The oyster genome reveals stress adaptation and complexity of shell formation

Nature

Volumn 490, Issue 7418, 2012, Pages 49-54

  Wang, Jun ^b,l,m   Zhang, Guofan ^a   Fang, Xiaodong ^b   Guo, Ximing ^c   Li, Li ^a   Luo, Ruibang ^b,d   Xu, Fei ^a   Yang, Pengcheng ^b   Zhang, Linlin ^a   Wang, Xiaotong ^a   Qi, Haigang ^a   Xiong, Zhiqiang ^b   Que, Huayong ^a   Xie, Yinlong ^b,d   Holland, Peter W H ^e   Paps, Jordi ^e   Zhu, Yabing ^b   Wu, Fucun ^a   Chen, Yuanxin ^b   Wang, Jiafeng ^a   Peng, Chunfang ^b   Meng, Jie ^a   Yang, Lan ^b   Liu, Jun ^a   Wen, Bo ^b   Zhang, Na ^a   Huang, Zhiyong ^b   Zhu, Qihui ^a   Feng, Yue ^b   Mount, Andrew ^f   Hedgecock, Dennis ^g   Xu, Zhe ^h   Liu, Yunjie ^b   Domazet Lošo, Tomislav ⁱ   Du, Yishuai ^a   Sun, Xiaoqing ^b   Zhang, Shoudu ^a   Liu, Binghang ^b,d   Cheng, Peizhou ^a   Jiang, Xuanting ^b   Li, Juan ^a   Fan, Dingding ^b   Wang, Wei ^a   Fu, Wenjing ^b   Wang, Tong ^a   Wang, Bo ^b   Zhang, Jibiao ^a   Peng, Zhiyu ^b   Li, Yingxiang ^a   Li, Na ^b   Wang, Jinpeng ^a   Chen, Maoshan ^b   He, Yan ^c   Tan, Fengji ^b   Song, Xiaorui ^a   Zheng, Qiumei ^b   Huang, Ronglian ^a   Yang, Hailong ^b   Du, Xuedi ^a   Chen, Li ^b   Yang, Mei ^a   Gaffney, Patrick M ^j   Wang, Shan ^c   Luo, Longhai ^b   She, Zhicai ^a   Ming, Yao ^b   Huang, Wen ^a   Zhang, Shu ^b   Huang, Baoyu ^a   Zhang, Yong ^b   Qu, Tao ^a   Ni, Peixiang ^b   Miao, Guoying ^a   Wang, Junyi ^b   Wang, Qiang ^a   Steinberg, Christian E W ^k   Wang, Haiyan ^a   Li, Ning ^b   Qian, Lumin ^c   Zhang, Guojie ^b   Li, Yingrui ^b   Yang, Huanming ^b   Liu, Xiao ^a   Yin, Ye ^b   Wang, Jian ^b   more..

^a INSTITUTE OF OCEANOLOGY   (China)

^b BGI SHENZHEN   (China)

^c RUTGERS UNIVERSITY   (United States)

^d Department of Computer Science   (Hong Kong)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f CLEMSON UNIVERSITY   (United States)

^g UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^h Atlantic Cape Community College   (United States)

ⁱ RUDER BO KOVI INSTITUTE   (Croatia)

^j UNIVERSITY OF DELAWARE   (United States)

^k HUMBOLDT UNIVERSITY   (Germany)

^l UNIVERSITY OF COPENHAGEN   (Denmark)

^m Capital Region   (Denmark)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENT COMPONENT C1Q; HEAT SHOCK PROTEIN 70; HOX PROTEIN; INHIBITOR OF APOPTOSIS PROTEIN; PROTEOME; RAS PROTEIN; TRANSCRIPTOME;

ADAPTATION; APOPTOSIS; BIVALVE; COMPLEXITY; ENVIRONMENTAL STRESS; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; HEAT SHOCK; INHIBITOR; INTERTIDAL ENVIRONMENT; POLYMORPHISM; PROTEIN; PROTEOMICS; SHELL;

ADAPTATION; ANIMAL SHELL; ARTICLE; ENVIRONMENTAL STRESS; EXOSOME; EXTRACELLULAR MATRIX; FEMALE; GENE EXPRESSION; GENE SEQUENCE; GENETIC CODE; GENOME; INTERTIDAL ZONE; LOPHOTROCHOZOA; NONHUMAN; OYSTER; PRIORITY JOURNAL; SESSILE SPECIES; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSPOSON;

ADAPTATION, PHYSIOLOGICAL; ANIMAL SHELLS; ANIMALS; APOPTOSIS REGULATORY PROTEINS; CRASSOSTREA; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, HOMEOBOX; GENOME; GENOMICS; HSP70 HEAT-SHOCK PROTEINS; HUMANS; LARVA; MASS SPECTROMETRY; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME;

CRASSOSTREA GIGAS; LOPHOTROCHOZOA; MOLLUSCA; OSTREIDAE;

EID: 84867088834     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature11413     Document Type: Article

References (47)

1. Ponder, W. F. & Lindberg, D. R. in Phylogeny and Evolution of the Mollusca (eds Ponder, W. & Lindberg, D. R.) Ch. 1, 1-18 (Univ. of California Press, 2008).
2. Walters, E. T. & Moroz, L. L. Molluscan memory of injury: evolutionary insights into chronic pain and neurological disorders. Brain Behav. Evol. 74, 206-218 (2009).
3. Talmage, S. C. & Gobler, C. J. Effects of past, present, and future ocean carbon dioxide concentrations on the growth and survival of larval shellfish. Proc. Natl Acad. Sci. USA 107, 17246-17251 (2010).
4. Caldeira, K. & Wickett, M. E. Anthropogenic carbon and ocean pH. Nature 425, 365-365 (2003).
5. Marin, F., Luquet, G., Marie, B. & Medakovic, D. Molluscan shell proteins: primary structure, origin, and evolution. Curr. Top. Dev. Biol. 80, 209-276 (2008).
6. Hedgecock, D. et al. The case for sequencing the Pacific oyster genome. J. Shellfish Res. 24, 429-441 (2005). (Pubitemid 41209447)
7. Sodergren, E. et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314, 941-952 (2006). (Pubitemid 44749930)
8. Small, K. S., Brudno, M., Hill, M. M. & Sidow, A. Extreme genomic variation in a natural population. Proc. Natl Acad. Sci. USA 104, 5698-5703 (2007). (Pubitemid 47175743)
9. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
10. Xu, X. et al. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195 (2011).
11. Bonasio, R. et al. Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science 329, 1068-1071 (2010).
12. Dalloul, R. A. et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 8, e1000475 (2010).
13. Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207-210 (2011).
14. Harris, R. S. Improved Pairwise Alignment of Genomic DNA. PhD thesis, Pennsylvania State Univ. (2007).
15. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
16. Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnol. 29, 59-63 (2010).
17. Suk, E. K. et al. A comprehensively molecular haplotype-resolved genome of a European individual. Genome Res. 21, 1672-1685 (2011).
18. Sauvage, C., Bierne, N., Lapègue, S.& Boudry, P. Single nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 406, 13-22 (2007). (Pubitemid 350216291)
19. McGoldrick, D. J.&Hedgecock, D. Fixation, segregationand linkage of allozymeloci in inbred families of the Pacific oyster Crassostrea gigas (Thunberg): implications for the causes of inbreeding depression. Genetics 146, 321-334 (1997). (Pubitemid 27194410)
20. Hillier, L. W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods 5, 183-188 (2008). (Pubitemid 351181748)
21. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
22. Gaffney, P. M., Pierce, J. C., Mackinley, A. G., Titchen, D. A. & Glenn, W. K. Pearl, a novel family of putative transposable elements in bivalvemollusks. J. Mol. Evol. 56, 308-316 (2003). (Pubitemid 36279036)
23. Han, Y. & Wessler, S. R. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 38, e199 (2010).
24. Barucca, M., Olmo, E. & Canapa, A. Hox and paraHox genes in bivalve molluscs. Gene 317, 97-102 (2003). (Pubitemid 37356922)
25. Ferrier, D. E. K. & Holland, P. W. H. Ciona intestinalis ParaHox genes: evolution of Hox/ParaHox cluster integrity, developmental mode, and temporal colinearity. Mol. Phylogenet. Evol. 24, 412-417 (2002).
26. Goldstone, J. V. et al. The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome. Dev. Biol. 300, 366-384 (2006). (Pubitemid 44827001)
27. Carland, T. M. & Gerwick, L. The C1q domain containing proteins: where do they come from and what do they do? Dev. Comp. Immunol. 34, 785-790 (2010).
28. Hanington, P. C. & Zhang, S. M. The primary role of fibrinogen-related proteins in invertebrates is defense, not coagulation. J. Innate Immun. 3, 17-27 (2011).
29. Zhang, S. M., Adema, C. M., Kepler, T. B. & Loker, E. S. Diversification of Ig superfamily genes in an invertebrate. Science 305, 251-254 (2004). (Pubitemid 38886740)
30. Kourtis, N. & Tavernarakis, N. Cellular stress response pathways and ageing: intricate molecular relationships. EMBO J. 30, 2520-2531 (2011).
31. Lee, E. F. et al. Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes. Proc.Natl Acad. Sci.USA 108, 6999-7003(2011).
32. Bender, C. E. et al. Mitochondrial pathway of apoptosis is ancestral in metazoans. Proc. Natl Acad. Sci. USA 109, 4904-4909 (2012).
33. Galtsoff, P. S. The American oyster Crassostrea virginica Gmelin. Fishery Bull., 64, 1-480 (United States Govt Printing Office, 1964).
34. Mosser, D. D., Caron, A. W., Bourget, L., Denis-Larose, C. & Massie, B. Role of the human heat shock protein hsp70 in protection against stress-induced apoptosis. Mol. Cell. Biol. 17, 5317-5327 (1997). (Pubitemid 27357630)
35. Weiner, S., Traub, W. & Parker, S. Macromolecules in mollusc shells and their functions in biomineralization. Phil. Trans. R. Soc. Lond. B 304, 425-434 (1984).
36. Furuhashi, T., Schwarzinger, C., Miksik, I., Smrz, M. & Beran, A. Molluscan shell evolution with review of shell calcification hypothesis. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 154, 351-371 (2009).
37. Mount, A. S., Wheeler, A. P., Paradkar, R. P. & Snider, D. Hemocyte-mediated shell mineralization in the eastern oyster. Science 304, 297-300 (2004). (Pubitemid 38452183)
38. Stark, M. et al. Macroscopic fibers self-assembled from recombinant miniature spider silk proteins. Biomacromolecules 8, 1695-1701 (2007). (Pubitemid 46865144)
39. Lemmon, C. A., Chen, C. S. & Romer, L. H. Cell traction forces direct fibronectin matrix assembly. Biophys. J. 96, 729-738 (2009).
40. Keller, S., Sanderson, M. P., Stoeck, A.&Altevogt, P. Exosomes: frombiogenesisand secretion to biological function. Immunol. Lett. 107, 102-108 (2006). (Pubitemid 44779821)
41. Mathivanan, S., Fahner, C. J., Reid, G. E. & Simpson, R. J. ExoCarta 2012: database of exosomal proteins, RNA and lipids. Nucleic Acids Res. 40, D1241-D1244 (2012).
42. Mount, A. S.,Gohad, N. V.,Hansen, D. C.,Mueller, K.&Johnstone, M. B.Depositionof nanocrystalline calcite on surfaces by a tissue and cellular biomineralization. US patent 2010/0150982 A1 (2010).
43. Sauvage, E., Kerff, F., Terrak, M., Ayala, J. A. & Charlier, P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol. Rev. 32, 234-258 (2008). (Pubitemid 351257821)
44. Nagai, K., Yano, M., Morimoto, K.& Miyamoto, H. Tyrosinase localization inmollusc shells. Comp. Biochem. Physiol. B 146, 207-214 (2007).
45. Chang, T. S. An updated review of tyrosinase inhibitors. Int. J. Mol. Sci. 10, 2440-2475 (2009).
46. Waite, J. H. in The Mollusca Vol. I (eds Hochachka, P. & Wilbur, K. M.) Ch. 11, 467-504 (Academic, 1983).
47. Zhang, G. et al. Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030 (2012).