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

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.

Transcriptomic and Physiological Analysis Reveal Melanin Synthesis-Related Genes and Pathways in Pacific Oysters (Crassostrea gigas)

Shell color is one of the shell traits of molluscs, which has been regarded as an economic trait in some bivalves. Pacific oysters (Crassostrea gigas) are important aquaculture shellfish worldwide. In the past decade, several shell color strains of C. gigas were developed through selective breeding, which provides valuable materials for research on the inheritance pattern and regulation mechanisms of shell color. The inheritance patterns of different shell colors in C. gigas have been identified in certain research; however, the regulation mechanism of oyster pigmentation and shell color formation remains unclear. In this study, we performed transcriptomic and physiological analyses using black and white shell oysters to investigate the molecular mechanism of melanin synthesis in C. gigas. Several pigmentation-related pathways, such as cytochrome P450, melanogenesis, tyrosine metabolism, and the cAMP signaling pathway were found. The majority of differentially expressed genes and some signaling molecules from these pathways exhibited a higher level in the black shell oysters than in the white, especially after L-tyrosine feeding, suggesting that those differences may cause a variation of tyrosine metabolism and melanin synthesis. In addition, the in vitro assay using primary cells from mantle tissue showed that L-tyrosine incubation increased cAMP level, gene and protein expression, and melanin content. This study reveals the difference in tyrosine metabolism and melanin synthesis in black and white shell oysters and provides evidence for the potential regulatory mechanism of shell color in oysters.

Effects of ocean acidification and tralopyril on bivalve biomineralization and carbon cycling: A study of the Pacific Oyster (Crassostrea gigas)

The combined effects of emerging pollutants and ocean acidification (OA) on marine organisms and marine ecosystems have attracted increasing attention. However, the combined effects of tralopyril and OA on marine organisms and marine ecosystems remain unclear. In this study, Crassostrea gigas (C. gigas) were exposed to tralopyril (1 μg/L) and/or OA (PH = 7.7) for 21 days and a 14-day recovery acclimation. To investigate the stress response and potential molecular mechanisms of C. gigas to OA and tralopyril exposure alone or in combination, as well as the effects of OA and/or tralopyril on bivalve biomineralization and marine carbon cycling. The results showed that the combined toxicity was between that of acidification and tralopyril alone. Single or combined exposure activated the general stress defense responses of C. gigas mantle, affected energy metabolism and biomineralization of the organism and the carbon cycle of the marine ecosystem. Moreover, acidification-induced and tralopyril-induced toxicity showed potential recoverability at molecular and biochemical levels. This study provides a new perspective on the molecular mechanisms of tralopyril toxicity to bivalve shellfish and reveals the potential role of tralopyril and OA on marine carbon cycling.

DNA Methylation Analyses Unveil a Regulatory Landscape in the Formation of Nacre Color in Pearl Oyster Pinctada fucata martensii

Pearl color is regulated by genetics, biological pigments, and organic matrices and an important factor that influences the pearl economic value. The epigenetic regulation mechanism underlying pearl pigmentation remains poorly understood. In this study, we collected the mantle pallial (MP) and mantle central (MC) of the golden-lipped strain, and MP of the silver-lipped strain of pearl oyster Pinctada fucata martensii. The whole-genome bisulfite sequencing (WGBS) technology was employed to investigate the possible implication of epigenetic factors regulating nacre color variation. Our results revealed approximately 2.5% of the cytosines in the genome of the P. fucata martensii were methylated, with the CG methylation type was in most abundance. Overall, we identified 12, 621 differentially methylated regions (DMRs) corresponding to 3,471 DMR-associated genes (DMGs) between the two comparison groups. These DMGs were principally enriched into KEGG metabolic pathways including ABC transporters, Terpenoid backbone biosynthesis, and fatty acid degradation. In addition, integrating information about DMGs, DEGs, and function annotation indicated eight genes LDLR, NinaB, RDH, CYP, FADS, fn3, PU-1, KRMP as the candidate genes related to pigmentation of nacre color. A further study proved that the pigment in nacre is violaxanthin. The results of our study provide the support that there is an association between nacre color formation and DNA methylation profiles and will help to reveal the epigenetic regulation of nacre pigmentation formation in pearl oyster P. fucata martensii.

Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas)

Molluscan shell color polymorphism is important in genetic breeding, while the molecular information mechanism for shell coloring is unclear. Here, high-throughput RNA sequencing was used to compare expression profiles of coding and non-coding RNAs (ncRNAs) from Pacific oyster Crassostrea gigas with orange and black shell, which were from an F2 family constructed by crossing an orange shell male with a black shell female. First, 458, 13, and 8 differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, respectively. Functional analysis suggested that the DEGs were significantly enriched in 9 pathways including tyrosine metabolism and oxidative phosphorylation pathways. Several genes related to melanin synthesis and biomineralization expressed higher whereas genes associated with carotenoid pigmentation or metabolism expressed lower in orange shell oyster. Then, based on the ncRNA analysis, 163 and 20 genes were targeted by 13 and 8 differentially expressed lncRNAs (DELs) and miRNAs (DEMs), severally. Potential DELs-DEMs-DEGs interactions were also examined. Seven DEMs-DEGs pairs were detected, in which tyrosinase-like protein 1 was targeted by lgi-miR-133-3p and lgi-miR-252a and cytochrome P450 was targeted by dme-miRNA-1-3p. These results revealed that melanin synthesis-related genes and miRNAs-mRNA interactions functioned on orange shell coloration, which shed light on the molecular regulation of shell coloration in marine shellfish.