Colorful seashells: Identification of haem pathway genes associated with the synthesis of porphyrin shell color in marine snails

Protoporphyrin IX metabolism mediated via translocator protein (CgTspO) involved in orange shell coloration of pacific oyster (Crassostrea gigas)

Mollusc shell color polymorphism is influenced by various factors. Pigments secreted in vivo by animals play a critical role in shell coloration. Among the different shell-color hues, orange pigmentation has been partially attributed to porphyrins. However, the detailed causal relationship between porphyrins and orange-shell phenotype in molluscs remains largely unexplored. The various strains of Pacific oyster (Crassostrea gigas) with different shell color provide useful models to study the molecular regulation of mollusc coloration. Accordingly, oysters with orange and gold-shells, exhibiting distinct porphyrin distributions, were selected for analysis of total metabolites and gene expression profile through mantle metabolomic and transcriptomic studies. Translocator protein (TspO) and protoporphyrin IX (PPIX) were identified as potential factors influencing oyster shell-color. The concentration of PPIX was measured using HPLC, while expression profiling of CgTspO was analyzed by qPCR, in situ hybridization, Western blotting, and immunofluorescence techniques. Moreover, the roles of CgTspO in regulating PPIX metabolism and affecting the orange-shell-coloration were investigated in vitro and in vivo. These studies indicate that PPIX and its associated metabolic protein, CgTspO may serve as new regulators of orange-shell-coloration in C. gigas. Data of this study offer new insights into oyster shell coloration and enhancing understandings of mollusc shell color polymorphism.

Research progress on formation mechanism of pearl

Pearls are deeply cherished for their rich color and gorgeous luster, and their quality directly affects their value. Currently, the evaluation of pearl quality is mainly based on four aspects: color, shape, size and smoothness. The quality of pearls is influenced by a variety of factors, categorized into internal factors, such as the structural composition of the nacreous layer and genetic factors of the mussels, and external factors, including the aquaculture environment. Existing research results indicates that genetic factors are the dominant factor controlling the pearl quality. However, the macromolecules such as metal ions, organic pigments and various physical and chemical factors in the aquaculture water environment will also significantly impact pearl quality. Among these, matrix proteins are organic macromolecules found in the nacreous layer that play an important role in pearl quality. They participate in the deposition of calcium carbonate and the construction of the organic framework, affecting the pearls' size and shape. The color of pearls is influenced by the deposition of metal ions, the transport of organic pigments and the regulation of microstructure.

Mitf involved in shell pigmentation by activating tyrosinase-mediated melanin synthesis in Pacific oyster (Crassostrea gigas)

Pigmentation is frequently observed in the molluscan shells, whereas the molecular regulation about these shell pigments formation is not clear. The microphthalmia-associated transcription factor (Mitf) is an important transactivator in melanin synthesis in vertebrates. Here, the Mitf containing a highly conserved basic helix-loop-helixleucine zipper (bHLH-LZ) domain was identified in an economically important marine bivalve Pacific oyster Crassostrea gigas. The Mitf was found to widespread tissue distribution and the expression was higher in the marginal mantle than in the central mantle. Particularly, the expression level of Mitf was high in black shell color oysters compared with white shell oysters. After injecting siRNA, the expression of Mitf decreased significantly, and the efficiency of RNA interference reached 53%. Besides, knockdown Mitf obviously decreased expression of tyrosinase family genes and tyrosinase activity of mantles, indicating a potential regulatory relationship between Mitf and Tyr or Typs. Simultaneously, there was a sharply reduce in the number of the melanosomes in the outer fold of mantle by silencing of Mitf. Luciferase assays in cell culture further verified that Mitf was involved in transcriptional regulation of Typ-2 and Typ-3 genes through binding to their specific promoter regions. These data argue that Mitf is involved in shell pigmentation through activating tyrosinase-mediated melanin synthesis in C. gigas.

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.

Effects of Dietary Cystine and Tyrosine Supplementation on Melanin Synthesis in the Pacific Oyster (Crassostrea gigas)

Melanogenesis is a multistep process to produce melanin for dark pigmentation in skin coloration. Previous studies in vertebrates demonstrated that cystine and tyrosine amino acids are involved in the melanin synthesis. However, very little is known about the melanogenesis in bivalve. In this study, cystine supplementation for 30 days significantly upregulated the expression of CgB-aat1, CgCbs and CgTyr and pheomelanin content in the Pacific oyster Crassostrea gigas. Transmission electron microscope (TEM) results revealed more melanosomes in the connective tissue and melanin granules were secreted in epithelium of mantle. In contrast, tyrosine supplementation had no clear effect on melanogenesis except the gene expression changes of CgB-aat1 and CgCbs. In addition, prolonged supplementation of cystine or tyrosine for 60 days had a negative impact on melanogenesis. Indeed, after 60 days, expression of most of the melanin synthesis-related genes under study was decreased, and melanin content was significantly reduced, indicating that cystine and tyrosine might inhibit production of eumelanin and pheomelanin, respectively. In addition, in vitro analysis using primary cell culture from mantle tissue indicated that incubation with cystine, tyrosine, or B-AAT1 polypeptide, CBS/TYR recombinant proteins induced the increase of CgB-aat1 and CgCbs expression in a dose-dependent manner, suggesting the presence of a regulatory network in response to cystine and tyrosine amino acids intakes in pheomelanin synthesis-related gene expression. Taken together, these data indicate that cystine-CgB-aat1-CgCbs-CgTyr axis is a potential regulator of the pheomelanin biosynthesis pathway, and thus plays an important role in the mantle pigmentation in C. gigas. This work provides a new clue for selective cultivation of oyster strains with specific shell colors in bivalve breeding.

Transcription factor CgPOU3F4-like regulates expression of pheomelanin synthesis related gene CgB-aat1 in the Pacific oyster (Crassostrea gigas)

Previous study has found that b (0, +) -type amino acid transporter 1 (CgB-aat1) plays an essential role on mantle pigmentation in the Pacific oyster Crassostrea gigas. However, the molecular regulation of CgB-aat1 gene expression remains unclear. Herein, three POU domain family members, CgPOU2F1, CgPOU3F4-like and CgPOU4F3-X1 were characterized and they all had POUs and HOX domains, respectively, which were important in transcriptional regulation. CgPOU3F4-like gene expression was the highest in mantle edge. Subsequently, the dual-luciferase reporter result showed that the core regulatory region of CgB-aat1 gene was from -632 to -350 bp of promoter. In transient co-transfection assays, the strongest activity was activated only by CgPOU3F4-like, suggesting CgPOU3F4-like was a valid transcriptional activator of CgB-aat1 gene promoter. And the structural integrity of CgPOU3F4-like was essential for its activation function. In addition, site directed mutagenesis assay was applied to detect three key binding sites between CgPOU3F4-like and core region of CgB-aat1 gene promoter, and this interaction was verified by ChIP test. Furthermore, CgPOU3F4-like knockdown by RNA interference led to obvious decreases in CgB-aat1 and cystathionine beta-synthase (CgCbs) expressions at both mRNA and protein levels. Collectively, these results indicate that CgPOU3F4-like positively regulate CgB-aat1 gene expression and it may be a critical upstream transcriptional regulation factor in pheomelanin synthesis in C. gigas.

Shell color polymorphism in marine gastropods

Marine gastropods are characterized by an incredible variation in shell color. In this review, we aim to introduce researchers to previous studies of shell color polymorphism in this group of animals, trying to provide an overview of the topic and highlighting some potential avenues for future research. For this, we tackle the different aspects of shell color polymorphism in marine gastropods: its biochemical and genetic basis, its patterns of spatial and temporal distribution, as well as its potential evolutionary causes. In particular, we put special emphasis on the evolutionary studies that have been conducted so far to reveal the evolutionary mechanisms responsible for the maintenance of shell color polymorphism in this group of animals, as it constitutes the least addressed aspect in existing literature reviews. Several general conclusions can be drawn from our review: First, natural selection is commonly involved in the maintenance of gastropod color polymorphism; second, although the contribution of neutral forces (gene flow-genetic drift equilibrium) to shell color polymorphism maintenance do not seem to be particularly important, it has rarely been studied systematically; third, a relationship between shell color polymorphism and mode of larval development (related to dispersal capability) may exist. As for future studies, we suggest that a combination of both classical laboratory crossing experiments and -Omics approaches may yield interesting results on the molecular basis of color polymorphism. We believe that understanding the various causes of shell color polymorphism in marine gastropods is of great importance not only to understand how biodiversity works, but also for protecting such biodiversity, as knowledge of its evolutionary causes may help implement conservation measures in those species or ecosystems that are threatened.

Evolutionary loss of shell pigmentation, pattern, and eye structure in deep-sea snails in the dysphotic zone

Adaptations to habitats lacking light, such as the reduction or loss of eyes and pigmentation, have fascinated biologists for centuries, yet have rarely been studied in the deep sea, the earth's oldest and largest light-limited habitat. Here, we investigate the evolutionary loss of shell pigmentation, pattern, and eye structure across a family of deep-sea gastropods (Solariellidae). We show that within our phylogenetic framework, loss of these traits evolves without reversal, at different rates (faster for shell traits than eye structure), and over different depth ranges. Using a Bayesian approach, we find support for correlated evolution of trait loss with increasing depth within the dysphotic region. A transition to trait loss occurs for pattern and eye structure at 400-500 m and for pigmentation at 600-700 m. We also show that one of the sighted, shallow-water species, Ilanga navakaensis, which may represent the "best-case" scenario for vision for the family, likely has poor spatial acuity and contrast sensitivity. We therefore propose that pigmentation and pattern are not used for intraspecific communication but are important for camouflage from visual predators, and that the low-resolution vision of solariellids is likely to require high light intensity for basic visual tasks, such as detecting predators.

The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation

Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows important variation in shell color across Northeast Atlantic. In this study, we constructed a high-density genetic map, as a tool for screening common cockle genome, which was applied to ascertain the genetic basis of color variation in the species. The consensus genetic map comprised 19 linkage groups (LGs) in accordance with the cockle karyotype (2n = 38) and spanned 1073 cM, including 730 markers per LG and an inter-marker distance of 0.13 cM. Five full-sib families showing segregation for several color-associated traits were used for a genome-wide association study and a major QTL on chromosome 13 associated to different color-traits was detected. Mining on this genomic region revealed several candidate genes related to shell construction and color. A genomic region previously reported associated with divergent selection in cockle distribution overlapped with this QTL suggesting its putative role on adaptation.

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

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

Identification of a coproporphyrinogen-III oxidase gene and its correlation with nacre color in Hyriopsis cumingii

Pearl color is an important factor influencing pearl value, and is affected by the nacre color of the shell in Hyriopsis cumingii. Coproporphyrinogen-III oxidase (CPOX) is a key enzyme in porphyrin synthesis, and porphyrins are involved in color formation in different organisms, including in the nacre color of mussels. In this study, a CPOX gene (HcCPOX) was identified from H. cumingii, and its amino acid sequence was found to contain a coprogen-oxidase domain. HcCPOX mRNA was expressed widely in the tissues of white and purple mussels, and the highest expression was found in the gill, followed by the fringe mantle. The expression of HcCPOX in all tissues of purple mussels (except in the middle mantle) was higher than that of white mussels. Strong hybridization signals for HcCPOX were observed in the dorsal epithelial cells of the outer fold of the mantle. The activity of CPOX in the gill, fringe mantle, and foot of purple mussels was significantly higher than that in white mussels. Moreover, the expression of HcCPOX and CPOX activity were decreased in RNA interference experiments. The findings indicate that HcCPOX might contributes to nacre color formation in H. cumingii by being involved in porphyrin synthesis.

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.

Shell Biosynthesis and Pigmentation as Revealed by the Expression of Tyrosinase and Tyrosinase-like Protein Genes in Pacific Oyster (Crassostrea gigas) with Different Shell Colors

The widely recognized color polymorphisms of molluscan shell have been appreciated for hundreds of years by collectors and scientists, while molecular mechanisms underlying shell pigmentation are still poorly understood. Tyrosinase is a key rate-limiting enzyme for the biosynthesis of melanin. Here, we performed an extensive multi-omics data mining and identified two tyrosinase genes, including tyrosinase and tyrosinase-like protein 2 (Tyr and Typ-2 respectively), in the Pacific oyster Crassostrea gigas, and investigated the expression patterns of tyrosinase during adults and embryogenesis in black and white shell color C. gigas. Tissue expression analysis showed that two tyrosinase genes were both specifically expressed in the mantle, and the expression levels of Tyr and Typ-2 in the edge mantle were significantly higher than that in the central mantle. Besides, Tyr and Typ-2 genes were black shell-specific compared with white shell oysters. In situ hybridization showed that strong signals for Tyr were detected in the inner surface of the outer fold, whereas positive signals for Typ-2 were mainly localized in the outer surface of the outer fold. In the embryos and larvae, the high expression of Tyr mRNA was detected in eyed-larvae, while Typ-2 mRNA was mainly expressed at the trochophore and early D-veliger. Furthermore, the tyrosinase activity in the edge mantle was significantly higher than that in the central mantle. These findings indicated that Tyr gene may be involved in shell pigmentation, and Typ-2 is more likely to play critical roles not only in the formation of shell prismatic layer but also in shell pigmentation. In particular, Typ-2 gene was likely to involve in the initial non-calcified shell of trochophores. The work provides valuable information for the molecular mechanism study of shell formation and pigmentation in C. gigas.

RNA Interference by Ingested Dsrna-Expressing Bacteria to Study Porphyrin Pigmentation in Crassostrea gigas

Porphyrins are a widespread group of pigments in nature which are believed to contribute to shell colors in mollusks. Previous studies have provided candidate genes for porphyrin shell coloration, however, the linkage analysis between functional genes and porphyrin pigmentation remains unclear in mollusks. RNA interference is a powerful molecular tool for analyzing the loss of functions of genes in vivo and alter gene expression. In this study, we used unicellular alga Platymonas subcordiformis and Nitzschia closterium f. minutissima as vectors to feed oysters with Escherichia coli strain HT115 engineered to express double-stranded RNAs targeting specific genes involved in porphyrin synthesis. A strain of Crassostrea gigas with orange shell was used to target key haem pathway genes expression using the aforementioned approach. We show here that feeding the oysters with E. coli, containing dsRNA targeting pigmentation genes, can cause changes in the color of the newly deposited shell. For example, the RNAi knockdown of CgALAS and CgPBGD resulted in the loss of uroporphyrin pigmentation from the shell due to the accumulation of the pigment in the oyster's mantle. The study probed the crucial role of ALAS and PBGD genes potential functions of uroporphyrin production and shell color pigmentation in C. gigas.

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.

Identification and characterization of key haem pathway genes associated with the synthesis of porphyrin in Pacific oyster (Crassostrea gigas)

Molluscs exhibit diverse shell colors. The molecular regulation of shell coloration is however not well understood. To investigate the connection of shell coloration with pigment synthesis, we analyzed the distribution of porphyrins, a widespread group of pigments in nature, in four Pacific oyster strains of different shell colors including black, orange, golden, and white. The porphyrin distribution was analyzed in oyster mantles and shells by fluorescence imaging and UV spectrophotometer. The results showed that red fluorescence emitted by porphyrins under the UV light was detected only on the nacre of the orange-shell strain and mantles of orange, black and white-shell strains. Extracts from newly deposit shell, nacre and mantle tissue from orange-shell specimens showed peaks in UV-vis spectra that are characteristic of porphyrins, but these were not observed for the other shell-color strains. In addition, genes of the haem synthetic pathway were isolated and characterized. Phylogenetic analysis of CgALAS, CgALAD, CgPBGD, CgUROS, and CgUROD provide further evidence for a conserved genetic pathway of haem synthesis during evolution. Differential expression of the haem genes expressed in mantle tissues support these findings and are consistent with porphyrins being produced by the orange strain only. Tissue in situ hybridization demonstrated the expression of these candidate genes at the outer fold of C. gigas mantles where shell is deposited. Our studies provide a better understanding of shell pigmentation in C. gigas and candidate genes for future mechanistic analysis of shell color formation in molluscs.

Molecular Pathways and Pigments Underlying the Colors of the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus 1758)

The shell color of the Mollusca has attracted naturalists and collectors for hundreds of years, while the molecular pathways regulating pigment production and the pigments themselves remain poorly described. In this study, our aim was to identify the main pigments and their molecular pathways in the pearl oyster Pinctada margaritifera—the species displaying the broadest range of colors. Three inner shell colors were investigated—red, yellow, and green. To maximize phenotypic homogeneity, a controlled population approach combined with common garden conditioning was used. Comparative analysis of transcriptomes (RNA-seq) of P. margaritifera with different shell colors revealed the central role of the heme pathway, which is involved in the production of red (uroporphyrin and derivates), yellow (bilirubin), and green (biliverdin and cobalamin forms) pigments. In addition, the Raper–Mason, and purine metabolism pathways were shown to produce yellow pigments (pheomelanin and xanthine) and the black pigment eumelanin. The presence of these pigments in pigmented shell was validated by Raman spectroscopy. This method also highlighted that all the identified pathways and pigments are expressed ubiquitously and that the dominant color of the shell is due to the preferential expression of one pathway compared with another. These pathways could likely be extrapolated to many other organisms presenting broad chromatic variation.

Melanins as Sustainable Resources for Advanced Biotechnological Applications

Melanins are a class of biopolymers that are widespread in nature and have diverse origins, chemical compositions, and functions. Their chemical, electrical, optical, and paramagnetic properties offer opportunities for applications in materials science, particularly for medical and technical uses. This review focuses on the application of analytical techniques to study melanins in multidisciplinary contexts with a view to their use as sustainable resources for advanced biotechnological applications, and how these may facilitate the achievement of the United Nations Sustainable Development Goals.

Evo-devo of shell colour in gastropods and bivalves

Recent technical innovations are revealing surprising patterns in mollusc shell pigmentation, such as an unexpectedly modest role for melanins and rapid divergences in the mix of pigments used to achieve similar colour patterns. The elucidation of the molecular genetic basis of shell pigmentation has been slow, probably because of the high genome complexity of gastropods and bivalves. Recent work within the old field of evolutionary ecology of shell pigmentation allows a greater role for the analysis of large-geographic-scale patterns (sometimes employing citizen-science data), as well as experimental field studies. However, the field remains dominated by land snails as model organisms, while colour pattern evolution in marine gastropods and bivalves, particularly those not exposed to visual predators, remains mysterious.

Integrated proteomic and transcriptomic analysis reveals that polymorphic shell colors vary with melanin synthesis in Bellamya purificata snail

The snail Bellamya purificata is an ecologically and economically important freshwater gastropod species. However, limited genomic resources are available for this snail. In this study, the transcriptome of mantle tissues and proteome of shells of B. purificata with two shell colors (namely light-cyan line (LC) and light-purple line (LP)) were deeply sequenced and characterized. A total of 5.72 million contigs were assembled into 157,015 unigenes, 21,455 (13.66%) of these unigenes were significantly matched to NR, Swiss-Prot, KOG, GO and KEGG database. 1807 differentially expressed genes (DEGs) were identified between the two different shell color lines. These DEGs were significantly enriched in five KEGG pathways including tyrosine metabolism, tryptophan metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and histidine metabolism, which suggested that the shell color polymorphism in B. purificata was a result of melanin synthesis variation. A total of 1521 proteins were identified in B. purificata here as well. The differentially expressed protein analysis showed that the tyrosinase content in LP was significantly decreased in comparison to LC, which agreed with the transcriptome analysis results. This study provides valuable genomic resources of B. purificata and improves our understanding of molecular mechanisms of biomineralization and shell color polymorphism in snail.

Chemical evidence of rare porphyrins in purple shells of Crassostrea gigas oyster

The colour of oyster shells is a very diverse characteristic morphotype, forming intriguing vivid patterns both on the inside and outside of the shell. In the present study, we have identified for the first time, the presence of several porphyrins as constituents of the shell pigmentation of the Crassostrea gigas oyster consumed worldwide. The precise molecular structures of halochromic, fluorescent and acid-soluble porphyrins, such as uroporphyrin and turacin, are unambiguously determined by reverse phase liquid chromatography combined with high resolution mass spectrometry. Their presence account for the purple colouration of shells but also for the dark colouration of adductor muscle scars. We have also defined the endogenous origin of these porphyrins, specifically secreted or accumulated by the shell forming tissue. These findings are pioneering analytical proofs of the existence of the haem pathway in the edible oyster Crassostrea gigas, evidenced by the chemical identification of haem side-products and supported by the recent publication of the corresponding oyster genome.

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.

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.

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.

Colour plasticity in the shells and pearls of animal graft model Pinctada margaritifera assessed by HSV colour quantification

The bivalve Pinctada margaritifera has the capacity to produce the most varied and colourful pearls in the world. Colour expression in the inner shell is under combined genetic and environmental control and is correlated with the colour of pearls produced when the same individual is used as a graft donor. One major limitation when studying colour phenotypes is grader subjectivity, which leads to inconsistent colour qualification and quantification. Through the use of HSV (Hue Saturation Value) colour space, we created an R package named 'ImaginR' to characterise inner shell colour variations in P. margaritifera. Using a machine-learning protocol with a training dataset, ImaginR was able to reassign individual oysters and pearls to predefined human-based phenotype categories. We then tested the package on samples obtained in an experiment testing the effects of donor conditioning depth on the colour of the donor inner shell and colour of the pearls harvested from recipients following grafting and 20 months of culture in situ. These analyses successfully detected donor shell colour modifications due to depth-related plasticity and the maintenance of these modifications through to the harvested pearls. Besides its potential interest for standardization in the pearl industry, this new method is relevant to other research projects using biological models.

Colorful seashells: Identification of haem pathway genes associated with the synthesis of porphyrin shell color in marine snails

Very little is known about the evolution of molluskan shell pigments, although Mollusca is a highly diverse, species rich, and ecologically important group of animals comprised of many brightly colored taxa. The marine snail genus Clanculus was chosen as an exceptional model for studying the evolution of shell color, first, because in Clanculus margaritarius and Clanculus pharaonius both shell and foot share similar colors and patterns; and second, because recent studies have identified the pigments, trochopuniceus (pink‐red), and trochoxouthos (yellow‐brown), both comprised of uroporphyrin I and uroporphyrin III, in both shell and colored foot tissue of these species. These unusual characteristics provide a rare opportunity to identify the genes involved in color production because, as the same pigments occur in the shell and colored foot tissue, the same color‐related genes may be simultaneously expressed in both mantle (which produces the shell) and foot tissue. In this study, the transcriptomes of these two Clanculus species along with a third species, Calliostoma zizyphinum, were sequenced to identify genes associated with the synthesis of porphyrins. Calliostoma zizyphinum was selected as a negative control as trochopuniceus and trochoxouthos were not found to occur in this species. As expected, genes necessary for the production of uroporphyrin I and III were found in all three species, but gene expression levels were consistent with synthesis of uroporphyrins in mantle and colored foot tissue only in Clanculus. These results are relevant not only to understanding the evolution of shell pigmentation in Clanculus but also to understanding the evolution of color in other species with uroporphyrin pigmentation, including (mainly marine) mollusks soft tissues and shells, annelid and platyhelminth worms, and some bird feathers.