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Identification and Differential Expression of Biomineralization Genes in the Mantle of Pearl Oyster Pinctada fucata

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Abstract

A series of proteins are involved in shell formation of the pearl oyster Pinctada fucata, but the involved mechanisms and the relative expression levels of these proteins have not been elucidated. In this study, we sequenced and characterized the transcriptome of P. fucata mantle tissue. A total of 100,679 unique transcripts were assembled, 43687 Unigenes were annotated, and 48654 CDSs were determined. Of these, GO annotated 16353 Unigenes, COG defined 11585 unigenes into 25 categories, and KEGG sorted 25053 unigenes into 258 pathways. In total, 67 biomineralization-related genes were identified, of which 23 genes were newly described in P. fucata. These genes included ones that expressed shell matrix proteins, regulatory factors, and uncharacterized genes. Differential expression of these 67 genes and 9 other biomineralization-related genes was confirmed using qPCR. Of the 8 nacreous layer-related genes, MSI60 (774.00) was expressed at a much higher level than the others. KRMP2-4 and MSI31 were the most highly expressed of the 13 prismatic layer-related genes and KRMP2 was expressed at nearly 10000 times of the level of the 18S gene. For genes related to both layers, shematrin 2 (3977.84), nacrein (2404.75), PFMG 10 (2113.93), and PFMG 4 (1015.89) were highly expressed, and ferritin-like protein (877.54) and PFMG 8 (516.48) were highly expressed among the 16 undefined genes. The expression levels of regulation factors were generally low, and the highest level was 324.09 (EF-hand) and the lowest occurred in the BMP and wnt families. The expression levels of the prismatic matrix proteins were much higher than those of nacreous ones, consistent with a thicker prismatic layer. MSI60 and nacrein are likely the main components of the nacreous layer, and KRMP2-4, MSI31, shematrin 2, and PFMG 10 gene products are the main components of the prismatic layer. This is the first report of transient expression levels of a large number of biomineralization-related genes at the same time in mantle tissue of P. fucata. These findings provide a novel perspective to understand the molecular mechanisms of shell formation and will be beneficial to genetic improvement of P. fucata for the production of high-quality pearls as well.

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Reference

  • Addadi L, Winer S (1997) A pavement of pearl. Nature 389:912–913

    Article  CAS  Google Scholar 

  • Baeuerlein E, Epple M, Behrens P (2007) Handbook of biomineralization. Wiley, Weinheima

    Book  Google Scholar 

  • Conesa A, Gotz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Fang D, Xu G, Hu Y, Pan C, Xie L, Zhang R (2011) Identification of genes directly involved in shell formation and their functions in pearl oyster, Pinctada fucata. PLoS One 6(7):e21860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang J, Zhang C, Ma Z, Xie L, Zhang R (2007) A novel extracellular EF-hand protein involved in the shell formation of pearl oyster. Biochim Biophys Acta 1770:1037–1044

    Article  CAS  PubMed  Google Scholar 

  • Huang XD, Zhao M, Liu WG, Guan YY, Shi Y, Wang Q, Wu SZ, He MX (2012) Gigabase-scale transcriptome analysis on four species of pearl oysters. Mar Biotechnol 15:253–264

    Article  PubMed  Google Scholar 

  • Iseli C, Jongeneel C, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999:138–148

  • Jackson D, McDougall C, Green K, Simpson F, Worheide G (2006) A rapidly evolving secretome builds and patterns a sea shell. BMC Biol 4:40

    Article  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  CAS  PubMed  Google Scholar 

  • Kinoshita S, Ning W, Inoue H, Maeyama K, Okamoto K, Nagai K (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(6):e21238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kong Y, Jing G, Yan Z, Li C, Gong N (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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu HL, Liu SF, Ge YJ, Liu J, Wang XY, Xie LP, Zhang RQ, Wang Z (2007) Identification and characterization of a biomineralization related gene PFMG1 highly expressed in the mantle of Pinctada fucata. Biochemistry 46:844–851

    Article  CAS  PubMed  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using realtime quantitative PCR and 2 (−Delta Delta C(T)) method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • Ma Z, Huang J, Sun J, Wang G, Li C (2007) A novel extrapallial fluid protein controls the morphology of nacre lamellae in the pearl oyster, Pinctada fucata. J Biol Chem 282:23253–23263

    Article  CAS  PubMed  Google Scholar 

  • Marin F, Luquet G (2004) Molluscan shell proteins. Comptes Rendus Palevol 3:469–492

    Article  Google Scholar 

  • Miyamoto H, Miyashita T, Okushima M, Nakano S, Morita T (1996) A carbonic anhydrase from the nacreous layer in oyster pearls. Proc Natl Acad Sci U S A 93:9657–9660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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. Zool Sci 22:311–315

    Article  CAS  PubMed  Google Scholar 

  • Miyashita T, Takagi Y, Miyamoto H, Matsushiro A (2000) Complementary DNA cloning and characterization of Pearlin, a new class of matrix protein in the nacreous layer of oyster pearls. Mar Biotechnol 2:409–418

    CAS  PubMed  Google Scholar 

  • Miyazaki Y, Nishida T, Aoki H, Samata T (2010) Expression of genes responsible for biomineralization of Pinctada fucata during development. Comp Biochem Physiol B 155:241–224

    Article  PubMed  Google Scholar 

  • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27:29–34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ozaki N, Sakuda S, Nagasawa H (2001) Isolation and some characterization of an acidic polysaccharide with anti-calcification activity from coccoliths of a marine alga, Pleurochrysis carterae. Biosci Biotechnol Biochem 65:2330–2333

    Article  CAS  PubMed  Google Scholar 

  • Pertea G, Huang X, Liang F (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19(5):651–652

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Shi Y, Yu C, Gu Z, Zhan X, Wang Y, Wang A, Wang Y (2012) Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes. Mar Biotechnol 15:175–187

    Article  PubMed  Google Scholar 

  • Shi Y, Zheng X, Zhan X, Wang A, Gu Z (2016) cDNA microarray analysis revealing candidate biomineralization genes of the pearl oyster, Pinctada fucata martensii. Mar Biotechnol 18:336–348

    Article  CAS  PubMed  Google Scholar 

  • Sigel H, Sigel A, Sigel RKO (2008) Biomineralization: from nature to application. Wiley, Chichester

    Book  Google Scholar 

  • Song D, Ding Y, Pang Y, Sun D (2006) Flourier transformation infrared spectroscopy study on the prismatic and nacreous layers of the shell. J Dalian Maritime Univ 32(4):110–113

    CAS  Google Scholar 

  • Sudo S, Fujikawa T, Nagakura T, Tanaka M, Nakashima K, Takahashi T (1997) Structure of mollusk shell framework proteins. Nature 387:563–564

    Article  CAS  PubMed  Google Scholar 

  • Suzuki M, Murayama E, Inoue H, Ozaki N, Tohse 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suzuki M, Sakuda S, Nagasawa H (2007) Identification of chitn in the prismatic layer of the shell and a chitin synthase gene from the japanese pearl oyster, Pinctada fucata. Biosci Biotechnol Biochem 71(7):1735–1744

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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 Biotechnol 8:52–61

    Article  CAS  PubMed  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    Article  PubMed  PubMed Central  Google Scholar 

  • Treccani L, Mann K, Heinemann F, Fritz M (2006) Perlwapin, an abalone nacre protein with three four-disulfide core (whey acidic protein) domins, inhibits the growth of calcium carbonate crystals. Biophys J 91:2601–2608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsukamoto D, Sarashina I, Endo K (2004) Structure and expression of an unusually acidic matrix protein of pearl oyster shells. Biochem Biophys Res Commun 320:1175–1180

    Article  CAS  PubMed  Google Scholar 

  • Weiss IM, Schönitzer W, Eichner N, Sumper M (2006) The chitin synthase involved in marine bivalve mollusk shell formation contains a myosin domain. FEBS Lett 580:1846–1852

    Article  CAS  PubMed  Google Scholar 

  • Yano M, Nagai K, Morimoto K, Miyamoto H (2007) A novel nacre protein N19 in the pearl oyster Pinctada fucata. Biochem Biophys Res Commun 362:158–163

    Article  CAS  PubMed  Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhan X, Gu ZF, Yu CC, Wen HY, Shi YH, Wang AM (2015) Expressed sequence tags 454 sequencing and biomineralization gene expression for pearl sac of the pearl oyster, Pinctada fucata martensii. Aquac Res 46:745–758

    Article  CAS  Google Scholar 

  • Zhang C, Zhang R (2006) Matrix proteins in the outer shells of molluscs. Mar Biotechnol (NY) 8:572–586

    Article  Google Scholar 

  • Zhang Y, Xie L, Meng Q, Jiang T, Pu R (2003a) 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

    Article  PubMed  Google Scholar 

  • Zhang Y, Meng Q, Jiang T, Wang H, Xie L, Zhang R (2003b) A novel ferritin subunit involved in shell formation from the pearl oyster (Pinctada fucata). Comp Biochem Physiol B: Biochem Mol Biol 135(1):43–54

    Article  Google Scholar 

  • Zhang C, Xie L, Huang J, Liu X, Zhang R (2006) A novel matrix protein family participating in the prismatic layer framework formation of pearl oyster, Pinctada fucata. Biochem Biophys Res Commun 344(3):735–740

    Article  CAS  PubMed  Google Scholar 

  • 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 14:730–739

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the Earmarked Fund for China Agriculture Research System (CARS-48), the National Natural Science Foundation of China (31372525), and the Special Fund for Marine Fisheries Research and Extension of Guangdong Province (Z2014006, Z2015009, and Z2015010).

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Authors and Affiliations

  1. Qinzhou University, Qinzhou, Guangxi, 535011, China

    Haimei Li & Dahui Yu

  2. Shanghai Ocean University, Shanghai, 201306, China

    Haimei Li & Dahui Yu

  3. Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture, Guangzhou, Guangdong, 510300, China

    Haimei Li, Bo Zhang, Sigang Fan, Baosuo Liu, Jiaqi Su & Dahui Yu

  4. South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, Guangdong, 510300, China

    Dahui Yu

  5. South China Sea Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510300, China

    Dahui Yu

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  1. Haimei Li
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  4. Baosuo Liu
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Correspondence to Dahui Yu.

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Additional file 1

KEGG pathway annotation of unigenes from Pteria penguin mantle tissue. KEGG, Kyoto Encyclopedia of Genes and Genomes database. (XLSX 22 kb)

Additional file 2

Primers and Tm value of genes used for qPCR. (DOC 188 kb)

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Li, H., Zhang, B., Fan, S. et al. Identification and Differential Expression of Biomineralization Genes in the Mantle of Pearl Oyster Pinctada fucata . Mar Biotechnol 19, 266–276 (2017). https://doi.org/10.1007/s10126-017-9748-6

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  • DOI: https://doi.org/10.1007/s10126-017-9748-6

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