with ∼2.43 Gbp in Pinctada maxima, and ∼25.9 million reads with ∼2.33 Gbp in Pteria penguin, respectively. After sequence assembly and blastx alignment, the numbers of annotated unigenes ≥200 bp were 33,882 in P. fucata, 30,666 in P. margaritifera, 26,420 in P. maxima, and 29,928 in P. penguin. Based on these annotated unigenes among four species of pearl oysters, CDSs were extracted and predicted and furthermore, analyses of GO and KEGG assignments were performed. In addition, 60 putative genes of growth factors and their receptors from four species of pearl oysters were predicted. This study established an excellent resource for gene discovery and expression in pearl oysters, but also offered a significant platform for functional genomics and comparative genomic studies for mollusks.

Transcriptome sequencing of Zhikong scallop (Chlamys farreri) and comparative transcriptomic analysis with Yesso scallop (Patinopecten yessoensis)

Background

Bivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri), and conducted the first transcriptome comparison for scallops.

Results

In a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO) and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis) revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs) and 350 simple sequence repeats (SSRs) were also detected.

Conclusion

Our study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.