Characterization of the mantle transcriptome of yesso scallop (Patinopecten yessoensis): identification of genes potentially involved in biomineralization and pigmentation

A functional role for myostatin in muscle hyperplasia and hypertrophy revealed by comparative transcriptomics in Yesso scallop Patinopecten yessoensis

Elucidating the molecular regulatory mechanisms underlying muscle growth and development is of profound significance in aquaculture. Yesso scallop is a cold-water bivalve of considerable economic importance, having its primary edible component of adductor muscle. In this study, comparative transcriptomics and histological analysis at different sampling times after Myostatin (MSTN) interference were performed to identify the potential candidate genes potentially involved in muscle growth and development. The comparative transcriptomics revealed that growth factors and cytokines, extracellular matrix proteins and ubiquitin-proteasome system are potentially involved in muscle hypertrophy and hyperplasia. After MSTN interference, striated adductor muscle displays significant muscle hypertrophy (51.77 % increase on day 7 and 59.83 % increase on day 21) and muscle hyperplasia (59.36 % increase on day 7 and 61.83 % increase on day 21). WGCNA identifies the key darkolivegreen module, which may play crucial roles in muscle hyperplasia and hypertrophy within the striated muscle of the scallop. Five key transcription factors (zf-CCCH, zf-C2H2, PPP1R10, LRRFIP2, and Gon4) are identified by analyzing the co-expression patterns of core genes within the module. These findings will aid in understanding the regulatory mechanisms of muscle growth in scallops and provide a basis for genetic improvement in shellfish aquaculture.

A Functionally Conserved yet Dynamically Evolving Toolkit Underpinning Molluscan Biomineralization: Insights From Shell and Radula

The molluscan shell and radula constitute pivotal molluscan innovations, each characterized by distinct functions and diverse forms, regulated by the highly specific biomineralization regulatory networks. Despite their paramount importance, the conserved components and adaptive evolutionary processes governing these regulatory networks remain unresolved. To address this knowledge gap, we advocate for the integration of data from less-explored lineages, such as Scaphopoda, as an essential step. This study presents the inaugural comprehensive transcriptome analysis of Pictodentalium vernedei, a representative species of Scaphopoda distinguished by a unique and evolutionarily conserved shell morphology and radula structure. Furthermore, comparative transcriptome/genome analyses are employed to unravel the conservatism and evolutionary innovation of the involved biomineralization regulatory elements. Our findings underscore the central role of secretomes in governing biomineralization processes, and we identified a fundamental set of 26 domains within molluscan secretomes, forming an essential functional protein domain repertoire necessary for the transformation of inorganic ions into biomineralized structures. This core biomineralization toolkit has undergone independent expansion and lineage-specific recruitment, giving rise to novel, modular domain architectures. This may be essential for the functional specialization and morphological diversification of shell and radula structures. These evolutionary processes are driven by the independent co-option of ancient genes and the emergence of novel de novo genes. This comprehensive investigation not only contributes insights into the evolution of molluscan biomineralization structures but also establishes avenues for further scholarly exploration.

Understanding Mantle Edge Pigmentation Through Comprehensive Transcriptomic Profiling of the Chilean Oyster (Ostrea chilensis)

The Chilean oyster (Ostrea chilensis) is a flat oyster native to Chile and New Zealand. Over-exploitation has led to local extinctions in some areas. Two phenotypes, distinguished by dark or white mantle edge pigmentation, have been identified, with the dark-edged mantle oysters being more commercially valuable due to perceived quality. In this study, transcriptomic data were obtained from the mantles of both phenotypes. Total RNA was extracted of adult Chilean Oyster mantle, and samples were sequenced using HiSeq X Illumina technology. A total of 935,620,583 paired-end reads were de novo assembled, 50,908 transcripts produced, and a reference transcriptome created with 37.92% GC content and an N50 of 1929 bp. Functional annotation showed a total of 51,315 GO terms, with 21,322 annotations on Biological Process, 14,578 annotations on Molecular Functions, and 15,415 annotations on Cellular Component. The RNA-seq analysis revealed 746 differentially expressed transcripts, 573 up-regulated and 173 transcripts down-regulated, between dark- and white-mantle edge Chilean Oyster. KEGG enrichment analysis revealed notable differences in the expression profiles allowing the detection of differential expressed transcripts associated with specific pathways such as Ribosome, Citrate cycle, and Protein processing in endoplasmic reticulum. Other interesting differentially represented pathways include Tyrosine metabolism, Tryptophan metabolism, cAMP signaling pathway, ABC transporters, Notch signaling pathway, Endocytosis, and Calcium signaling pathway. This dataset provides a valuable molecular resource for O. chilensis and the understanding of the molecular mechanisms involved in mantle edge pigmentation.

Proteomic characterization of a foraminiferal test's organic matrix

Foraminifera are unicellular protists capable of precipitating calcite tests, which fossilize and preserve geochemical signatures of past environmental conditions dating back to the Cambrian period. The biomineralization mechanisms responsible for the mineral structures, which are key to interpreting palaeoceanographic signals, are poorly understood. Here, we present an extensive analysis of the test-bound proteins. Using liquid chromatography-tandem mass spectrometry, we identify 373 test-bound proteins in the large benthic foraminifer Amphistegina lobifera, the majority of which are highly acidic and rich in negatively charged residues. We detect proteins involved in vesicle formation and active Ca2+ trafficking, but in contrast, do not find similar proteins involved in Mg2+ transport. Considering findings from this study and previous ones, we propose a dual ion transport model involving seawater vacuolization, followed by the active release of Ca2+ from the initial vacuoles and subsequent uptake into newly formed Ca-rich vesicles that consequently enrich the calcification fluid. We further speculate that Mg2+ passively leaks through the membrane from the remaining Mg-rich vesicles, into the calcifying fluid, at much lower concentrations than in seawater. This hypothesis could not only explain the low Mg/Ca ratio in foraminiferal tests compared to inorganic calcite, but could possibly also account for its elevated sensitivity to temperature compared with inorganically precipitated CaCO3.

Multi-tissue metabolomic profiling reveals the crucial metabolites and pathways associated with scallop growth

BACKGROUND

Bivalves represent a vital economic resource in aquaculture for their high productivity and extensive market demand. Growth is one of the most important and desired aquaculture traits for bivalves, regulated by multiple levels, notably intricate metabolic processes. However, the understanding of the metabolic profiles that influence bivalve growth is limited, particularly from a multi-tissue perspective.

RESULTS

In this study, metabolic profiles of multiple tissues of Chlamys farreri with different growth performance were systematically investigated by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Through comparing the metabolic variation between fast-growing (FG) scallops and slow-growing (SG) scallops, 613, 509, 105, and 192 significantly different metabolites (SDMs) were identified in the mantle, gill, adductor muscle, and digestive gland, respectively. Growth-related metabolic pathways including sphingolipid metabolism, fatty acid biosynthesis, and ABC transporter pathway, along with 11 SDMs associated with growth traits were identified in all four tissues, implying they were involved in the growth of multiple tissues in scallops. Tissue-specific metabolic profiling indicated that sulfur-containing amino acid metabolism in the mantle potentially contributed to shell growth, while the gill synergistically participated with the mantle through various metabolic processes, such as tyrosine metabolism, glycine, serine, and threonine metabolism and melanogenesis; energy metabolism was crucial for adductor muscle growth; and nutrients digestion and absorption in the digestive gland were linked to scallop growth.

CONCLUSIONS

Our results represent the first comprehensive analysis of the crucial pathways and metabolites associated with the growth of C. farreri, offering valuable insights for future bivalve aquaculture production.

Characterization of two carbonic anhydrase isoforms in the pulmonate snail (Lymnaea Stagnalis) and their involvement in Molluskan calcification

Calcifying organisms are suffering from negative impacts induced by climate change, such as CO2-induced acidification, which may impair external calcified structures. Freshwater mollusks have the potential to suffer more from CO2-induced acidification than marine calcifiers due to the lower buffering capacity of many freshwater systems. One of the most important enzymes contributing to the biomineralization reaction is carbonic anhydrase (CA), which catalyzes the reversible conversion of CO2 to bicarbonate, the major carbon source of the calcareous structure in calcifiers. In this study we characterized two α-CA isoforms (LsCA1 and LsCA4) from the freshwater snail Lymnaea stagnalis using a combination of gene sequencing, gene expression, phylogenetic analysis and biochemical assays. Both CA isoforms demonstrated high expression levels in the mantle tissue, the major site for biomineralization. Furthermore, expression of LsCA4 during development parallels shell formation. The primary protein structure analysis, active site configuration and the catalytic activity of LsCA4 together suggest that the LsCA4 is embedded in the apical and basolateral membranes of mantle cells; while LsCA1 is proposed to be cytosolic and might play an important role in acid-base regulation. These findings of LsCA isoforms form a strong basis for a more detailed physiological understanding of the effects of elevated CO2 on calcification in freshwater mollusks.

Integrative proteome and metabolome analyses reveal molecular basis underlying growth and nutrient composition in the Pacific oyster, Crassostrea gigas

In order to comprehend the molecular basis of growth, nutrient composition, and color pigmentation in oysters, comparative proteome and metabolome analyses of two selectively bred oyster strains with contrasting growth rate and shell color were used in this study. A total of 289 proteins and 224 metabolites were identified differentially expressed between the two strains. We identified a series of specifically enriched functional clusters implicated in protein biosynthesis (RPL4, MRPS7, and CARS), fatty acid metabolism (ACSL5, PEX3, ACOXI, CPTIA, FABP6, and HSD17B12), energy metabolism (FH, PPP1R7, CLAM2, and RGN), cell proliferation (MYB, NFYC, DOHH, TOP2a, SMARCA5, and SMARCC2), material transport (ABCB1, ABCB8, VPS16, and VPS33a), and pigmentation (RDH7, RDH13, Retsat, COX15, and Cyp3a9). Integrated proteome and metabolome analyses indicate that fast-growing strain utilize energy-efficient mechanisms of ATP generation while promoting protein and polyunsaturated fatty acid synthesis, activating the cell cycle to increase cell proliferation and thus promoting their biomass increase. These results uncovered molecular mechanisms underlying growth regulation, nutrition quality, and pigmentation and provided candidate biomarkers for molecular breeding in oysters. SIGNIFICANCE: Rapid growth has always been the primary breeding objective to increase the production profits of Pacific oyster (Crassostrea gigas), while favorable nutritional quality and beautiful color add commercial value. In recent years, proteomic and metabolomic techniques have been widely used in marine organisms, although these techniques are seldom utilized to study oyster growth and development. In this study, two C. gigas strains with contrasted phenotypes in growth and shell color provided an ideal model for unraveling the molecular basis of growth and nutrient composition through a comparison of the proteome and metabolome. Since proteins and metabolites are the critical undertakers and the end products of cellular regulatory processes, identifying the differentially expressed proteins and metabolites would allow for discovering biomarkers and pathways that were implicated in cell growth, proliferation, and other critical functions. This work provides valuable resources in assistance with molecular breeding of oyster strains with superior production traits of fast-growth and high-quality nutrient value.

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

BACKGROUND

Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species has recently been seriously affected by the frequent outbreaks of Polydora disease, causing great economic losses. Long non-coding RNAs (lncRNAs) exhibit exhibit crucial effects on diverse biological processes, but still remain poorly studied in scallops, limiting our understanding of the molecular regulatory mechanism of P. yessoensis in response to Polydora infestation.

RESULTS

In this study, a high-throughput transcriptome analysis was conducted in the mantles of healthy and Polydora-infected P. yessoensis by RNA sequencing. A total of 19,133 lncRNAs with 2,203 known and 16,930 novel were identified. The genomic characterizations of lncRNAs showed shorter sequence and open reading frame (ORF) length, fewer number of exons and lower expression levels in comparison with mRNAs. There were separately 2280 and 1636 differentially expressed mRNAs and lncRNAs (DEGs and DELs) detected in diseased individuals. The target genes of DELs were determined by both co-location and co-expression analyses. Functional enrichment analysis revealed that DEGs involved in melanization and biomineralization were significantly upregulated; further, obviously increased melanin granules were observed in epithelial cells of the edge mantle in diseased scallops by histological and TEM study, indicating the crucial role of melanizaiton and biomineralization in P. yessoensis to resist against Polydora infestation. Moreover, many key genes, such as Tyrs, Frizzled, Wnts, calmodulins, Pifs, perlucin, laccase, shell matrix protein, mucins and chitins, were targeted by DELs. Finally, a core lncRNA-mRNA interactive network involved in melanization and biomineralization was constructed and validated by qRT-PCR.

CONCLUSIONS

This work provides valuable resources for studies of lncRNAs in scallops, and adds a new insight into the molecular regulatory mechanisms of P. yessoensis defending against Polydora infestation, which will contribute to Polydora disease control and breeding of disease-resistant varieties in molluscs.

Outer fold is sole effective tissue among three mantle folds with regard to oyster shell colour

Molluscs constitute the second largest phylum of animals in the world, and shell colour is one of their most important phenotypic characteristics. In this study, we found among three folds on the mantle edge of oyster, only the outer fold had the same colour as the shell. Transcriptome and mantle cutting experiment indicated that the outer fold may be mainly reflected in chitin framework formation and biomineralisation. There were obvious differences in SEM structure and protein composition between the black and white shell periostraca. The black shell periostraca had more proteins related to melanin biosynthesis and chitin binding. Additionally, we identified an uncharacterized protein gene (named as CgCBP) ultra-highly expressed only in the black outer fold and confirmed its function of chitin-binding and CaCO₃ precipitation promoting. RNAi also indicated that CgCBP knockdown could change the structure of shell periostracum and reduce shell pigmentation. All these results suggest that the mantle outer fold plays multiple key roles in shell periostraca bioprocessing, and shell periostracum structure affected by chitin-binding protein is functionally correlated with shell pigmentation. The investigation of oyster shell periostracum structure and shell colour will provide a better understanding in pigmentation during biological mineralisation in molluscs.

Identifying genes associated with genetic control of color polymorphism in the pearl oyster Pinctada margaritifera var. cumingii (Linnaeus 1758) using a comparative whole genome pool-sequencing approach

For hundreds of years, the color diversity of Mollusca shells has been a topic of interest for humanity. However, the genetic control underlying color expression is still poorly understood in mollusks. The pearl oyster Pinctada margaritifera is increasingly becoming a biological model to study this process due to its ability to produce a large range of colors. Previous breeding experiments demonstrated that color phenotypes were partly under genetic control, and while a few genes were found in comparative transcriptomics and epigenetic experiments, genetic variants associated with the phenotypes have not yet been investigated. Here, we used a pooled-sequencing approach on 172 individuals to investigate color-associated variants on three color phenotypes of economic interest for pearl farming, in three wild and one hatchery populations. While our results uncovered SNPs targeting pigment-related genes already identified in previous studies, such as PBGD, tyrosinases, GST, or FECH, we also identified new color-related genes occurring in the same pathways, like CYP4F8, CYP3A4, and CYP2R1. Moreover, we identified new genes involved in novel pathways unknown to be involved in shell coloration for P. margaritifera, like the carotenoid pathway, BCO1. These findings are essential to possibly implement future breeding programs focused on individual selection for specific color production in pearl oysters and improve the footprint of perliculture on the Polynesian lagoon by producing less but with a better quality.

Heme-Peroxidase 2 Modulated by POU2F1 and SOX5 is Involved in Pigmentation in Pacific Oyster (Crassostrea gigas)

Color polymorphism is frequently observed in molluscan shellfish, while the molecular regulation of shell pigmentation is not well understood. Peroxidase is a key enzyme involved in melanogenesis. Here, we identified a heme-peroxidase 2 gene (CgHPX2), and characterized the expression patterns and transcriptional regulation of CgHPX2 in the Pacific oyster Crassostrea gigas. Tissues expression analysis showed that CgHPX2 was a mantle-specific gene and primarily expressed in the edge mantle in black shell color oyster compared with white shell oyster. In situ hybridization showed that strong signals for CgHPX2 were detected in the both inner and outer surface of the outer fold of mantle in the black shell color oyster, whereas positive signals in white shell oyster were mainly localized in the outer surface of the outer fold of mantle. In the embryos and larvae, a high expression level of CgHPX2 was detected in the trochophore stage in both black and white shell color oysters. The temporal localization of CgHPX2 was mainly detected in the shell gland and edge mantle of trochophore and calcified shell larvae, respectively. In addition, a 2227 bp of 5' flanking region sequence of CgHPX2 was cloned, which contained a presumed core promoter region and many potential transcription factor binding sites. Further luciferase assay experiment confirmed that POU domain, class 2, transcription factor 1 (POU2F1), and SRY-box transcription factor 5 (SOX5) were involved in transcriptional regulation of CgHPX2 gene through binding to its specific promoter region. After CgPOU2F1 and CgSOX5 RNA interference, the CgHPX2 gene expression was significantly decreased. These results suggested that CgPOU2F1 and CgSOX5 might be two important transcription factors that positively regulated the expression of CgHPX2 gene, improving our understanding of the transcriptional regulation of molluscan shell pigmentation.

Transcriptome analysis of the bivalve Placuna placenta mantle reveals potential biomineralization-related genes

The shells of window pane oyster Placuna placenta are very thin and exhibit excellent optical transparency and mechanical robustness. However, little is known about the biomineralization-related proteins of the shells of P. placenta. In this work, we report the comprehensive transcriptome of the mantle tissue of P. placenta for the first time. The unigenes of the mantle tissue of P. placenta were annotated by using the public databases such as nr, GO, KOG, KEGG, and Pfam. 24,343 unigenes were annotated according to Pfam database, accounting for 21.48% of the total unigenes. We find that half of the annotated unigenes of the mantle tissue of P. placenta are consistent to the annotated unigenes from pacific oyster Crassostrea gigas according to nr database. The unigene sequence analysis from the mantle tissue of P. placenta indicates that 465,392 potential single nucleotide polymorphisms (SNPs) and 62,103 potential indel markers were identified from 60,371 unigenes. 178 unigenes of the mantle tissue of P. placenta are found to be homologous to those reported proteins related to the biomineralization process of molluscan shells, while 18 of them are highly expressed unigenes in the mantle tissue. It is proposed that four unigenes with the highest expression levels in the mantle tissue are very often related to the biomineralization process, while another three unigenes are potentially related to the biomineralization process according to the Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) analysis. In summary, the transcriptome analysis of the mantle tissue of P. Placenta shows the potential biomineralization-related proteins and this work may shed light for the shell formation mechanism of bivalves.

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

BACKGROUND

Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation.

RESULTS

In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the "gold standard" of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in ^mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop.

CONCLUSIONS

This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.

Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shells

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we report a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50 = 2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the haemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

Identification of shell-color-related microRNAs in the Manila clam Ruditapes philippinarum using high-throughput sequencing of small RNA transcriptomes

Shell-color polymorphism is a common phenomenon in several mollusk species and has been associated with thermal capacity, developmental stability, shell strength, and immunity. Shell-color polymorphism has been related to the differential expression of genes in several signal transduction pathways; however, the functions of micro-RNAs (miRNAs) in shell-color formation remain unclear. In the present study, we compared high-quality, small-RNA transcriptomes in three strains of the Manila clam Ruditapes philippinarum with specific shell-color patterns, artificially selected for six generations. Totals of 114 known and 208 novel miRNAs were identified by high-throughput sequencing, of which nine known and one novel miRNA were verified by stem-loop quantitative real time-polymerase chain reaction. Predicted miRNA targets were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. miR-137 and miR-216b and the Hedgehog signaling pathway and Wnt signaling pathway were identified as being potentially involved in pigment formation and regulation in R. philippinarum. These results may help to clarify the role of miRNAs in shell coloration and shed light on the mechanisms regulating color formation in bivalve shells.

Comparative Transcriptomic and Expression Profiles Between the Foot Muscle and Mantle Tissues in the Giant Triton Snail Charonia tritonis

The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Limited research on molecular mechanisms can be conducted because the complete genomic information on this species is unavailable. Hence, we performed transcriptome sequencing of the C. tritonis foot muscle and mantle using the Illumina HiSeq sequencing platform. In 109,722 unigenes, we detected 7,994 (3,196 up-regulated and 4,798 down-regulated) differentially expressed genes (DEGs) from the C. tritonis foot muscle and mantle transcriptomes. These DEGs will provide valuable resources to improve the understanding of molecular mechanisms involved in biomineralization of C. tritonis. In the Gene Ontology (GO) database, DEGs were clustered into three main categories (biological processes, molecular functions, and cellular components) and were involved in 50 functional subcategories. The top 20 GO terms in the molecular function category included sulfotransferase activity, transferring sulfur-containing groups, and calcium ion binding, which are terms considered to be related to biomineralization. In KEGG classifications, transcriptomic DEGs were mainly enriched in glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate, and sulfur metabolism pathway, which may be related to biomineralization. The results of qPCR showed that three of the eight genes examined were significantly up-regulated in the mantle. The phylogenetic tree of BMP1 suggested a significant divergence between homologous genes in C. tritonis. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms such as reproduction.

Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

BACKGROUND

Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the black-lipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression. The relationship of shell colour with resulting cultured pearl colour is of great economic interest in P. margaritifera, on which a pearl industry is based. Hence, the albino phenotype provides a useful way to examine the molecular mechanisms underlying pigmentation.

RESULTS

Whole transcriptome RNA-sequencing analysis comparing albino and black wild-type phenotypes at three stages over the culture cycle of P. margaritifera revealed a total of 1606, 798 and 187 differentially expressed genes in whole juvenile, adult mantle and pearl sac tissue, respectively. These genes were found to be involved in five main molecular pathways, tightly linked to known pigmentation pathways: melanogenesis, calcium signalling pathway, Notch signalling pathway, pigment transport and biomineralization. Additionally, significant phenotype-associated SNPs were selected (N = 159), including two located in the Pif biomineralization gene, which codes for nacre formation. Interestingly, significantly different transcript splicing was detected between juvenile (N = 1366) and adult mantle tissue (N = 313) in, e.g., the tyrosinase Tyr-1 gene, which showed more complex regulation in mantle, and the Notch1 encoding gene, which was upregulated in albino juveniles.

CONCLUSION

This multiple RNA-seq approach provided new knowledge about genes associated with the P. margaritifera albino phenotype, highlighting: 1) new molecular pathways, such as the Notch signalling pathway in pigmentation, 2) associated SNP markers with biomineraliszation gene of interest like Pif for marker-assisted selection and prevention of inbreeding, and 3) alternative gene splicing for melanin biosynthesis implicating tyrosinase.

Genome-wide identification, characterisation and expression analysis of the ALAS gene in the Yesso scallop (Patinopecten yessoensis) with different shell colours

Porphyrins, one of the most common shell pigments, are by-products of the haem pathway. 5-Aminolaevulinate synthase (ALAS) is the first and rate-limiting enzyme in this pathway and has been well studied in vertebrate species. However, the function of ALAS in shell colouration has been poorly studied in molluscs, which are renowned for their colourful shells. In the present study, an ALAS gene, named PyALAS, was identified through whole-genome scanning in the Yesso scallop (Patinopecten yessoensis), an economically and evolutionarily important bivalve species in which the shell colour represents polymorphism. Two conserved domains were detected in the PyALAS protein sequence, including a Preseq-ALAS domain and a 5-ALAS domain, confirming the identification of PyALAS. Phylogenetic analysis of the ALAS proteins among various invertebrate and vertebrate species revealed a high consistency between the molecular evolution of ALAS and the species taxonomy. PyALAS was ubiquitously expressed in most adult tissues of the Yesso scallop. The left mantle expressed a significantly higher level of PyALAS than the right side in brown scallops, whereas there was no significant difference in white scallops. Significantly different expression levels of PyALAS was also detected between the two different shell colour strains. These data indicate that PyALAS plays an important role in shell colouration in Yesso scallops and the present study provides new insights into the molecular mechanism of shell colouration in molluscs.

Molecular cloning and expression analysis of tyrosinases (tyr) in four shell-color strains of Manila clam Ruditapes philippinarum

The Manila clam (Ruditapes philippinarum) is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene (tyr 9) was cloned and the expression level of tyr genes (tyr 6, tyr 9, tyr 10, and tyr 11) were investigated in different shell colors. Quantitative real-time PCR showed that tyr genes were significantly expressed in the mantle, a shell formation and pigmentation-related tissue. Moreover, the expression pattern of the tyr genes in the mantle of different shell-color strains was different, suggesting that tyrosinases might be involved in different shell-color formation. In addition, the expression profile of tyr 6, tyr 9, tyr 10, and tyr 11 genes were detected at different early developmental stages and the expression level varied with embryonic and larval growth. RNA interference (RNAi) results showed that the expression level of tyr 9 in the RNAi group was significantly down-regulated compared to control and negative control groups, indicating that Rptyr 9 might participate in shell-color formation. Our results indicated that tyr genes were likely to play vital roles in the formation of shell and shell-color in R. philippinarum.

Transcriptome analysis reveals the pigmentation-related genes in two shell color strains of the Manila clam Ruditapes philippinarum

The Manila clam, Ruditapes philippinarum, is an ecologically and economically important marine bivalve species. In this study, we conducted transcriptomic sequencing of two different shell color strains (O and Z) before color appearance (uncolored juvenile clam) and pigmented shell color (colored juvenile clam) and investigated the analysis of the differential expression patterns of specific genes associated with pigmentation by RNA-seq and time course qPCR analysis. The transcription level of 16 differentially expressed genes (DEGs) related with shell color was analyzed by qRT-PCR to validate the performance of RNA-seq from Illumina sequence data where most of them were up-regulated. Two genes were down-regulated after the occurrence of zebra clam stripes compared with uncolored zebra clam. The trend of gene expression obtained by qPCR was basically consistent with that of RNA-seq. The synthesis of melanin in bivalves plays potential roles in the pigmentation of the shell and is closely related to the formation of the surface pattern. The porphyrin metabolism combined with tyrosinase and melanogenesis signaling pathway is a novel finding in shell color determination of R. philippinarum. This study sheds light on the pigmentation and coloration mechanism of the Manila clam.

Histological and Expression Differences Among Different Mantle Regions of the Yesso Scallop (Patinopecten yessoensis) Provide Insights into the Molecular Mechanisms of Biomineralization and Pigmentation

The molecular mechanisms of shell formation and pigmentation are issues of great interest in molluscan studies due to the unique physical and biological properties of shells. The Yesso scallop, Patinopecten yessoensis, is one of the most important maricultural bivalves in Asian countries, and its shell color shows polymorphism. To gain more information about the underlying mechanisms of shell formation and pigmentation, this study presents the first analyses of histological and transcriptional differences between different mantle regions of the Yesso scallop, which are thought to be responsible for the formation of different shell layers. The results showed major microstructural differences between the edge and central mantles, which were closely associated with their functions. Different biomineralization-related GO functions, which might participate in the formation of different shell layers, were significantly enriched in the different mantle regions, indicating the different molecular functions of the two mantle regions in shell formation. The melanogenesis pathway, which controls melanin biosynthesis, was the most significantly enriched pathway in the DEGs between the two mantle regions, indicating its important role in shell pigmentation. Tyr, the key and rate-limiting gene in melanogenesis, was expressed at a remarkably high level in the central mantle, while the upstream regulatory genes included in melanogenesis were mainly upregulated in the edge mantle, suggesting the different molecular functions of the two mantle regions in shell pigmentation.

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

Microstructure and in-depth proteomic analysis of Perna viridis shell

For understanding the structural characteristics and the proteome of Perna shell, the microstructure, polymorph, and protein composition of the adult Perna viridis shell were investigated. The P. viridis shell have two distinct mineral layers, myostracum and nacre, with the same calcium carbonate polymorph of aragonite, determined by scanning electron microscope, Fourier transform infrared spectroscopy, and x-ray crystalline diffraction. Using Illumina sequencing, the mantle transcriptome of P. viridis was investigated and a total of 69,859 unigenes was generated. Using a combined proteomic/transcriptomic approach, a total of 378 shell proteins from P. viridis shell were identified, in which, 132 shell proteins identified with more than two matched unique peptides. Of the 132 shell proteins, 69 are exclusive to the nacre, 12 to the myostracum, and 51 are shared by both. The Myosin-tail domain containing proteins, Filament-like proteins, and Chitin-binding domain containing proteins represent the most abundant molecules. In addition, the shell matrix proteins (SMPs) containing biomineralization-related domains, such as Kunitz, A2M, WAP, EF-hand, PDZ, VWA, Collagen domain, and low complexity regions with abundant certain amino acids, were also identified from P. viridis shell. Collagenase and chitinase degradation can significantly change the morphology of the shell, indicating the important roles of collagen and chitin in the shell formation and the muscle-shell attachment. Our results present for the first time the proteome of P. viridis shell and increase the knowledge of SMPs in this genus.

Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii

BACKGROUND

The pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed transcriptomic sequencing and proteomic analyses using mantle edge tissues.

RESULTS

A total of 56,969 unigenes were obtained from transcriptomic, of which 21,610 were annotated, including 385 annotated significant up-regulated genes and 227 significant down-regulated genes in yellow shell oysters (| log2 (fold change) | ≥2 and false discovery rate < 0.001). Tyrosine metabolism, calcium signalling pathway, phototransduction, melanogenesis pathways and rhodopsin related Gene Ontology (GO) terms were enriched with significant differentially expressed genes (DEGs) in transcriptomic. Proteomic sequencing identified 1769 proteins, of which 51 were significantly differentially expressed in yellow shell oysters. Calmodulin, N66 matrix protein, nacre protein and Kazal-type serine protease inhibitor were up-regulated in yellow shell oysters at both mRNA and protein levels, while glycine-rich protein shematrin-2, mantle gene 4, and sulphide: quinone oxidoreductase were down-regulated at two omics levels. Particularly, calmodulin, nacre protein N16.3, mantle gene 4, sulphide: quinone oxidoreductase, tyrosinase-like protein 3, cytochrome P450 3A were confirmed by quantitative real-time PCR. Yellow shell oysters possessed higher total carotenoid content (TCC) compared than black shell oyster based on spectrophotography.

CONCLUSIONS

The yellow phenotype of pearl oysters, characterised by higher total carotenoids content, may reflect differences in retinal and rhodopsin metabolism, melanogenesis, calcium signalling pathway and biomineralisation. These results provide insights for exploring the relationships between calcium regulation, biomineralisation and yellow shell colour pigmentation.

Transcriptomic and proteomic analyses of genetic factors influencing adductor muscle coloration in QN Orange scallops

Background

Color polymorphism, a high-valued trait, is frequently observed in molluscan shellfish. The QN Orange scallop, a new scallop strain successively selected from the interspecific hybrids of the bay scallop (Argopecten irradians irradians) and the Peruvian scallop (Argopecten purpuratus), is distinguished from other scallops by its orange adductor muscles. In this study, to reveal the mechanisms of the formation of adductor muscle coloration in the QN Orange scallops, we compared the proteome and transcriptome of orange adductor muscles of the QN Orange and those of white adductor muscles of the Bohai Red scallop, another strain selected from the interspecific hybrids of the bay scallop and the Peruvian scallop.

Results

Transcriptomic analysis revealed 416 differentially expressed genes (DEGs) between white and orange adductor muscles, among which 216 were upregulated and 200 were downregulated. Seventy-four differentially expressed proteins (DEPs), including 36 upregulated and 38 downregulated proteins, were identified through label-free proteomics. Among the identified DEGs and DEPs, genes related to carotenoids biosynthesis including apolipophorin, and Cytochrome P450 and those related to melanin biosynthesis including tyrosinase and Ras-related protein Rab-11A were found to express at higher levels in orange adductor muscles. The high expression levels of VPS (vacuolar protein sorting) and TIF (translation initiation factor) in orange adductor muscle tissues indicated that carotenoid accumulation may be affected by proteins outside of the carotenoid pathway.

Conclusions

Our results implied that the coloration of orange adductor muscles in the QN Orange scallops may be controlled by genes modulating accumulation of carotenoids and melanins. This study may provide valuable information for understanding the mechanisms and pathways underlying adductor muscle coloration in molluscan shellfish.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5717-y) contains supplementary material, which is available to authorized users.

Acute effects of UVB radiation on the survival, growth, development, and reproduction of Daphniopsis tibetana Sars (Crustacea: Cladocera)

Daphniopsis tibetana Sars lives in elevation, usually with strong solar UV radiation. We speculate that UV may have an effect on the ecology and evolutionary biology of this species. However, the regulatory effect and mechanism of UV on D. tibetana have not been studied previously. Here, our results showed that UVB could act as a positive factor in the relative body lengths, reproductive parameters, and population growth parameters of D. tibetana when UVB radiation is 20-170 mJ cm^-2, compared with the control group. Strikingly, these parameters were highest at 120 mJ cm^-2. To explore the mechanism underlying the UVB irradiation effects, we conducted a transcriptome analysis using the Trinity platform. The results indicated that differentially regulated genes were mostly enriched in lipid transport and lipid localization by Gene Ontology (GO) enrichment analysis of 146 differentially expressed genes (83 upregulated and 63 downregulated). This is the first study of UVB radiation of D. tibetana to reveal genes that may have crucial roles in survival, growth, and reproduction and could be candidates for future functional studies. Additionally, the study could supply a substantial resource for investigating and elucidating lipids that could play important roles in a physiological context.

Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes

In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.

Genome-wide identification, characterization and expression analysis of the MITF gene in Yesso scallops (Patinopecten yessoensis) with different shell colors

The microphthalmia-associated transcription factor (MITF) is the center of the regulator network of melanin synthesis in vertebrates. However, the role of MITF in shell color formation is poorly studied in mollusks. In the present study, an MITF gene, PyMITF, was first identified at the whole-genome level in Yesso scallop (Patinopecten yessoensis), an evolutionarily and economically important species, the shell color of which shows polymorphism. The PyMITF is a large gene spanning ~37 kb in the genome with 7 introns and 8 exons. A basic helix-loop-helix leucine zipper (bHLH-LZ) domain was detected in the PyMITF protein sequence, which can bind the canonical E-box sequence in the promoter region of the downstream genes. Phylogenetic analysis of the MITFs among vertebrates and invertebrates revealed that the molecular evolution of MITFs was consistent with the species taxonomy. Different expression levels of PyMITF were detected among different shell color strains, indicating the important role of PyMITF involved in shell pigmentation. Besides, PyMITF was expressed at a significantly higher level in the central mantle than that in the edge mantle, proving the participation of the central mantle in shell color formation in molecular level for the first time. The work provides valuable information for the molecular mechanism study of shell color formation.

Transcriptional changes in the Japanese scallop (Mizuhopecten yessoensis) shellinfested by Polydora provide insights into the molecular mechanism of shell formation and immunomodulation

The Japanese scallop (Mizuhopecten yessoensis) is one of the most important aquaculture species in Asian countries; however, it has suffered severe infection by Polydora in northern China in recent years, causing great economic losses. The Polydora parasitizes the shell of scallops, badly destroying the shell's structure. To investigate the molecular response mechanism of M. yessoensis to Polydora infestion, a comprehensive and niche-targeted cDNA sequence database for diseased scallops was constructed. Additionally, the transcriptional changes in the edge mantle, central mantle and hemocytes, tissues directly related to the disease, were first described in this study. The results showed that genes involved in shell formation and immunomodulation were significantly differentially expressed due to the infestation. Different transcriptional changes existed between the two mantle regions, indicating the different molecular functions likely responsible for the formation of different shell layers. The differential expression of genes for immune recognition, signal transduction and pathogen elimination presented an integrated immune response process in scallops. Moreover, neuromodulation and glycometabolism involved in the regulation process with relevant function significantly enriched. The study provides valuable information for mechanism study of shell formation and immunomodulation in scallops.

Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas

Background

Conchiferan molluscs construct a biocalcified shell that likely supported much of their evolutionary success. However, beyond broad proteomic and transcriptomic surveys of molluscan shells and the shell-forming mantle tissue, little is known of the spatial and ontogenetic regulation of shell fabrication. In addition, most efforts have been focused on species that deposit nacre, which is at odds with the majority of conchiferan species that fabricate shells using a crossed-lamellar microstructure, sensu lato.

Results

By combining proteomic and transcriptomic sequencing with in situ hybridization we have identified a suite of gene products associated with the production of the crossed-lamellar shell in Lymnaea stagnalis. With this spatial expression data we are able to generate novel hypotheses of how the adult mantle tissue coordinates the deposition of the calcified shell. These hypotheses include functional roles for unusual and otherwise difficult-to-study proteins such as those containing repetitive low-complexity domains. The spatial expression readouts of shell-forming genes also reveal cryptic patterns of asymmetry and modularity in the shell-forming cells of larvae and adult mantle tissue.

Conclusions

This molecular modularity of the shell-forming mantle tissue hints at intimate associations between structure, function, and evolvability and may provide an elegant explanation for the evolutionary success of the second largest phylum among the Metazoa.

Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics

BACKGROUND

Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis.

RESULTS

Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle. For the same comparison, iTRAQ-based proteomics reveals 474 differentially expressed proteins (DEPs), 198 up- and 276 downregulated. These DEPs mainly comprise muscle-specific proteins of the sarcoplasmic reticulum, extracellular matrix, and metabolic pathways. A group of conventional muscle proteins-myosin heavy chain, myosin regulatory light chain, myosin essential light chain, and troponin-are enriched in fast muscle. In contrast, paramyosin, twitchin, and catchin are preferentially expressed in slow muscle. The association analysis of proteomic and transcriptomic data provides the evidences of regulatory events at the transcriptional and posttranscriptional levels in fast and slow muscles. Among 1236 differentially expressed unigenes, 22.7% show a similar regulation of mRNA levels and protein abundances. In contrast, more unigenes (53.2%) exhibit striking differences between gene expression and protein abundances in the two muscles, which indicates the existence of fiber-type specific, posttranscriptional regulatory events in most of myofibrillar proteins, such as myosin heavy chain, titin, troponin, and twitchin.

CONCLUSIONS

This first, global view of protein and mRNA expression levels in scallop fast and slow muscles reveal that regulatory mechanisms at the transcriptional and posttranscriptional levels are essential in the maintenance of muscle structure and function. The existence of fiber-type specific, posttranscriptional regulatory mechanisms in myofibrillar proteins will greatly improve our understanding of the molecular basis of muscle contraction and its regulation in non-model invertebrates.

Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp ( Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Cr (VI), the pathogenicity factor, is widely known to cause toxic effects in living organisms. Given the economic importance of the mantis shrimp ( Oratosquilla oratoria), the understanding of impacts by Cr (VI) is considered important. In this study, transcriptome of mantis shrimp was characterized by a comparison between control and Cr (VI)-treated samples using RNA-seq approach. Totally, 88 234 826 bp and 13.24G clean reads were obtained. The total length and number of unigenes were 68 411 206 bp and 100 918, respectively. The maximal and average length of unigenes was 24 906 bp and 678 bp, respectively (N50, 798 bp). 7115 of these unigenes accounted for 7.05% of the total that were annotated in all databases. After annotation of assembled unigenes, 35 619 of them were assigned into 3 functional categories and 56 subcategories using Gene Ontology; 18 580 of them were assigned into 26 functional categories using Clusters of Orthologous Groups of proteins; 16 864 of them were assigned into 5 major categories and 32 subclasses using KEGG. Finally, 1730 genes were differentially expressed (DGEs), 9 up-regulated pathways (protein digestion and absorption, neuroactive ligand-receptor interaction, pancreatic secretion, tyrosine metabolism, amoebiasis, ECM-receptor interaction, riboflavin metabolism, amino sugar and nucleotide sugar metabolism and AGE-RAGE signaling pathway in diabetic complications) were significantly enriched ( q < 0.05), and one down-regulated pathway ( Staphylococcus aureus infection) was significantly enriched ( q < 0.05). Up-regulation of genes in pathways of protein digestion/absorption ( PepT1/SLC15A and ATP1B) and environment information processing ( COL1AS, COL4A; LAMA3_5, LAMB3; FN1 and TN) may imply the potentially positive toxicity resistance mechanisms.

Bias and Correction in RNA-seq Data for Marine Species

RNA-seq is a recently developed approach widely used for transcriptome profiling in biological analyses that use next-generation sequencing technologies. Accurate estimation of gene expression levels is critical for answering biological questions. Here, we show that the commonly used measure of gene expression levels, fragments per kilobase of transcript per million mapped reads (FPKM), is biased in transcript length, GC content, and dinucleotide frequencies in the RNA-seq analysis of marine species. We used a generalized linear model to correct the observed biases of FPKM. We used RNA-seq data sets from eight species obtained by different sequencing methods to evaluate the correction methods. Our work contributes to the understanding of potential technical artifacts in RNA-seq experiments for marine species, and presents a means by which more accurate gene expression measures can be obtained.

Genome-wide identification and expression profiling of the SOX gene family in a bivalve mollusc Patinopecten yessoensis

SOX family is composed of transcription factors that play vital roles in various developmental processes. Comprehensive understanding on evolution of the SOX family requires full characterization of SOX genes in different phyla. Mollusca is the second largest metazoan phylum, but till now, systematic investigation on the SOX family is still lacking in this phylum. In this study, we conducted genome-wide identification of the SOX family in Yesso scallop Patinopecten yessoensis and profiled their tissue distribution and temporal expression patterns in the ovaries and testes during gametogenesis. Seven SOX genes were identified, including SOXB1, B2, C, D, E, F and H, representing the first record in protostomes with SOX members identical to that proposed to exist in the last common ancestor of chordates. Genomic structure analysis identified relatively conserved exon-intron structures, accompanied by intron insertion. Quantitative real-time PCR analysis revealed possible involvement of scallop SOX in various functions, including neuro-sensory cell differentiation, hematopoiesis, myogenesis and gametogenesis. This study represents the first systematic characterization of SOX gene family in Mollusca. It will assist in a better understanding of the evolution and function of SOX family in metazoans.

Molecular Cloning and Characterization of Full-Length cDNA of Calmodulin Gene from Pacific Oyster Crassostrea gigas

The shell of the pearl oyster (Pinctada fucata) mainly comprises aragonite whereas that of the Pacific oyster (Crassostrea gigas) is mainly calcite, thereby suggesting the different mechanisms of shell formation between above two mollusks. Calmodulin (CaM) is an important gene for regulating the uptake, transport, and secretion of calcium during the process of shell formation in pearl oyster. It is interesting to characterize the CaM in oysters, which could facilitate the understanding of the different shell formation mechanisms among mollusks. We cloned the full-length cDNA of Pacific oyster CaM (cgCaM) and found that the cgCaM ORF encoded a peptide of 113 amino acids containing three EF-hand calcium-binding domains, its expression level was highest in the mantle, hinting that the cgCaM gene is probably involved in shell formation of Pacific oyster, and the common ancestor of Gastropoda and Bivalvia may possess at least three CaM genes. We also found that the numbers of some EF hand family members in highly calcified species were higher than those in lowly calcified species and the numbers of these motifs in oyster genome were the highest among the mollusk species with whole genome sequence, further hinting the correlation between CaM and biomineralization.

Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture.

Transcriptome Sequencing and Comparative Analysis of Ovary and Testis Identifies Potential Key Sex-Related Genes and Pathways in Scallop Patinopecten yessoensis

Bivalve mollusks have fascinatingly diverse modes of reproduction. However, research investigating sex determination and reproductive regulation in this group of animals is still in its infancy. In this study, transcriptomes of three ovaries and three testes of Yesso scallop were sequenced and analyzed. Transcriptome comparison revealed that 4394 genes were significantly different between ovaries and testes, of which 1973 were ovary-biased (upregulated in the ovaries) and 2421 were testis-biased. Crucial sex-determining genes that were previously reported in vertebrates and putatively present in bivalves, namely FOXL2, DMRT, SOXH, and SOXE, were investigated. The genes all possessed conserved functional domains and were detected in the gonads. Except for PySOXE, the other three genes were significantly differentially expressed between the ovaries and testes. PyFOXL2 was ovary-biased, and PyDMRT and PySOXH were testis-biased, suggesting that these three genes are likely to be key candidates for scallop sex determination/differentiation. Furthermore, GO and KEGG enrichment analyses were conducted for both ovary- and testis-biased genes. Interestingly, both neurotransmitter transporters and GABAergic synapse genes were overrepresented in the ovary-biased genes, suggesting that neurotransmitters, such as GABA and glycine, are likely to participate in scallop ovary development. Our study will assist in better understanding of the molecular mechanisms underlying bivalve sex determination and reproductive regulation.

Characterization of the mantle transcriptome in bivalves: Pecten maximus, Mytilus edulis and Crassostrea gigas

The calcareous shells secreted by bivalve molluscs display diverse and species specific structural compositions, which indicates possible divergent biomineralization processes. Thus, studying multiple mollusc species will provide a more comprehensive understanding of shell formation. Here, the transcriptomes of the mantle tissues responsible for shell deposition were characterized in three commercially relevant bivalve species. Using high-throughput sequencing and bioinformatics tools, de novo transcriptome assemblies of mantle tissues were generated for the mussel Mytilus edulis, the oyster Crassostrea gigas and the scallop Pecten maximus. These transcriptomes were annotated, and contigs with similarity to proteins known to have shell formation roles in other species were identified. Comparison of the shell formation specific proteins in the three bivalves indicates the possibility of species specific shell proteins.

Evaluation of the 2b-RAD method for genomic selection in scallop breeding

The recently developed 2b-restriction site-associated DNA (2b-RAD) sequencing method provides a cost-effective and flexible genotyping platform for aquaculture species lacking sufficient genomic resources. Here, we evaluated the performance of this method in the genomic selection (GS) of Yesso scallop (Patinopecten yessoensis) through simulation and real data analyses using six statistical models. Our simulation analysis revealed that the prediction accuracies obtained using the 2b-RAD markers were slightly lower than those obtained using all polymorphic loci in the genome. Furthermore, a small subset of markers obtained from a reduced tag representation (RTR) library presented comparable performance to that obtained using all markers, making RTR be an attractive approach for GS purpose. Six GS models exhibited variable performance in prediction accuracy depending on the scenarios (e.g., heritability, sample size, population structure), but Bayes-alphabet and BLUP-based models generally outperformed other models. Finally, we performed the evaluation using an empirical dataset composed of 349 Yesso scallops that were derived from five families. The prediction accuracy for this empirical dataset could reach 0.4 based on optimal GS models. In summary, the genotyping flexibility and cost-effectiveness make 2b-RAD be an ideal genotyping platform for genomic selection in aquaculture breeding programs.

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation

BACKGROUND

Shell color polymorphisms of Mollusca have contributed to development of evolutionary biology and population genetics, while the genetic bases and molecular mechanisms underlying shell pigmentation are poorly understood. The Pacific oyster (Crassostrea gigas) is one of the most important farmed oysters worldwide. Through successive family selection, four shell color variants (white, golden, black and partially pigmented) of C. gigas have been developed. To elucidate the genetic mechanisms of shell coloration in C. gigas and facilitate the selection of elite oyster lines with desired coloration patterns, differentially expressed genes (DEGs) were identified among the four shell color variants by RNA-seq.

RESULTS

Digital gene expression generated over fifteen million reads per sample, producing expression data for 28,027 genes. A total number of 2,645 DEGs were identified from pair-wise comparisons, of which 432, 91, 43 and 39 genes specially were up-regulated in white, black, golden and partially pigmented shell of C. gigas, respectively. Three genes of Abca1, Abca3 and Abcb1 which belong to the ATP-binding cassette (ABC) transporters super-families were significantly associated with white shell formation. A tyrosinase transcript (CGI_10008737) represented consistent up-regulated pattern with golden coloration. We proposed that white shell variant of C. gigas could employ "endocytosis" to down-regulate notch level and to prevent shell pigmentation.

CONCLUSION

This study discovered some potential shell coloration genes and related molecular mechanisms by the RNA-seq, which would provide foundational information to further study on shell coloration and assist in selective breeding in C. gigas.