Comparative Analysis of the Transcriptome in Tissues Secreting Purple and White Nacre in the Pearl Mussel Hyriopsis cumingii

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Bai, Zhiyi ^a   Zheng, Hanfeng ^a,b   Lin, Jingyun ^a   Wang, Guiling ^a   Li, Jiale ^a  

^a SHANGHAI OCEAN UNIVERSITY   (China)

^b SOUTH CHINA SEA FISHERIES RESEARCH INSTITUTE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; TRANSCRIPTOME;

ANIMAL SHELL; ANIMAL TISSUE; ARTICLE; BIOMINERALIZATION; CELLULAR SECRETION; COMPARATIVE STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE LIBRARY; GENETIC LINKAGE; GENETIC MARKER; HYRIOPSIS CUMINGII; MUSSEL; NACRE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; RNA ANALYSIS; RNA SEQUENCE; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; NACRE; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; REPETITIVE SEQUENCES, AMINO ACID; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; UNIONIDAE;

HYRIOPSIS CUMINGII;

EID: 84872320266     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053617     Document Type: Article

References (70)

1. Addadi L, Weiner S, (1997) Biomineralization: A pavement of pearl. Nature 389: 912-915.
2. Jackson A, Vincent J, Turner R, (1988) The mechanical design of nacre. Proceedings of the Royal society of London Series B Biological sciences 234: 415-440.
3. Sanchez C, Arribart H, Guille MMG, (2005) Biomimetism and bioinspiration as tools for the design of innovative materials and systems. Nature materials 4: 277-288.
4. Oaki Y, Imai H, (2005) The hierarchical architecture of nacre and its mimetic material. Angewandte Chemie International Edition 44: 6571-6575.
5. Rousseau M, Lopez E, Stempflé P, Brendlé M, Franke L, et al. (2005) Multiscale structure of sheet nacre. Biomaterials 26: 6254-6262.
6. Marin F, Luquet G, Marie B, Medakovic D, (2008) Molluscan shell proteins: primary structure, origin, and evolution. Current topics in developmental biology 80: 209-276.
7. Cartwright JHE, Checa AG, (2007) The dynamics of nacre self-assembly. Journal of the Royal Society Interface 4: 491-504.
8. Jackson D, Wörheide G, Degnan B, (2007) Dynamic expression of ancient and novel molluscan shell genes during ecological transitions. BMC evolutionary biology 7: 160.
9. Jackson DJ, McDougall C, Woodcroft B, Moase P, Rose RA, et al. (2010) Parallel evolution of nacre building gene sets in molluscs. Molecular biology and evolution 27: 591-608.
10. Samata T, (2004) Recent Advances in Studies on Nacreous Layer Biomineralization Molecular and Cellular Aspects. Thalassas: An international journal of marine sciences 20: 25-44.
11. Joubert C, Piquemal D, Marie B, Manchon L, Pierrat F, et al. (2010) Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization. BMC genomics 11: 613.
12. Liu YY (1979) Economic fauna of China (Freshwater Mollusk). Beijing: Science Press.
13. Li J, Li Y, (2009) Aquaculture in China-Freshwater pearl mussel. World Aquaculture 40: 60-62.
14. Li J, Liu Y, (2011) The main influencing factors on the quality of cultured pearls. Journal of Fisheries of China 35: 1753-1760.
15. Ji L, Liu J, Song W, Li S, Miao D, (2012) Effects of dietary Europium complex and Europium (III) on cultured pearl colour in the pearl oyster Pinctada martensii. Aquaculture Research.
16. Karampelas S, Fritsch E, Mevellec JY, Sklavounos S, Soldatos T, (2009) Role of polyenes in the coloration of cultured freshwater pearls. European Journal of Mineralogy 21: 85-97.
17. Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, et al. (2010) Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome biology 11: R8.
18. Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141-145.
19. Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, et al. (2003) Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proceedings of the National Academy of Sciences 100: 8007.
20. Wang S, Sha Z, Sonstegard T, Liu H, Xu P, et al. (2008) Quality assessment parameters for EST-derived SNPs from catfish. BMC genomics 9: 450.
21. Liu Z, Cordes J, (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238: 1-37.
22. Hou R, Bao Z, Wang S, Su H, Li Y, et al. (2011) Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX. PLoS ONE 6: e21560.
23. Bai Z, Yin Y, Hu S, Wang G, Zhang X, et al. (2010) Identification of Genes Potentially Involved in Pearl Formation by Expressed Sequence Tag Analysis of Mantle from Freshwater Pearl Mussel (Hyriopsis Cumingii Lea). Journal of Shellfish Research 29: 527-534.
24. Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al. (2005) Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature methods 2: 105-111.
25. Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
26. Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends in genetics: TIG 16: 276-277.
27. Chen Z, Xue C, Zhu S, Zhou F, Liu G, et al. (2005) GoPipe: streamlined gene ontology annotation for batch anonymous sequences with statistics. Progress in Biochemistry and Biophysics 32: 187-191.
28. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic acids research 38: D355.
29. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic acids research 39: D225-229.
30. Newman A, Cooper J, (2007) XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences. BMC bioinformatics 8: 382.
31. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods 5: 621-628.
32. Wang L, Feng Z, Wang X, Zhang X, (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
33. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, et al. (1999) A general approach to single-nucleotide polymorphism discovery. Nat Genet 23: 452-456.
34. Bai Z, Yin Y, Hu S, Wang G, Zhang X, et al. (2009) Identification of genes involved in immune response, microsatellite, and SNP markers from expressed sequence tags generated from hemocytes of freshwater pearl mussel (Hyriopsis cumingii). Marine biotechnology 11: 520-530.
35. Basrai MA, Hieter P, Boeke JD, (1997) Small open reading frames: beautiful needles in the haystack. Genome research 7: 768-771.
36. Addadi L, Joester D, Nudelman F, Weiner S, (2006) Mollusk shell formation: a source of new concepts for understanding biomineralization processes. Chemistry 12: 980-987.
37. Levi-Kalisman Y, Falini G, Addadi L, Weiner S, (2001) Structure of the nacreous organic matrix of a bivalve mollusk shell examined in the hydrated state using cryo-TEM. Journal of structural biology 135: 8-17.
38. Marin F, Amons R, Guichard N, Stigter M, Hecker A, et al. (2005) Caspartin and calprismin, two proteins of the shell calcitic prisms of the Mediterranean fan mussel Pinna nobilis. The Journal of biological chemistry 280: 33895-33908.
39. Suzuki M, Saruwatari K, Kogure T, Yamamoto Y, Nishimura T, et al. (2009) An acidic matrix protein, Pif, is a key macromolecule for nacre formation. Science 325: 1388-1390.
40. Takeuchi T, Endo K, (2006) Biphasic and dually coordinated expression of the genes encoding major shell matrix proteins in the pearl oyster Pinctada fucata. Marine biotechnology 8: 52-61.
41. 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. Zoological science 22: 311-315.
42. Nagai K, Yano M, Morimoto K, Miyamoto H, (2007) Tyrosinase localization in mollusc shells. Comparative biochemistry and physiology Part B, Biochemistry & molecular biology 146: 207-214.
43. Marxen JC, Nimtz M, Becker W, Mann K, (2003) The major soluble 19.6 kDa protein of the organic shell matrix of the freshwater snail Biomphalaria glabrata is an N-glycosylated dermatopontin. Biochimica et biophysica acta 1650: 92-98.
44. Blank S, Arnoldi M, Khoshnavaz S, Treccani L, Kuntz M, et al. (2003) The nacre protein perlucin nucleates growth of calcium carbonate crystals. Journal of microscopy 212: 280-291.
45. Fang D, Pan C, Lin H, Lin Y, Zhang G, et al. (2012) Novel basic protein, PfN23, functions as key macromolecule during nacre formation. The Journal of biological chemistry 287: 15776-15785.
46. Yang YM, Guo SG, Shi LY, Wang WZ, (2004) Study on compositions and colour ing mechan ism of freshwater cultured pearls. Journal of gems and gemmology 6: 10-13.
47. Gong N, Ma Z, Li Q, Yan Z, Xie L, et al. (2008) Characterization of calcium deposition and shell matrix protein secretion in primary mantle tissue culture from the marine pearl oyster Pinctada fucata. Mar Biotechnol 10: 457-465.
48. Addadi L, Raz S, Weiner S, (2003) Taking advantage of disorder: amorphous calcium carbonate and its roles in biomineralization. Advanced Materials 15: 959-970.
49. Aizenberg J, Lambert G, Weiner S, Addadi L, (2002) Factors involved in the formation of amorphous and crystalline calcium carbonate: a study of an ascidian skeleton. Journal of the American Chemical Society 124: 32-39.
50. Tao J, Zhou D, Zhang Z, Xu X, Tang R, (2009) Magnesium-aspartate-based crystallization switch inspired from shell molt of crustacean. Proceedings of the National Academy of Sciences of the United States of America 106: 22096-22101.
51. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57-63.
52. Velculescu VE, Kinzler KW, (2007) Gene expression analysis goes digital. Nature biotechnology 25: 878-880.
53. Milet C, Berland S, Lamghari M, Mouries L, Jolly C, et al. (2004) Conservation of signal molecules involved in biomineralisation control in calcifying matrices of bone and shell. Comptes Rendus Palevol 3: 493-501.
54. Zhang X, Tamasi J, Lu X, Zhu J, Chen H, et al. (2011) Epidermal growth factor receptor plays an anabolic role in bone metabolism in vivo. Journal of Bone and Mineral Research 26: 1022-1034.
55. Hopkins DR, Keles S, Greenspan DS, (2007) The bone morphogenetic protein 1/Tolloid-like metalloproteinases. Matrix Biology 26: 508-523.
56. Lallier T, (2004) Semaphorin profiling of periodontal fibroblasts and osteoblasts. Journal of dental research 83: 677-682.
57. Yazdani U, Terman JR, (2006) The semaphorins. Genome Biol 7: 211.
58. Hikiji H, Ishii S, Yokomizo T, Takato T, Shimizu T, (2009) A distinctive role of the leukotriene B4 receptor BLT1 in osteoclastic activity during bone loss. Proceedings of the National Academy of Sciences 106: 21294-21299.
59. Zhang Y, Dong C, (2007) Regulatory mechanisms of mitogen-activated kinase signaling. Cellular and molecular life sciences 64: 2771-2789.
60. Schnorr O, Suschek CV, Kolb-Bachofen V, (2003) The importance of cationic amino acid transporter expression in human skin. Journal of investigative dermatology 120: 1016-1022.
61. Moreau A, Yotov WV, Glorieux FH, St-Arnaud R, (1998) Bone-specific expression of the alpha chain of the nascent polypeptide-associated complex, a coactivator potentiating c-Jun-mediated transcription. Molecular and cellular biology 18: 1312.
62. Rospert S, Dubaquie Y, Gautschi M, (2002) Nascent-polypeptide-associated complex. Cellular and molecular life sciences 59: 1632-1639.
63. Bennett V, Baines AJ, (2001) Spectrin and Ankyrin-Based Pathways: Metazoan Inventions for Integrating Cells Into Tissues. Physiological Reviews 81: 1353-1392.
64. Mann S, (1988) Molecular recognition in biomineralization. Nature 332: 119-124.
65. Mason JM, Arndt KM, (2004) Coiled coil domains: stability, specificity, and biological implications. ChemBioChem 5: 170-176.
66. Frank S, Schulthess T, Landwehr R, Lustig A, Mini T, et al. (2002) Characterization of the matrilin coiled-coil domains reveals seven novel isoforms. Journal of Biological Chemistry 277: 19071.
67. Schrauwen I, Ealy M, Huentelman MJ, Thys M, Homer N, et al. (2009) A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis. The American Journal of Human Genetics 84: 328-338.
68. Seth A, Lee BK, Qi S, Vary CPH, (2000) Coordinate expression of novel genes during osteoblast differentiation. Journal of Bone and Mineral Research 15: 1683-1696.
69. Addadi L, Weiner S, (1985) Interactions between acidic proteins and crystals: stereochemical requirements in biomineralization. Proceedings of the National Academy of Sciences of the United States of America 82: 4110-4114.
70. Weiner S, Addadi L, (1991) Acidic macromolecules of mineralized tissues: the controllers of crystal formation. Trends in biochemical sciences 16: 252-256.