リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Global gene expression analysis on the formation of pearl sac and pearl by allografting in Pinctada fucata」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。
リケラボ

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Global gene expression analysis on the formation of pearl sac and pearl by allografting in Pinctada fucata

MARIOM 東京大学 DOI:10.15083/0002004435

2022.06.22

概要

The bivalve mollusk, Pinctada fucata is renowned worldwide for its ability of producing high quality spherical pearl and accounts for more than 90% of seawater pearl production. Pearls are the result of mollusk’s capability to produce calcified shell materials in response to an injury to the mantle tissue. Mollusk shell is mainly composed of calcium carbonate (CaCO3) crystals (>90% w/w) surrounded by an organic matrix (0.01% to 5% w/w) of proteins, lipids and polysaccharides. As in shell biomineralization, pearl formation is also regulated by the extracellular organic matrix secreted by the mantle tissue of mollusk.

Mantle grafting is the commonly practiced method for producing spherical pearls. The process involves a surgical implantation where a small piece (3 × 3 mm) of mantle tissue is excised from a suitable donor oyster and then implanted into the gonad of a host oyster along with an inorganic nucleus. Once transplanted, the outer epithelial cells of the graft start to proliferate and differentiate to give rise a monolayer of the secretory epithelium around the nucleus termed as ‘pearl sac’. The newly formed pearl sac gradually secretes various matrix proteins onto the nucleus in order to produce a lustrous pearl. Therefore, it is very reasonable to claim that pearl sac formation is the critical step of pearl culture which eventually determines the success of culture.

Under normal condition, outer epithelium of the mantle is a stable and mitotically inactive tissue, whereas the inner epithelial cells, contrarily, proliferate intermittently for the renewal of the tissue. Upon a mantle injury, the outer epithelial cells multiply actively to regenerate the injured site. The pearl sac formation simply resembles the wound healing process that occurs after a mantle injury. During mantle grafting, the external epithelial cells of the graft become active soon after surgical implantation and start to proliferate into a pearl sac. Other components of the graft, such as inner epithelial cells, muscle fibres and connective tissues eventually disappear. It is assumed that the outer epithelium contains proliferating stem cells, but the feature of those cells is unclear. So, identification of genes involved in epithelial cell proliferation and differentiation is of utmost important to understand the mechanisms of pearl formation.

Shell or pearl biomineralization is a highly controlled biological process regulated by the cascades of a substantial number of genes. Though the mechanism of pearl formation has been studied largely, but the complex physiological process by which pearl sac and pearl is formed has not been properly understood yet. Using an RNAseq approach, here, we aimed to reveal the genes involved in the development of pearl sac and pearl, and the sequential expression patterns of different shell matrix proteins (SMPs) secreted from the pearl sac during different stages of pearl formation. We also examined the pearl layers to scrutinize the microstructural characterization of the surface depositions on pearls. In the last part of the study, we tried to establish a suitable method of gene editing in P. fucata using CRISPR/Cas9 system.

1. Genes expressed during the proliferation of mantle epithelial cells into pearl sac
To describe the genes engaged in pearl sac formation, we performed RNA sequencing of mantle graft and the later pearl sac at different stages of pearl formation. During grafting experiments for three months, we collected nine samples: donor mantle epithelial cells, donor mantle pallium, donor mantle pallium on grafting, and mantle pallium each from the host at 24 hours, 48 hours, 1 week, 2 weeks, 1 months and 3 months post grafting. In the wound healing process, pearl sac was developed by two weeks of culture as indicated by the up-regulated Gene Ontology (GO) terms relevant to epithelial cell proliferation and differentiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that immune genes were highly expressed (P < 0.05) between 0 h – 24 h in a donor dependent-manner and 48 h – 1 w in a host dependent-manner.

We screened out a number of genes including JAG1, RFX3, STRC, FGFR2, SAV1, RAC1, DMD, RGMA, PTK7, MAF, MEF2A, SFRP5, TGM1, FZD1, GRHL2, TEAD1, PRKDC, LAMC1, EGFR, CASP8, CDC42, RSPO2, MTSS1, MATN1, SULF1, SPG20 and LRP6 that may be involved in the proliferation and differentiation of mantle epithelial cells into pearl sac. Furthermore, it is the first time that we identified some stem cell marker genes including ABCG2, SOX2, MEF2A, HES1, MET, NRP1, ESR1, STAT6, PAX2, FZD1 and PROM1 that were expressed differentially during pearl sac development. RT-PCR data showed ubiquitous expression of these stem cell marker genes in P. fucata, which further proposed their cell proliferation-related functions in different tissues. Additionally, qPCR results demonstrated that all these genes were highly expressed in mantle tissue, suggesting their potential role in the proliferation of the mantle epithelium into pearl sac. Furthermore, PAX2 and FZD1 were expressed higher in mantle compared to other tissues such as gonad and muscle.

2. Gene expression profiles at different stages of pearl formation during 3 months pearl culture
More than 200 molluscan biomineralization-related genes that contribute to the formation of shell and pearl have been identified till date. In this study, we screened out 192 genes likely involved in pearl biomineralization by blast search against a list of reference biomineralization genes prepared beforehand. It has been clearly defined that, the biomineralization genes are being secreted by the pearl sac developed from donor mantle graft, not by the host gonad tissue. So, the identified biomineralization-related genes in our study were expressed in the pearl sac, i.e., in the donor mantle epithelium.

Though the mantle tissue is primarily responsible for shell/pearl biomineralization, recent studies have also been reported that oyster hemocytes can mediate shell biomineralization by secreting and transporting CaCO3 crystals to the site of mineralization. Therefore, the interaction observed between donor mantle graft and surrounding host hemocytes immediately after grafting is very essential for the proper development of pearl sac and pearl.

Principal component analysis (PCA) precisely elucidates that the mineralization process during the first 3 months of culture is regulated differently. Further hierarchical clustering of 192 biomineralization-related genes showed clearly different expression profiles between the earlier (before 1 week) and later stages (1 week to 3 months) of pearl grafting. Detailed expression analysis of the major SMPs demonstrated that most of the prismatic layer forming SMPs were first up-regulated and then gradually down-regulated, indicating their involvement in the development of pearl sac and the onset of pearl mineralization. Most of the nacreous layer forming SMPs were up-regulated after the formation of pearl sac with the highest expression at 1 month, suggesting the completion of the nacreous layer formation. Nacrein, MSI7 and shematrin involved in both layer formation were highly expressed during 0 h – 24 h, down-regulated up to 1 week and then up-regulated again after maturation of pearl sac. Actually, these SMPs control and mediate the CaCO3 crystal formation. However, the genes highly expressed in the pearl sac may not be highly expressed in the mantle pallium. Therefore, the expression profiling of the SMPs can be used as a marker of the shell and pearl formation.

3. Microstructural characterization of pearl layers recapitulates the mineralization sequence of pearl
Clear morphological differences were observed among the pearls obtained at 1 month and 3 months of culture. Surface examination of 1 month pearls revealed the variation in the initial mineralization among the pearls. Moreover, the nacre deposition at the early stage of pearl formation was not uniform throughout the surroundings of a given pearl. But at 3 months, the pearl surface became smoother and more regular with a pearl luster.

Scanning electron microscopy (SEM) demonstrated that an initial organic layer was deposited onto the nucleus surface before the secretion of prismatic and nacreous layers. But, the thickness of the organic material layer was variable among different pearls and even in different parts of the same pearl. Thus the initial mineralization of pearl is not simply the reappearance of the nacreous structures, rather it is more complex. The metabolic changes that occur in the mantle epithelial cells during its differentiation into a pearl sac may result in the formation of a new mineralizing sequence that is comparable to the structure of the shell. However, the prismatic layer of pearl is more diversified compared to the regular brick-wall like structures of nacre that develops later on it. Unlike the canonical mollusk shell, prismatic layer in pearl was composed of both aragonite and calcite prisms, organic materials and some unknown compounds.

The study recapitulates the mineralization sequence of pearl, where a heterogeneous prismatic layer is secreted first and followed by nacreous layer. Additionally, SEM imaging confirmed the deposition of nacreous layer around the nucleus by 1 month that we predicted from our gene expression study.

4. CRISPR/Cas9 mediated gene editing in P. fucata
We tried to establish a suitable method of gene editing in pearl oyster using high-throughput CRISPR/Cas9 system. Here, we showed that direct injection of Cas9 protein and appropriate sgRNA into the adductor muscle of adult oyster can induce noticeable mutation in desired gene. DNA sequencing results from two representative mutants indicated a large deletion (45 bp) on the targeted gene, nacrein. We got 3 mutant oysters among 4 injected with sgRNA-Cas9 complex. The notable success rate suggests that, this tool can function in pearl oyster in vivo through a simple but efficient approach of direct injection.

This is the first and a preliminary trial of CRISPR-mediated gene alteration in bivalve mollusk. Therefore, further study is needed to make the method more appropriate.

Conclusion
The findings of the present study conclude two consecutive stages during the 3 months pearl culture. One is the initiation of pearl sac formation as part of the wound healing process in response to the oyster defense mechanism (before 1 week post grafting). Another is the maturation of pearl sac and deposition of organic matrices on the bare nucleus (2 week to 3 months). We figured out the key genes including some stem cell marker genes engaged in proliferation and differentiation of mantle epithelial cells into pearl sac. We also described the notable immune genes and pathways that provide insight into the increased understanding of the host immune reaction in response to accepting a graft.

The expression pattern of the key genes involved in the development of pearl sac and pearl elucidated that immune and cell proliferation related-genes were mostly enriched during earlier stages (before 2 weeks), whereas biomineralization genes were expressed in later stages (2 weeks to 3 months) of pearl grafting. The expression profiling of 192 biomineralization genes indicates that first 3 months of pearl biogenesis are very crucial when the pearl sac forms and secretes significant amount of nacre for making a lustrous pearl. Microstructural characterization of pearls explains the order of mineralization where a periostracum-like layer is secreted first before the deposition of the heterogeneous prismatic layer and the outermost nacreous layer onto the nucleus. CRISPR/Cas9 mediated gene editing suggests that it can be a simple but efficient tool for gene editing in pearl oyster towards improving the quality of cultured pearl.

The improved understanding of the molecular mechanisms underlying the formation of pearl sac and pearl obtained from this study will provide a basis for future research towards upgrading the pearl culture practice and pearl quality. The study also gives some valuable information for identifying the functional genes implicated for pearl sac formation. However, further functional analyses are needed to verify the functions of the identified stem cell marker genes in pearl sac development.

論文の公開元へ

この論文で使われている画像

関連論文

関連論文をもっと見る

参考文献

Addadi, L., Joester, D., Nudelman, F., Weiner, S., 2006. Mollusk shell formation: a source of new concepts for understanding biomineralization processes. Chem. Eur. J. 12, 980-987.

Addadi, L., Weiner, S., 1997. A pavement of pearl. Nature 389, 912-915.

Alagarswami, K., 1987. Cultured pearls-production and quality, in: K. Alagarswami (Eds.), Pearl Culture, Central Marine Fisheries Research Institute, Cochin, pp. 105-113.

Ansai, S., Kinoshita, M., 2014. Targeted mutagenesis using CRISPR/Cas system in medaka. Biol. Open 3, 362-371.

Aoki, S., 1966. Comparative histological observations on the pearl-sac tissues forming nacreous, prismatic and periostracal pearls. Nippon Suisan Gakkaishi 32, 1-10.

Armstrong, D.A., Armstrong, J.L., Krassner, S.M., Pauley, G.B., 1971. Experimental wound repair in the black abalone, Haliotis cracherodii. J. Invertebrate Pathol. 17, 216-227.

Ausubel, F.M., 2005. Are innate immune signaling pathways in plants and animals conserved? Nat. Immunol. 6, 973-979.

Avruch, J., Khokhlatchev, A., Kyriakis, J.M., Luo, Z., Tzivion, G., Vavvas, D., 2001. Ras activation of the raf kinase: tyrosine kinase recruitment of the MAP kinase cascade. Recent Prog Horm Res. 56(1), 127-155.

Awaji, M., Machii, A., 2011. Fundamental studies on in vivo and in vitro pearl formation- contribution of outer epithelial cells of pearl oyster mantle and pearl sacs. Aqua-BioScience Monographs (ABSM) 4(1), 1-39.

Awaji, M., Suzuki, T., 1995. The pattern of cell proliferation during pearl sac formation in the pearl oyster. Fish. Sci. 61(5), 747-751.

Bédouet, L., Schuller, M.J., Marin, F., Milet, C., Lopez, E., Giraud, M., 2001. Soluble proteins of the nacre of the giant oyster Pinctada maxima and of the abalone Haliotis tuberculata: extraction and partial analysis of nacre proteins. Comp.

Biochem. Physiol. B Biochem. Mol. Biol. 128(3), 389-400.

Bédouet, L., Rusconi, F., Rousseau, M., Duplat, D., Marie, A., Dubost, L., Le Ny, K., Berland, S., Péduzzi, J., Lopez, E., 2006. Identification of low molecular weight molecules as new components of the nacre organic matrix. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 144(4), 5 32-43.

Beer, A.C., Southgate, P.C., 2000. Collection of pearl oyster (family Pteriidae) spat at Orpheus Island Great Barrier Reef (Australia). J. Shellfish Res. 19, 821-826.

Belcher, A.M., Wu, X.H., Christensen, R.J., Hansma, P.K., Stucky, G.D. Morse, D.E., 1996. Control of crystal phase switching and orientation by soluble mollusc-shell proteins. Nature 381, 56-58.

Bénédicte, L., Salmena, L., Bidère, N., Su, H., Matysiak-Zablocki, E., Murakami, K., 2007. Essential role for caspase-8 in toll-like receptors and NF-κB signaling. J. Biol. Chem. 282(10), 7416-7423.

Beniash, E., Ivanina, A., Lieb, N.S., Kurochkin, I., Sokolova, I.M., 2010. Elevated level of carbon dioxide affects metabolism and shell formation in oysters Crassostrea virginica (Gmelin). Mar. Ecol. Prog. Ser. 419, 95-108.

Bhattacharya, D., Marfo, C.A., Li, D., Lane, M., Khokha, M.K., 2015. CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus. Dev. Biol. 408, 196-204.

Blay, C., Planes, S., Ky, C.L., 2017. Donor and recipient contribution to phenotypic traits and the expression of biomineralisation genes in the pearl oyster model Pinctada margaritifera. Sci. Rep. 7(1), 2696.

Blay, C., Planes, S., Ky, C.L., 2018. Cultured pearl surface quality profiling by the shell matrix protein gene expression in the biomineralised pearl sac tissue of Pinctada margaritifera. Mar. Biotechnol. 20(4), 490-501.

Bray, N.L., Pimentel, H., Melsted, P., Pachter, L., 2016. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34(5), 525-527.

Carter, J., 1980. Environmental and biological controls of bivalve shell mineralogy and microstructure. In: Skeletal growth of aquatic organisms. Rhoads, D.C., Lutz, R.A. (Eds.), New York, Plenum Press, 69-113.

Cavelier, P., Cau, J., Morin, N., Delsert, C., 2017. Early gametogenesis in the Pacific oyster: new insights using stem cell and mitotic markers. J. Exp. Biol. 220, 3988-3996.

Chang, N., Sun, C., Gao, L., Zhu, D., Xu, X., Zhu, X., Xiong, J.W., Xi, J.J., 2013. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res. 23, 465-472.

Checa, A., 2000. A new model for periostracum and shell formation in Unionidae (Bivalvia, Mollusca). Tissue Cell 32, 405-416.

Checa, A.G., Cartwright, J.H.E. Willinger, M.G., 2009. The key role of the surface membrane in why gastropod nacre grows in towers. Proc. Natl. Acad. Sci. U.S.A. 106, 38-43.

Checa, A.G., Cartwright, J.H.E., Willinger, M.G., 2013. Mineral bridges in nacre revisited. In: Watabe, S., Maeyama, K., Nagasawa, H. (eds), Recent Advances in Pearl Research. Proc. International Symposium Pearl Res. 2011. TERRAPUB, Tokyo, pp 109-123.

Chellam, A., Victor, A., Dharmaraj, S., Velayudhan, T., Rao, K.S., 1991. Pearl oyster farming and pearl culture. FAO Corporate Doc. Repository. http://eprints.cmfri.org.in/id/eprint/6847.

Chen, C., Fenk, L.A., de Bono, M., 2013. Efficient genome editing in Ceanorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res. 41, e193.

Chen, S., Lee, B., Lee, A.Y., Modzelewski, A.J., He, L., 2016 .Highly efficient mouse genome editing by CRISPR ribonucleoprotein electroporation of zygotes. J. Biol. Chem. 291, 14457-14467.

Chen, Y.F., Qian, G.Y., 2009. Studies on the formation of pearl sac in vitro of epithelial cells and tissue from mantle. J. Hydroecol. 2, 74-77.

Cho, S.W., Kim, S., Kim, J.M., Kim, J.S., 2013. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 31, 230-232.

Cho, S.W., Lee, J., Carroll, D., Kim, J.S., Lee, J. 2013. Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 195, 1177-1180.

Choi, Y.H., Chang, Y.J., 2003. Gametogenic cycle of the transplanted-cultured pearl oyster, Pinctada fucata martensii (Bivalvia: Pteriidae) in Korea. Aquaculture 220, 781-790.

Clark, M.S., Thorne, M.A., Vieira, F.A., Cardoso, J.C., Power, D.M., Peck, L.S., 2010. Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics 11, 362.

Cochennec-Laureau, N., Montagnani, C., Saulnier, D., Fougerouse, A., Levy, P., Lo, C., 2010. A histological examination of grafting success in pearl oyster Pinctada margaritifera in French Polynesia. Aquat. Living Resour. 23, 131-140.

Cochennec-Laureau, N., Montagnani, C., Saulnier, D., Fougerouse, A., Levy, P., Lo, C.A., 2010. Histological examination of grafting success in pearl oyster Pinctada

margaritifera in French Polynesia. Aquat Living Resour. 23, 131-140.

Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., Zhang, F., 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823.

Crenshaw, M.A., 1972. The inorganic composition of molluscan extrapallial fluid. Biol. Bull. 143, 506-512.

Cuif, J.P., Ball, A.P., Dauphin, Y., Farre, B., Nouet, J., Perez-Huerta, A., Salomé, M., Williams, C.T., 2008. Structural, mineralogical and biochemical diversity in the lower part of the pearl layer of cultivated seawater pearls from Polynesia. Microsc Microanal. 14, 405-417.

Cuif, J.P., Dauphin, Y., Howard, L., Nouet, J., Rouziere, S., Salome, M., 2011. Is the pearl layer a reversed shell? A re-examination of the theory of pearl formation through physical characterizations of pearl and shell developmental stages in Pinctada margaritifera. Aquat Living Resour. 24, 41-424.

Dakin, W.J., 1913. Pearls. In: Giles, P., Litt, D., Seward, A.C. (Eds.), The Cambridge Manuals of Science and Literature. Cambridge University Press, London. 103 pp.

Dang, Y., Jia, G., Choi, J., Ma, H., Anaya, E., Ye, C., Shankar, P., Wu, H., 2015. Optimizing sgRNA structure to improve CRISPR–Cas9 knockout efficiency. Genome Biol. 16, 280.

Dickinson, G. H., Matoo, O. B., Tourek, R. T., Sokolova, I. M., Beniash, E., 2013. Environmental salinity modulates the effects of elevated CO2 levels on juvenile hard-shell clams, Mercenaria mercenaria. J. Exp. Biol. 216, 2607-2618.

Dix, T. G., 1973. Histology of the mantle and pearl sac of pearl oysters Pinctada maxima (Lamellibranchia). J. Malacol. Soc. Aust. 2, 365-375.

Du, X., Jiao, Y., Deng, Y.W., Wang, Q.H.R., 2010. Ultrastructure of the pearl sac cells of pearl oyster Pinctada martensii. Acta Oceanol. Sin. 32, 160-164.

Duan, J., Lu, G., Xie, Z., Lou, M., Luo, J., Guo, L., Zhang, Y., 2014. Genome-wide identification of CRISPR/Cas9 off-targets in human genome. Cell Res. 24, 1009-1012.

Eddy, L., Affandi, R., Kusumorini, N., Sani, Y., Manal, W., 2015. The pearl sac formation in male and female Pinctada maxima host oysters implanted with allograft saibo. HAYATI J. Biosci. 22, 122-129.

Ellis, S., Haws, M., 1999. Producing pearls using the black-lip pearl oyster (Pinctada margaritifera). Aquafarmer Inf. Sheet. 8 pp.

Falini, G., Albeck, S., Weiner, S., Addadi, L., 1996. Control of aragonite or calcite polymorphism by mollusk shell macromolecules. Science. 271, 67-69.

Fang, Z., Feng, Q., Chi, Y., Xie, L., Zhang, R., 2008. Investigation of cell proliferation and differentiation in the mantle of Pinctada fucata (Bivalve, Mollusca). Mar Biol. 153, 745-754.

Fougerouse, A., Rousseau, M., Lucas, J.S., 2008. Soft tissue anatomy, shell structure and biomineralization. In: Southgate, P.C, Lucas, A.B. (Eds.), The pearl oyster. Elsevier, Amsterdam, 77-99 pp.

Fu Y, Foden, J.A., Khayter, C., Maeder, M.L., Reyon, D., Joung, J.K., Sander, J.D., 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31, 822-826.

Fu, D., Zhang, Y., Xiao, S., Yu, Z., 2011. The first homolog of a TRAF7 (TNF receptor associated factor 7) gene in a mollusk, Crassostrea hongkongensis. Fish Shellfish Immunol. 31, 1208-1210.

Funabara, D., Ohmori, F., Kinoshita, S., Koyama, H., Mizutani, S., Ota, A., Osakabe, Y., Nagai, K., Maeyama, K., Okamoto, K., Kanoh, S., Asakawa, S., Watabe, S., 2014. Novel genes participating in the formation of prismatic and nacreous layers in the pearl oyster as revealed by their tissue distribution and RNA interference knockdown. PLoS One. 9(1), e84706.

Funakoshi, S., 2000. Studies on the classification, structure and function of hemocytes in bivalves. Bull. Natl. Res. Inst. Aquaculture 29, 1-103.

Furuhashi, T., Schwarzinger, C., Miksik, I., Smrz, M., Beran, A., 2009. Molluscan shell evolution with review of shell calcification hypothesis. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 154, 351-371.

Gao, J., Chen, Y., Yang, Y., Liang, J., Xie, J., Liu, J., Li, S., Zheng, G., Xie, L., Zhang, R., 2016. The transcription factor Pf-POU3F4 regulates expression of the matrix protein genes aspein and prismalin-14 in pearl oyster (Pinctada fucata). FEBS J. 283(10), 1962-1978.

Garcia-Gasca, A., Ochoa-Baez, J.R.I., Betancourt, M., 1994. Microscopic anatomy of the mantle of the pearl oyster Pinctada magatianica (Hanley, 1856). J. Shellfish Res.13, 85-92.

Gasiunas, G., Barrangou, R., Horvath, P., Siksnys, V., 2012. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. PNAS 109, E2579-E2586.

Gervis, M.H., Sims, N.A., 1992. The biology and culture of pearl oysters (Bivalvia: Pteriidae). International Centre for Living Aquatic Resources Management (ICLARM) Studies and Reviews, 21: 49 pp.

Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E.,

Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., Regev, A., 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 29, 644-652.

Gratz, S.J., Cummings, A.M., Nguyen, J.N., Hamm, D.C., Donohue, L.K., Harrison, M.M., Wildonger, J., O'Connor-Giles, K.M., 2013. Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 4, 1029-1035.

Gregoire, C., 1972. Structure of the molluscan shell. In: Florkin, M., Scheer, B.T. (Eds.), Chemical Zoology. Academic Press, New York, 45-102 pp.

Gu, Z., Yin, X., Yu, C., Zhan, X., Shi, Y., Wang, A., 2016, Expression profiles of nine bio mineralization genes and their relationship with pearl nacre thickness in the pearl oyster, Pinctada fucata martensii Dunker. Aquaculture Res. 47, 1874-1884.

Gueguen, Y., Montagnani, C., Joubert, C., Marie, B., Belliard, C., Tayale, A., Fievet, J., Levy, P., Piquemal, D., Marin, F., Moullac, G.L., Ky, C.L., Garen, P., Lo, C., Saulnier, D., 2013. Characterization of molecular processes involved in the pearl formation in Pinctada margaritifera for a sustainable development of pearl farming industry in French Polynesia. In: Watabe, S., Maeyama, K., Nagasawa,

H. (Eds.), Recent advances in pearl research -Proceedings of the International Symposium on Pearl Research, 2011. 184-194 pp. Gyrd-Hansen, M., Meier, P., 2010. IAPs: from caspase inhibitors to modulators of NFκB, inflammation and cancer. Nat. Rev. Cancer. 10, 561-574.

Haszprunar, G., Wanninger, A., 2012. Molluscs. Curr. Biol. 22, 510-514.

Haynes, L.M., Moore, D.D., Kurt-Jones, E.A., Finberg, R.W., Anderson, L.J., Tripp, R.A., 2001. Involvement of toll-like receptor 4 in innate immunity to respiratory syncytial virus. J. Virol. 75, 10730-10737.

Herbst, R.S., 2004. Review of epidermal growth factor receptor biology. Int. J. Radiat. Oncol. Biol. Phys. 59, Suppl 2, 21-26.

Hoang, Q.Q., Sicheri, F., Howard, A.J., Yang, D.S., 2003. Bone recognition mechanism of porcine osteocalcin from crystal structure. Nature, 425(6961), 977-980.

Hongyan, M.A., Beili, Z., LEE, I.S., Zuolu, Q., Zhangfa, T., Shuheng, Q.I.U., 2007. Aragonite observed in the prismatic layer of seawater-cultured pearls. Front. Mater. Sci. China 1(3), 326-329.

Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., Li, Y., Fine, E.J., Wu, X., Shalem, O., Cradick, T.J., Marraffini, L.A., Bao, G., Zhang, F., 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827-832.

Huang, B., Zhang, L., Du, Y., Li, L., Qu, T., Meng, J., Zhang, G., 2014. Alternative splicing and immune response of Crassostrea gigas tumor necrosis factor receptor associated factor 3. Mol. Biol. Rep. 41, 6481-6491.

Huang, B., Zhang, L., Du, Y., Li, L., Tang, X., Zhang, G., 2016. Molecular characterization and functional analysis of tumor necrosis factor receptorassociated factor 2 in the Pacific oyster. Fish Shellfish Immunol. 48, 12-19.

Huang, D.X., Wei, G.J., He, M.X., 2015a. Cloning and gene expression of signal transducers and activators of transcription (STAT) homologue provide new insights into the immune response and nucleus graft of the pearl oyster Pinctada fucata. Fish Shellfish Immunol. 47, 847-854.

Huang, L., Li, G.Y., Mo, Z.L., Xiao, P., Li, J., Huang, J., 2015b. De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity. PLoS One 10(2), e0117642.

Huang, J., Li, S., Liu, Y., Liu, C., Xie, L., Zhang, R., 2018. Hemocytes in the extrapallial space of Pinctada fucata are involved in immunity and biomineralization. Sci. Rep. 8, 4657.

Huang, X.D., Liu W.G., Guan, Y.Y., Shi, Y., Wang, Q., Zhao, M., Wu, S.Z., He, M.X., 2012a. Molecular cloning, characterization and expression analysis of tumor necrosis factor receptor-associated factor 3 (TRAF3) from pearl oyster Pinctada fucata. Fish Shellfish Immunol. 33, 652-658.

Huang, X.D., Liu, W.G., Guan, Y.Y., Shi, Y., Wang, Q., Zhao, M., Wu, S.Z., He M.X., 2012b. Molecular cloning and characterization of class I NF-κB transcription factor from pearl oyster (Pinctada fucata). Fish Shellfish Immunol. 33:659-666.

Ikmi, A., McKinney, S.A., Delventhal, K.M., Gibson, M.C., 2014. TALEN and CRISPR/Cas9-mediated genome editing in the early branching metazoan Nematostella vectensis. Nat. Commun. 5, 5486.

Imler, J.L., Zheng, L., 2004. Biology of toll receptors: lessons from insects and mammals. J. Leukoc. Biol. 75, 18-26.

Inoue, N., Ishibashi, R., Ishikawa, T., Atsumi, T., Aoki, H., Komaru, A., 2011. Can the quality of pearls from the Japanese pearl oyster (Pinctada fucata) be explained by the gene expression patterns of the major shell matrix proteins in the pearl sac?. Mar. Biotechnol. (NY) 13(1), 48-55.

Ivanina, A.V., Borah, B.M., Vogts, A., Malik, I., Wu, J., Chin, A.R., Almarza, A.J., Kumta, P., Piontkivska, H., Beniash, E., Sokolova, I.M., 2018. Potential tradeoffs between biomineralization and immunity revealed by shell properties and gene expression profiles of two closely related Crassostrea species. J. Exp. Biol. 221, jeb183236.

Ivanina, A.V., Falfushynska, H.I., Beniash, E., Piontkivska, H., Sokolova, I.M., 2017. Biomineralization-related specialization of hemocytes and mantle tissues of the Pacific oyster Crassostrea gigas. J. Exp. Biol. 220, 3209-3221.

Jackson, A.P., Vincent, J.F.V., Turner, R.M., 1988. The mechanical design of nacre. Proc. R. Soc. Lond. B 23, 415-440.

Jasin, M., Haber, J.E., 2016. The democratization of gene editing: Insights from sitespecific cleavage and double-strand break repair. DNA Repair (Amst.) 44, 6-16.

Jiang, W., Bikard, D., Cox, D., Zhang, F., Marraffini, L.A., 2013. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233–239.

Jiao, Y., Tian, Q.L., Du, X.D., Wang, Q.H., Huang, R.L., Deng, Y.W., Shi, S.L., 2014. Molecular characterization of tumor necrosis factor receptor-associated factor (TRAF6) in pearl oyster Pinctada martensii. Genet. Mol. Res. 13(4), 10545-10555.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., Charpentier, E., 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821.

Jinek, M., Jiang, F., Taylor, D.W., Sternberg, S.H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., Kaplan, M., Iavarone, A.T., Charpentier, E., Nogales, E., Doudna, J.A., 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997.

Jones, D.B., Jerry, D.R., Forêt, S., Konovalov, D.A., Zenger, K.R., 2013. Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima. Marine Biotechnol. 15(6), 647–658.

Joubert, C., Piquemal, D., Marie, B., Manchon, L., Pierrat, F., Zanella-Cléon, I., Cochennec-Laureau, N., Gueguen, Y., Montagnani, C., 2010. Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization. BMC Genomics 11, 613.

Kamat, S., Su, X., Ballarini, R., Heuer, A.H., 2000. Structural basis for the fracture toughness of the shell of the conch Strombus gigas. Nature 405, 1036-1040.

Kanzok, S.M., Hoa, N.T., Bonizzoni, M., Luna, C., Huang, Y., Malacrida, A.R., Zheng, L., 2004. Origin of toll-like receptor-mediated innate immunity. J. Mol. Evol. 58, 442-448.

Kawakami, I.K., 1952. Studies on pearl formation. On the regeneration and transformation of the mantle piece in the pearl oyster. Mem Fac Kyushu Univ (Ser E) 1, 83-89.

Kawakami, I.K., 1953. Studies on pearl-sac formation II. The effect of water temperature and freshness of transplant on pearl-sac formation. Ann. Zool. Japan 26, 217-223.

Kiefert, L., McLaurin-Moreno, D., Arizmendi, E., Hanni, H.A., Elen, S., 2004. Cultured pearls from the Gulf of California, Mexico. Gems Gemmology 40, 26-38.

Kim, S., Kim, D., Cho, S.W., Kim, J., Kim, J.S., 2014. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012-1019.

Kinoshita, S., Wang, N., Inoue, H., Maeyama, K., Okamoto, K., Nagai, K., Kondo, H., Hirono, I., Asakawa, S., Watabe S., 2011. Deep sequencing of ESTs from nacreous and prismatic layer producing tissues and a screen for novel shell formation-related genes in the pearl oyster. PLoS ONE 6, e21238.

Kishore, P., Southgate, P.C., 2016. A detailed description of pearl-sac development in the black-lip pearl oyster, Pinctada margaritifera (Linnaeus 1758). Aquac. Res. 47, 2215-2226.

Kong, Y., Jing, G., Yan, Z., Li, C., Gong, N., Zhu, F., Li, D., Zhang, Y., Zheng, G., Wang, H., Xie, L., Zhang, R., 2009. Cloning and characterization of prisilkin-39, a novel matrix protein serving a dual role in the prismatic layer formation from the oyster Pinctada fucata. J. Biol. Chem. 284(16), 10841-10854.

Kotani, H., Taimatsu, K., Ohga, R., Ota, S., Kawahara, A., 2015. Efficient multiple genome modifications induced by the crRNAs, tracrRNA and Cas9 protein complex in zebrafish. PLoS One 10, e0128319.

Kripa, V., Mohamed, K.S., Appukuttan, K.K., Velayudhan, T.S., 2007. Production of Akoya pearls from the southwest coast of India. Aquaculture 262, 347-354.

Krishna, M., Narang, H., 2008. The complexity of mitogen-activated protein kinases (MAPKs) made simple. Cell Mol. Life Sci. 65, 3525-3544.

Kröger, N., Lorenz, S., Brunner, E., Sumper, M., 2002. Self-assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis. Science 298(5593), 584-586.

Ky, C., Broustal, F., Koua, M.S., Quillien, V., Beliaeff, B., 2018. Donor effect on cultured pearl nacre development and shell matrix gene expression in Pinctada margaritifera reared in different field sites. Aquac. Res. 49, 1934-1943.

Lee, J.S., Kwak, S.J., Kim, J., Kim, A.K., Noh, H.M., Kim, J.S., Yu, K., 2014. RNAguided genome editing in Drosophila with the purified Cas9 protein. G3 (Bethesda) 4, 1291-1295.

Lemaitre, B., Nicolas, E., Michaut, L., Reichhart, J.M., Hoffmann, J.A., 1996. The dorsoventral regulatory gene cassette spatzle/toll/cactus controls the potent antifungal response in Drosophila adults. Cell 86, 973-983.

Lewis, T.S., Shapiro, P.S., Ahn, N.G., 1998. Signal transduction through MAP kinase cascades. Adv. Canc. Res. 74, 49-139.

Li, C., Qu, T., Huang, B., Ji, P., Huang, W., Que, H., Li, L., Zhang, G., 2015. Cloning and characterization of a novel caspase-8-like gene in Crassostrea gigas. Fish Shellfish Immunol. 46, 486-492.

Li, H., Zhang, B., Fan, S., Liu, B., Su, J., Yu, D., 2017. Identification and Differential Expression of Bio mineralization Genes in the Mantle of Pearl Oyster Pinctada fucata. Marine Biotechnology 19(3): 266-276.

Li, S., Liu, C., Huang, J., Liu, Y., Zhang, S., Zheng, G., Xie, L., Zhang, R., 2016. Transcriptome and biomineralization responses of the pearl oyster Pinctada

fucata to elevated CO2 and temperature. Sci Rep. 6, 18943.

Li, S., Liu, Y., Huang, J., Zhan, A., Xie, L., Zhang, R., 2017. The receptor genes PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in the pearl oyster Pinctada fucata. Sci Rep. 7, 9219.

Li, S., Liu, Y., Liu, C., Huang, J., Zheng, G., Xie, L., 2016. Hemocytes participate in calcium carbonate crystal formation, transportation and shell regeneration in the pearl oyster Pinctada fucata. Fish Shellfish Immunol. 51, 263-270.

Liu, C., Li, S., Kong, J., Liu, Y., Wang, T., Xie, L., Zhang, R., 2015a. In-depth proteomic analysis of shell matrix proteins of Pinctada fucata. Sci Rep. 5, 17269.

Liu, J., Yang, D., Liu, S., Li, S., Xu, G., Zheng, G., Xie, L., Zhang, R., 2015b. Microarray: a global analysis of biomineralization related gene expression profiles during larval development in the pearl oyster, Pinctada fucata. BMC Genomics 16, 325.

Liu, X., Li, J., Xiang, L., 2012. The role of matrix proteins in the control of nacreous layer deposition during pearl formation. Proc. R. Soc. B. 279, 1000-1007.

Liu, X., Li, J., Xiang, L., Sun, J., Zheng, G., Zhang, G., Wang, H., Xie, L., Zhang, R., 2012. The role of matrix proteins in the control of nacreous layer deposition during pearl formation. Proc. Biol. Sci. 279, 1000-1007.

Livak, K.J., Schmittgen, T.D., 2001. Analysis of relative gene expression data using realtime quantitative PCR and the 2DDCT CT method. Methods 25, 402-408.

Love, M.I., Huber, W., Anders, S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550.

Lowenstam, H.A., 1981. Minerals formed by organisms. Science 211, 1126.

Lowenstam, H.A., Weiner, S., 1989. On Bio mineralization. Oxford University Press, London. pp. 7-23.

Luyer, J.L., Auffret, P., Quillien, V., Leclerc, N., Reisser, C., Vidal-Dupiol, J., Ky, C.L., 2019. Whole transcriptome sequencing and bio mineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera. BMC Genomics 20, 111.

Ma, H., Zhang, B., Lee, I.S., Qin, Z., Tong, Z., Qiu, S., 2007. Aragonite observed in the prismatic layer of seawater cultured pearls. Front. Mater. Sci. Chin. 1, 326-329.

Machii, A., 1968. Histological studies on the pearl sac formation. Bull. Nat. Pearl Res. Lab. 13, 1489-1539.

Machii, A., Nakahara, H., 1957. Studies on the histology of the pearl-sac, II. On the speed of the pearl-sac formation different by season. Bull. Nat. Pearl. Res. Lab. 2, 107-112.

Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E., Church, G.M., 2013. RNA-guided human genome engineering via Cas9. Science 339, 823-826.

Marie, B., Joubert, C., Tayalé, A., Zanella-Cléon, I., Belliard, C., Piquemal, D., Cochennec-Laureau, N., Marin, F., Gueguen, Y., Montagnani, C., 2012. Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell. Proc. Natl. Acad. Sci. 109, 20986-20991.

Marin, F., Luquet, G., 2004. Molluscan shell proteins. Comptes Rendus Palevol 3, 469-492.

Masaoka, T., Samata, T., Nogawa, C., Baba, H., Aoki, H., Kotaki, T., Nakagawa, A., Sato, M., Fujiwara, A., Kobayashi T., 2013. Shell matrix protein genes derived from donor expressed in pearl sac of Akoya pearl oysters (Pinctada fucata) under pearl culture. Aquaculture 384, 56-65.

Matlins, A., 2001. The pearl book: the definitive buying guide – how to select, buy, care for and enjoy pearls. Gemstone Press, 3-19 pp.

Mazzitelli, J.Y., Bonnafe, E., Klopp, C., Escudier, F., Geret, F., 2017. De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology 26, 127-140.

McGinty, E.L., Evans, B.S., Taylor, J.U., Jerry, D.R., 2010. Xenografts and pearl production in two pearl oyster species, P. maxima and P. margaritifera: effect on pearl quality and a key to understanding genetic contribution. Aquaculture 302, 175-181.

McGinty, E.L., Zenger, K.R., Jones, D.B., Jerry, D.R., 2012. Transcriptome analysis of biomineralisation-related genes within the pearl sac: host and donor oyster contribution. Mar. Genomics. 5, 27-33.

McGinty, E.L., Zenger, K.R., Taylor, J.U., Evans, B.S., Jerry, D.R., 2011. Diagnostic genetic markers unravel the interplay between host and donor oyster contribution in cultured pearl formation. Aquaculture 316, 20-24.

McIlwain, D.R., Berger, T., Mak, T.W., 2013. Caspase functions in cell death and disease. Cold Spring Harb Perspect Biol. 5, a008656.

Meyers, M.A., Lin, A.Y., Chen, P., Muyco, J., 2008. Mechanical strength of abalone nacre: role of the soft organic layer. J Mech Behav Biomed Mater 1, 76-85.

Miyamoto, H., Miyashita, T., Okushima, M., Nakano, S., Morita, T., Matsushiro, A., 1996. A carbonic anhydrase from the nacreous layer in oyster pearls. Proc. Natl. Acad. Sci. USA 93, 9657-9660.

Miyamoto, H., Miyoshi, F., Kohno, J., 2005. The carbonic anhydrase domain protein nacrein is expressed in the epithelial cells of the mantle and acts as a negative regulator in calcification in the mollusc Pinctada fucata. Zoolog. Sci. 22, 311-315.

Miyashita, T., Takagi, R., Miyamoto, H., Matsushiro, A., 2002. Identical carbonic anhydrase contributes to nacreous or prismatic layer formation in Pinctada fucata (Mollusca: Bivalvia). Veliger 45, 250-255.

Miyazaki, Y., Nishida, T., Aoki, H., Samata, T., 2010. Expression of genes responsible for biomineralization of Pinctada fucata during development. Comparative Biochemistry and Physiology, Part B 155, 241-248.

Mohamed, K.S., Kripa, V., Velayudhan, T.S., Appukuttan, K.K., 2006. Growth and biometric relationships of the pearl oyster, Pinctada fucata (Gould) on transplanting from the Gulf of Mannar to the Arabian Sea. Aquaculture Research 37, 725-741.

Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J., Almendros, C., 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740.

Montagnani, C., Marie, B., Marin, F., Belliard, C., Riquet, F., Tayalé, A., Zanella-Cléon, I., Fleury, E., Gueguen, Y., Piquemal, D., Cochennec-Laureau, N., 2011. Pmargpearlin is a matrix protein involved in nacre framework formation in the pearl oyster Pinctada margaritifera. Chembiochem. 12, 2033-2043.

Moreno-Mateos, M.A., Vejnar, C.E., Beaudoin, J.D., Fernandez, J.P., Mis, E.K, Khokha, M.K., Giraldez, A.J., 2015. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods. 12 (10): 982-988.

Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B., 2008. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621-628.

Mount, A.S., Wheeler, A.P., Paradkar, R.P., Snider, D., 2004. Hemocyte mediated shell mineralization in the eastern oyster. Science 304, 297-300.

Nagai, K., 2013. A history of the cultured pearl industry. Zoolog. Sci. 30(10), 783-93.

Nagai, K., 2013. The iridescence of pearls and the cultured-pearl industry. In S. Watabe, K. Maeyama, Nagasawa, H. (Eds.), Recent advances in pearl research (pp. 19– 35). Tokyo, Japan Terrapub.:

Nakahara, H & Machii, A, 1956, Studies on the histology of the pearl sac. I. Histological observations of pearl-sac tissues which produce normal and abnormal pearls. Bull. Natl. Pearl Res. Lab. 1, 10-13 (in Japanese with English abstract).

Nakahara, H., Bevelander, G., 1971. The formation and growth of the prismatic layer of Pinctada radiata. Calcif. Tissue Res. 7, 31-45.

Nishimasu, H., Ran, F.A.A., Hsu, P.D.D., Konermann, S., Shehata, S.I.I., Dohmae, N., Ishitani, R., Zhang, F., Nureki, O., 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949.

Niu Y, Shen, B., Cui, Y., Chen, Y., Wang, J., Wang, L., Kang, Y., Zhao, X., Si, W., Li, W., Xiang, A.P., Zhou, J., Guo, X., Bi, Y., Si, C., Hu, B., Dong, G., Wang, H., Zhou, Z., Li, T., Tan, T., Pu, X., Wang, F., Ji, S., Zhou, Q., Huang, X., Ji, W., Sha, J., 2014. Generation of gene-modified cynomolgus monkey via Cas9/RNAmediated gene targeting in one-cell embryos. Cell 156, 836-843.

Nogawa, C., Obara, M., Ozawa, M., Sato, A., Watanabe, A., Yamazaki, R., Yamada, D., Akiniwa, K., Samata, T., 2008. Characterization of organic matrix components of pearl oyster, Pinctada fucata and their implications in shell formation Frontiers of Material Science in China, 2: 156. of marine bivalves. Springer, Dordrecht, pp 73-93.

Nudelman, F., Gotliv, B.M., Addadi, L., Weiner, S., 2006. Mollusk shell formation: Mapping the distribution of organic matrix components underlying a single aragonitic tablet in nacre. J. Structural Biology 153, 176-187.

Ohashi, K., Burkart, V., Flohé, S., Kolb, H., 2000. Cutting edge: heat shock protein 60 is a putative endogenous ligand of the toll-like receptor-4 complex. J. Immunol. 164, 558-561.

Ohmori, F., Kinoshita, S., Funabara, D., Koyama, H., Nagai, K., Maeyama, K., Okamoto, K., Asakawa, S., Watabe, S., 2018. Novel isoforms of N16 and N19 families implicated for the nacreous layer formation in the pearl oyster Pinctada fucata. Mar. Biotechnol. 20, 155-167.

Okumura, T., Suzuki, M., Nagasawa, H., Kogure, T., 2012. Microstructural variation of biogenic calcite with intracrystalline organic macromolecules. Cryst. Growth Des. 12, 224-230.

Ota, S., Hisano, Y., Muraki, M., Hoshijima, K., Dahlem, T.J., Grunwald, D.J., Okada, Y., Kawahara, A., 2013. Efficient identification of TALEN-mediated genome modifications using heteroduplex mobility assays. Genes Cells 18, 450-458.

Paine, M.L., Snead, M.L., 1997. Protein interactions during assembly of the enamel organic extracellular matrix. J. Bone Miner. Res. 12(2), 221-227.

Pattanayak, V., Lin, S., Guilinger, J.P., Ma, E., Doudna, J.A., Liu, D.R., 2013. Highthroughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 31, 839-843.

Pauley, G.B., Heaton, L.H., 1969. Experimental wound repair in the freshwater mussel Anodonta oregonensis. J. Invertebrate Pathol. 13, 241-249.

Pe´rez-Huerta, A., Cuif, J., Dauphin, Y., Cusack, M., 2014. Crystallography of calcite in pearls. European Journal of Mineralogy 26, 507-516.

Peng, K., Liu, F., Wang, J., Hong, Y., 2018. Calmodulin highly expressed during the formation of pearl sac in freshwater pearl mussel (Hyriopsis schlegelii). Thalassas: An International Journal of Marine Sciences 34(1), 219.

Perry, K.J., Henry, J.Q., 2015. CRISPR/Cas9-mediated genome modification in the Mollusc, Crepidula fornicate. Genesis 53, 237-244.

Petit, H., Davis, W.L., Jones, R.G., Hagler, H.K., 1980. Morphological studies on the calcification process in the fresh-water mussel Amblema. Tissue Cell 12, 13-28.

Pimentel, H., Bray, N.L., Puente, S., Melsted, P., Pachter, L., 2017. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat. Methods 14(7), 687-690.

Qian, X., Ba, Y., Zhuang, Q.F., Zhong, G.F., 2014. RNA-seq technology and its application in fish transcriptomics. OMICS 18, 98-110.

Qu, F., Xiang, Z., Xiao, S., Wang, F., Li, J., Zhang, Y, Qin, Y., Yu, Z., 2017. c-Jun Nterminal kinase (JNK) is involved in immune defense against bacterial infection in Crassostrea hongkongensis. Dev. Comp. Immunol. 67, 77-85.

Qu, F., Xiang, Z., Zhang, Y., Li, J., Xiao, S., Zhang, Y., Mao, F., Ma, H., Yu, Z., 2016. A novel p38 MAPK indentified from Crassostrea hongkongensis and its involvement in host response to immune challenges. Mol. Immunol. 79, 113-124.

Qu, T., Huang, B., Zhang, L., Li, L., Xu, L., Huang, W., Li, C., Du, Y., Zhang, G., 2014. Identification and functional characterization of two executioner caspases in Crassostrea gigas. PLoS One 9, e89040.

Riedl, S.J., Shi, Y., 2004. Molecular mechanisms of caspase regulation during apoptosis. Nat. Rev. Mol. Cell Biol. 5, 897-907.

Ries, J. B., Cohen, A.L., McCorkle, D.C., 2009. Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. Geology 37, 1131-1134.

Roach, J.C., Glusman, G., Rowen, L., Kaur, A., Purcell, M.K., Smith, K.D, Hood, L.E., Aderem, A., 2005. The evolution of vertebrate toll-like receptors. Proc. Natl. Acad. Sci. 102, 9577-9582.

Rouet, P., Smih, F., Jasin, M., 1994. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol. Cell. Biol. 14, 8096-8106.

Rudin, N., Sugarman, E., Haber, J.E., 1989. Genetic and physical analysis of doublestrand break repair and recombination in Saccharomyces cerevisiae. Genetics 122, 519-534.

Ruiz-Rubio, H., Acosta-Salmón, H., Olivera, A., Southgate, P.C., Rangel-Dávalos, C., 2006. The influence of culture method and culture period on quality of half-pearls (‘mabé’) from the winged pearl oyster Pteria sterna, Gould, 1851. Aquaculture 254, 269-274.

Runnegar, B., 1985. Shell microstructures of Cambrian mollusc replicated by phosphate. Alcheringa 9, 245-257.

Saleuddin, A.S.M., Petit, H.P., 1983. The mode of formation and the structure of the periostracum. In: Saleuddin ASM, Wilbur KM (eds). Mollusca Vol. 4, Physiology Part 1. Academic Press, New York, 199–234.

Samata, T., Hayashi, N., Kono, M., Hasegawa, K., Horita, C., Akera, S., 1999. A new matrix protein family related to the nacreous layer formation of Pinctada fucata. FEBS Lett. 462, 225-229.

Saruwatari, K., Matsui, T., Mukai, H., Nagasawa, H., Kogure, T., 2009. Nucleation and growth of aragonite crystals at the growth front of nacres in pearl oyster, Pinctada fucata. Biomaterials 30(16), 3028–3034.

Schmitt, N., Marin, F., Thomas, J., Plasseraud, L., Demoy-Schneider, M., 2018. Pearl grafting: Tracking the biological origin of nuclei by straightforward immunological methods. Aquac. Res. 49, 692-700.

Scoones, R.J.S., 1990. Research on practices in the Western Australian cultured pearl industry. Fishing industry research project and development council project. NP12. July 1987 to June 1990. Broome Pearl Pty. Ltd. And MG Kailis Group of Companies. 74 pp.

Scoones, S.J.R., 1996. The development of the pearl sac in Pinctada maxima (Jameson,1901) (Lamellibranchia: Pteriidae) and the implications for the quality of cultured pearls. MSc Thesis, The University of Western Australia. Perth, 89 p. See N. Landman et al., Pearls (2001).

Shah, S.A., Erdmann, S., Mojica, F.J., Garrett, R.A., 2013. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 10, 891-899.

Shen, X., Belcher, A.M., Hansma, P.K., Stucky, G.D., Morse, D.E., 1997. (Title). J. Biol. Chem. 272, 32472-32481.

Shigeta, M., Sakane, Y., Iida, M., Suzuki, M., Kashiwagi, K., Kashiwagi, A., Fujii, S., Yamamoto, T., Suzuki, K.T., 2016. Rapid and efficient analysis of gene function using CRISPRCas9 in Xenopus tropicalis founders. Genes to Cells 21, 755-771.

Shuman, S., Glickman, M.S., 2007. Bacterial DNA repair by non-homologous end joining. Nat. Rev. Microbiol. 5, 852-861.

Silke, J., Meier, P., 2013. Inhibitor of apoptosis (IAP) proteins–modulators of cell death and inflammation. Cold Spring Harb Perspect Biol. 5, a008730.

Skelton, P.W., Benton, M.J., 1993. Mollusca: rostroconchia, scaphopoda and bivalvia. In: Benton M.J. (Eds.), The Fossil Record 2. Chapman & Hall, London: 237-263 pp.

Slaymaker, I.M., Gao, L., Zetsche, B., Scott, D.A., Yan, W.X., Zhang, F., 2016. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84-88.

Sminia, T., Pietersma, K., Scheerboom, J.E.M., 1973. Histological and ultrastructural observations on wound healing in the freshwater pulmonate Lymnaea stagnalis. Z. Zellforsch. 41, 561-573.

Song, L.S., Wang, L.L., Zhang, H., Wang, M.Q., 2015. The immune system and its modulation mechanism in scallop. Fish Shellfish Immunol. 46, 65-78. Southgate, P.C., Lucas, J.S., 2008. The pearl oyster. Oxford: Elsevier, 544 p.

Strack, E., 2008. Introduction. In: Southgate, P.C., Lucas, J.S. (Eds.), The pearl oyster. Elsevier Press, Oxford, 1-35 pp.

Sudo, S., Fujikawa, T., Nagakura, T., Ohkubo, T., Sakaguchi, K., Tanaka, M., Nakashima, K., Takahashi, T., 1997. Structures of mollusk shell framework proteins. Nature 387, 563-564.

Sun, J., Xu, G., Wang, Z., Li, Q., Cui, Y., Xie, L., Zhang, R., 2015. The effect of NF-κB signalling pathway on expression and regulation of nacrein in pearl oyster, Pinctada fucata. PLoS One 10(7), e0131711.

Sun, L., Huan, P., Wang, H., Liu, F., Liu, B., 2014. An EGFR gene of the Pacific oyster Crassostrea gigas functions in wound healing and promotes cell proliferation. Mol. Biol. Rep. 41(5), 2757-2765.

Suzuki, M., Murayama, E., Inoue, H., Ozaki, N., Tohse, H., Kogure, T., Nagasawa, H., 2004. Characterization of prismalin-14, a novel matrix protein from the prismatic layer of the Japanese pearl oyster (Pinctada fucata). Biochem. J. 382, 205-213.

Suzuki, M., Nagasawa, H., 2013. Mollusk shell structures and their formation mechanism. Can. J. Zool. 91, 349-366.

Suzuki, M., Saruwatari, K., Kogure, T., Yamamoto, Y., Nishimura, T., Kato, T., Nagasawa, H., 2009. An acidic matrix protein, Pif, is a key macromolecule for nacre formation. Science 325, 1388–1390.

Suzuki, T., Funakoshi, S. 1992. Isolation and a fibronectin-like molecule from a marine bivalve, Pinctada fucata, and its secretion by amebocytes. Zool. Sci. 9, 541-550.

Suzuki, T., Yoshinaka, R., Mizuta, S., Funakoshi, S., Wada, K., 1991. Extracellular matrix formation by amebocytes during epithelial regeneration in the pearl oyster Pinctada fucata. Cell Tissue Res. 266, 75-82.

Takeda, K., Akira, S., 2005. Toll-like receptors in innate immunity. Int. Immunol. 17, 1-14.

Takeuchi, T., Endo, K., 2006. Biphasic and dually coordinated expression of the genes encoding major shell matrix proteins in the pearl oyster Pinctada fucata. Mar. Biotechnology 8, 52-61.

Takeuchi, T., Kawashima, T., Koyanagi, R., Gyoja, F., Tanaka, M., Ikuta, T., Shoguchi, E., Fujiwara, M., Shinzato, C., Hisata, K., Fujie, M., Usami, T., Nagai, K., Maeyama, K., Okamoto, K., Aoki, H., Ishikawa, T., Masaoka, T., Fujiwara, A., Endo, K., Endo, H., Nagasawa, H., Kinoshita, S., Asakawa, S., Watabe, S., Satoh, N., 2012. Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res. 19(2), 117-130.

Takeuchi, T., Koyanagi, R., Gyoja, F., Kanda, M., Hisata, K., Fujie, M., Goto, H., Yamasaki, S., Nagai, K., Morino, Y., Miyamoto, H., Endo, K., Endo, H., Nagasawa, H., Kinoshita, S., Asakawa, S., Watabe, S., Satoh, N., Kawashima, T., 2016. Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle. Zoological Lett. 2, 3.

Takeuchi, T., Sarashina, I., Iijima, M., Endo, K., 2008. In vitro regulation of CaCO3 crystal polymorphism by the highly acidic molluscan shell protein aspein. FEBS Lett. 582, 591-596.

Tanguy, A., Guo, X., Ford, S.E., 2004. Discovery of genes expressed in response to Perkinsus marinus challenge in Eastern (Crassostrea virginica) and Pacific (C. gigas) oysters. Gene 338,121-131.

Tayale, A., Gueguen, Y., Treguier, C., Le Grand J.L., Cochennec-Laureau, N., Montagnani, C., Ky, C.L., 2012. Evidence of donor effect on cultured pearl quality from a duplicated grafting experiment on Pinctada margaritifera using wild donors. Aquat. Living Resour. 25, 269-280.

Taylor, J.D., Kennedy, W.J., 1969. The influence of the periostracum on the shell structure of bivalve molluscs. Calcif. Tissue Res. 3, 274-283.

Taylor, J.J., 2002. Producing golden and silver south sea pearls from Indonesian hatchery reared Pinctada maxima, in: World Aquaculture 2002 Book of Abstracts. Beijing, P. R. Of China, Apr 23-27, World Aquaculture Society, Baton Rouge LA.

Taylor, J.J., Strack, E., 2008. Pearl production. In: Southgate PC, Lucas JS, editors. The pearl oyster. Amsterdam: Elsevier, p. 273-302.

Torrey, R.D., Sheung, B., 2008. The pearl market. In: Southgate, P.C., Lucas, J.S., (Eds.). The pearl oyster. Elsevier, Amsterdam, 357-365 pp.

Tsan, M.F., Gao, B., 2004. Heat shock protein and innate immunity. Cell Mol. Immunol. 1(4), 274-279.

Van Noort, J.M., Bsibsi, M., Nacken, P., Gerritsen, W.H., Amor, S., 2012. The link between small heat shock proteins and the immune system. Int. J. Biochem. Cell Biol. 44, 1670-1679.

Varshney, G.K., Pei, W., LaFave, M.C., Idol, J., Xu, L., Gallardo, V., Carrington, B., Bishop, K., Jones, M., Li, M., Harper, U., Huang, S.C., Prakash, A., Chen, W., Sood, R., Ledin, J., Burgess, S.M., 2015. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 25, 1030-1042.

Vejnar C.E., Moreno-Mateos M.A., Cifuentes, D., Bazzini, A.A., Giraldez, A.J., 2016 Optimized CRISPR–Cas9 system for genome editing in zebrafish. Cold Spring Harb. Protoc. doi: 10.1101/pdb.prot086850.

Velayudhan, T.S., Chellam, A., Dharmaraj, S., Victor, A.C.C., Alagarswami, K., 1994. Histology of the mantle and pearl-sac formation in the Indian pearl oyster Pinctada fucata (Gould). Indian J Fish. 41(2), 70-75.

Wada, K., 1968. Mechanism of growth of nacre in bivalvia. Bull. Natl. Pearl Res. Lab. 13, 1561–1596.

Wada, K., Komaru, A., 1996. Color and weight of pearls produced by grafting the mantle tissue from a selected population for white shell color of the Japanese pearl oyster Pinctada fucata martensii (Dunker). Aquaculture 142(1), 25-32.

Wada, K.T., Temkin, I., 2008. Taxonomy and Phylogeny. In: Southgate, P.C., Lucas, J.S. (Eds.). The Pearl Oyster. Elsvier, Amsterdam, 37-66 pp.

Waller, T.R., 1980. SEM of the shell and mantle in the order Arcoida (Mollusca, Bivalvia). Smithson. Contrib. Zool. No. 313. pp. 1–58.

Wang, L., Song, X., Song, L., 2018a. The oyster immunity. Dev. and Comp. Immunol. 80, 99-118.

Wang, M., Wang, L., Jia, Z., Yi, Q., Song, L., 2018b. The various components implied the diversified toll-like receptor (TLR) signaling pathway in mollusk Chlamys farreri. Fish Shellfish Immun. 74, 205-212.

Wang, M., Yang, J., Zhou, Z., Qiu, L., Wang, L., Zhang, H., Gao, Y., Wang, X., Zhang, L., Zhao, J., Song, L., 2011. A primitive toll-like receptor signaling pathway in mollusk Zhikong scallop Chlamys farreri. Dev. Comp. Immunol. 35, 511-520.

Wang, M.Q., Wang, L.L., Guo, Y., Sun, R., Yue, F., Yi, Q.L., Song, L., 2015. The broad pattern recognition spectrum of the toll-like receptor in mollusk Zhikong scallop Chlamys farreri. Dev. Comp. Immunol. 52, 192-201.

Wang, N., Kinoshita, S., Riho, C., Maeyama, K., Nagai, K., Watabe, S., 2009. Quantitative expression analysis of nacreous shell matrix protein genes in the process of pearl biogenesis. Comp. Biochem. Physiol. B 154, 346-350.

Wang, W., Wu, Y., Lei, Q., Liang, H., Deng, Y., 2017. Deep transcriptome profiling sheds light on key players in nucleus implantation induced immune response in the pearl oyster Pinctada martensii. Fish Shellfish Immunol. 69, 67-77.

Wang, W., Zhang, T., Wang, L., Xu, J., Li, M., Zhang, A., Qiu, L., Song, L., 2016a. A new non-phagocytic TLR6 with broad recognition ligands from Pacific oyster Crassostrea gigas. Dev. Comp. Immunol. 65, 182-190. Ward, F., 1995. Pearls. Gem Book Publishers, 64 pp.

Watabe, N., 1965. Studies on shell formation. XI crystal–matrix relationships in the inner layer of mollusk shells. J. Ultrastruct. Res. 12, 351-370.

Watabe, N., 1983. Shell repair. In: Saleuddin ASM, Wilbur KM (eds). Mollusca Vol. 4, Physiology Part 1. Academic Press, New York, 289-316.

Wei, J., Liu, B., Fan, S., Li, H., Chen, M., Zhang, B., Su, J., Meng, Z., Yu, D., 2017a. Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis. Fish Shellfish Immunol. 62, 247-256.

Wei, J., Fan, S., Liu, B., Zhang, B., Su, J., Yu, D., 2017b. Transcriptome analysis of the immune reaction of the pearl oyster Pinctada fucata to xenograft from Pinctada maxima. Fish Shellfish Immunol. 67, 331-345.

Wu, Y., Liang, H., Wang, Z., Lei, Q., Xia, L., 2017. A novel toll-like receptor from the pearl oyster Pinctada fucata martensii is induced in response to stress. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 214, 19-26.

Xiang, Z., Qu, F., Qi, L., Zhang, Y., Tong, Y., Yu, Z., 2013. Cloning, characterization and expression analysis of a caspase-8 like gene from the Hong Kong oyster, Crassostrea hongkongensis. Fish Shellfish Immunol. 35, 1797-1803.

Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C.Y., Wei, L., 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39, W316-W322.

Xie, L., Zhang, R., 2009. Cloning and characterization of prisilkin-39, a novel matrix protein serving a dual role in the prismatic layer formation from the oyster Pinctada fucata. J. Biol. Chem. 284, 10841-10854.

Xin, L.S., Wang, M.Q., Zhang, H., Li, M.J., Wang, H., Wang, L.L., Song, L., 2016. The categorization and mutual modulation of expanded MyD88s in Crassostrea gigas. Fish Shellfish Immunol. 54, 118-127.

Yan, F., Jiao, Y., Deng, Y., Du, X., Huang, R., Wang, Q., Chen, W., 2014. Tissue inhibitor of metalloproteinase gene from pearl oyster Pinctada martensii participates in nacre formation. Biochem. Biophys. Res. Commun. 450, 300-305.

Yano, M., Nagai, K., Morimoto, K., Miyamoto, H., 2007. A novel nacre protein N19 in the pearl oyster Pinctada fucata. Biochem. Biophys. Res. Commun. 326, 158-163.

Yano, M., Nagain, K., Morimoto, K., Miyamoto, H., 2006. Shematrin: a family of glycine-rich structural proteins in the shell of the pearl oyster Pinctada fucata. Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 144, 254-262.

Yukihira, H., Klumpp, D.W., 2006. The pearl oysters, Pinctada maxima and Pinctada margaritifera, respond in different ways to culture in dissimilar environments. Aquaculture 252(2-4), 208-224.

Zhang, C., Zhang, R., 2006. Matrix proteins in the outer shells of molluscs. Mar. Biotechnology 8, 572-586.

Zhang, H., Huang, X., Shi, Y., Liu, W., He, M., 2018. Identification and analysis of an MKK4 homologue in response to the nucleus grafting operation and antigens in the pearl oyster, Pinctada fucata. Fish Shellfish Immunol. 73, 279-287.

Zhang, L.L., Li, L., Guo, X.M., Litman, G.W., Dishaw, L.J., Zhang, G.F., 2015. Massive expansion and functional divergence of innate immune genes in a protostome. Sci. Rep. 5, 8693.

Zhang, Y., He, X., Yu, F., Xiang, Z., Li, J., Thorpe, K.L., Yu, Z., 2013. Characteristic and functional analysis of toll-like receptors (TLRs) in the lophotrocozoan, Crassostrea gigas, reveals ancient origin of TLR-mediated innate immunity. PLoS One 8, e76464.

Zhang, Y., Xie, L., Meng, Q., Jiang, T., Pu, R., Chen, L., Zhang, R., 2003. A novel matrix protein participating in the nacre framework formation of pearl oyster Pinctada fucata. Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 135, 565-573.

Zhang, Y.L., Dong, C., 2005. MAP kinases in immune responses. Cell Mol. Immunol. 2(1), 20-27.

Zhao, M., He, M., Huang, X., Wang, Q., 2014. A homeodomain transcription factor gene, PfMSX, activates expression of pif gene in the pearl oyster Pinctada fucata. PLoS One 9(8), e103830.

Zhao, M., Shi, Y., He, M., Huang, X., Wang, Q., 2016. PfSMAD4 plays a role in biomineralization and can transduce bone morphogenetic protein-2 signals in the pearl oyster Pinctada fucata. BMC Dev. Biol. 16, 9.

Zhao, X., Wang, Q., Jiao, Y., Huang, R., Deng, Y., Wang, H., Du, X., 2012. Identification of genes potentially related to biomineralization and immunity by transcriptome analysis of pearl sac in pearl oyster Pinctada martensii. Mar. Biotechnol. (NY) 14, 730-739.

Zheng, Q., Wang, X.J., 2008. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 36, W358-W363.

Zheng, X., Cheng, M., Xiang, L., Liang, J., Xie, L., Zhang, R., 2015. The AP-1 transcription factor homolog Pf-AP-1 activates transcription of multiple biomineral proteins and potentially participates in Pinctada fucata biomineralization. Sci. Rep. 5, 14408.

Zhu, C., Southgate, P., Li, T., 2019. Production of pearls. In: Smaal, A. et al (eds) Goods and services.

Zhu, W., Fan, S., Huang, G., Zhang, D., Liu, B., Bi, X., Yu, D., 2015. Highly expressed EGFR in pearl sac may facilitate the pearl formation in the pearl oyster, Pinctada fucata. Gene 566(2), 201-211.

Zou, J., Wang, R., Li, R., Kong, Y., Wang, J., Ning, X., Zhang, L., Wang, S., Hu, X., Bao, Z., 2015. The genome-wide identification of mitogen-activated protein kinase kinase (MKK) genes in Yesso scallop Patinopecten yessoensis and their expression responses to bacteria challenges. Fish Shellfish Immunol. 45, 901-911.

参考文献をもっと見る