Bibliography
Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., Xiong, Z., Que, H., Xie, Y., Holland, P. W. H., Paps, J., Zhu, Y., Wu, F., Chen, Y., Wang, J., ⦠Wang, J. (2012). The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490(7418), 49â54.
Authors
85
- Guofan Zhang (first)
- Xiaodong Fang (additional)
- Ximing Guo (additional)
- Li Li (additional)
- Ruibang Luo (additional)
- Fei Xu (additional)
- Pengcheng Yang (additional)
- Linlin Zhang (additional)
- Xiaotong Wang (additional)
- Haigang Qi (additional)
- Zhiqiang Xiong (additional)
- Huayong Que (additional)
- Yinlong Xie (additional)
- Peter W. H. Holland (additional)
- Jordi Paps (additional)
- Yabing Zhu (additional)
- Fucun Wu (additional)
- Yuanxin Chen (additional)
- Jiafeng Wang (additional)
- Chunfang Peng (additional)
- Jie Meng (additional)
- Lan Yang (additional)
- Jun Liu (additional)
- Bo Wen (additional)
- Na Zhang (additional)
- Zhiyong Huang (additional)
- Qihui Zhu (additional)
- Yue Feng (additional)
- Andrew Mount (additional)
- Dennis Hedgecock (additional)
- Zhe Xu (additional)
- Yunjie Liu (additional)
- Tomislav Domazet-Lošo (additional)
- Yishuai Du (additional)
- Xiaoqing Sun (additional)
- Shoudu Zhang (additional)
- Binghang Liu (additional)
- Peizhou Cheng (additional)
- Xuanting Jiang (additional)
- Juan Li (additional)
- Dingding Fan (additional)
- Wei Wang (additional)
- Wenjing Fu (additional)
- Tong Wang (additional)
- Bo Wang (additional)
- Jibiao Zhang (additional)
- Zhiyu Peng (additional)
- Yingxiang Li (additional)
- Na Li (additional)
- Jinpeng Wang (additional)
- Maoshan Chen (additional)
- Yan He (additional)
- Fengji Tan (additional)
- Xiaorui Song (additional)
- Qiumei Zheng (additional)
- Ronglian Huang (additional)
- Hailong Yang (additional)
- Xuedi Du (additional)
- Li Chen (additional)
- Mei Yang (additional)
- Patrick M. Gaffney (additional)
- Shan Wang (additional)
- Longhai Luo (additional)
- Zhicai She (additional)
- Yao Ming (additional)
- Wen Huang (additional)
- Shu Zhang (additional)
- Baoyu Huang (additional)
- Yong Zhang (additional)
- Tao Qu (additional)
- Peixiang Ni (additional)
- Guoying Miao (additional)
- Junyi Wang (additional)
- Qiang Wang (additional)
- Christian E. W. Steinberg (additional)
- Haiyan Wang (additional)
- Ning Li (additional)
- Lumin Qian (additional)
- Guojie Zhang (additional)
- Yingrui Li (additional)
- Huanming Yang (additional)
- Xiao Liu (additional)
- Jian Wang (additional)
- Ye Yin (additional)
- Jun Wang (additional)
References
47
Referenced
1,931
-
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)
(
10.1525/california/9780520250925.001.0001
) / Phylogeny and Evolution of the Mollusca by WF Ponder (2008) -
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)
(
10.1159/000258667
) / Brain Behav. Evol. by ET Walters (2009) -
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)
(
10.1073/pnas.0913804107
) / Proc. Natl Acad. Sci. USA by SC Talmage (2010) -
Caldeira, K. & Wickett, M. E. Anthropogenic carbon and ocean pH. Nature 425, 365–365 (2003)
(
10.1038/425365a
) / Nature by K Caldeira (2003) -
Marin, F., Luquet, G., Marie, B. & Medakovic, D. Molluscan shell proteins: primary structure, origin, and evolution. Curr. Top. Dev. Biol. 80, 209–276 (2008)
(
10.1016/S0070-2153(07)80006-8
) / Curr. Top. Dev. Biol. by F Marin (2008) -
Hedgecock, D. et al. The case for sequencing the Pacific oyster genome. J. Shellfish Res. 24, 429–441 (2005)
(
10.2983/0730-8000(2005)24[429:TCFSTP]2.0.CO;2
) / J. Shellfish Res. by D Hedgecock (2005) -
Sodergren, E. et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314, 941–952 (2006)
(
10.1126/science.1133609
) / Science by E Sodergren (2006) -
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)
(
10.1073/pnas.0700890104
) / Proc. Natl Acad. Sci. USA by KS Small (2007) -
Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010)
(
10.1038/nature08696
) / Nature by R Li (2010) -
Xu, X. et al. Genome sequence and analysis of the tuber crop potato. Nature 475, 189–195 (2011)
(
10.1038/nature10288
) / Nature by X Xu (2011) -
Bonasio, R. et al. Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science 329, 1068–1071 (2010)
(
10.1126/science.1192428
) / Science by R Bonasio (2010) -
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)
(
10.1371/journal.pbio.1000475
) / PLoS Biol. by RA Dalloul (2010) -
Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207–210 (2011)
(
10.1038/nature10342
) / Nature by B Star (2011) - Harris, R. S. Improved Pairwise Alignment of Genomic DNA. PhD thesis, Pennsylvania State Univ. (2007)
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
(
10.1093/bioinformatics/btp324
) / Bioinformatics by H Li (2009) -
Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnol. 29, 59–63 (2010)
(
10.1038/nbt.1740
) / Nature Biotechnol. by JO Kitzman (2010) -
Suk, E. K. et al. A comprehensively molecular haplotype-resolved genome of a European individual. Genome Res. 21, 1672–1685 (2011)
(
10.1101/gr.125047.111
) / Genome Res. by EK Suk (2011) -
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)
(
10.1016/j.gene.2007.05.011
) / Gene by C Sauvage (2007) -
McGoldrick, D. J. & Hedgecock, D. Fixation, segregation and linkage of allozyme loci in inbred families of the Pacific oyster Crassostrea gigas (Thunberg): implications for the causes of inbreeding depression. Genetics 146, 321–334 (1997)
(
10.1093/genetics/146.1.321
) / Genetics by DJ McGoldrick (1997) -
Hillier, L. W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods 5, 183–188 (2008)
(
10.1038/nmeth.1179
) / Nature Methods by LW Hillier (2008) -
Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010)
(
10.1101/gr.097261.109
) / Genome Res. by R Li (2010) -
Gaffney, P. M., Pierce, J. C., Mackinley, A. G., Titchen, D. A. & Glenn, W. K. Pearl, a novel family of putative transposable elements in bivalve mollusks. J. Mol. Evol. 56, 308–316 (2003)
(
10.1007/s00239-002-2402-5
) / J. Mol. Evol. by PM Gaffney (2003) -
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)
(
10.1093/nar/gkq862
) / Nucleic Acids Res. by Y Han (2010) -
Barucca, M., Olmo, E. & Canapa, A. Hox and paraHox genes in bivalve molluscs. Gene 317, 97–102 (2003)
(
10.1016/S0378-1119(03)00657-7
) / Gene by M Barucca (2003) -
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)
(
10.1016/S1055-7903(02)00204-X
) / Mol. Phylogenet. Evol. by DEK Ferrier (2002) -
Goldstone, J. V. et al. The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome. Dev. Biol. 300, 366–384 (2006)
(
10.1016/j.ydbio.2006.08.066
) / Dev. Biol. by JV Goldstone (2006) -
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)
(
10.1016/j.dci.2010.02.014
) / Dev. Comp. Immunol. by TM Carland (2010) -
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)
(
10.1159/000321882
) / J. Innate Immun. by PC Hanington (2011) -
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)
(
10.1126/science.1088069
) / Science by SM Zhang (2004) -
Kourtis, N. & Tavernarakis, N. Cellular stress response pathways and ageing: intricate molecular relationships. EMBO J. 30, 2520–2531 (2011)
(
10.1038/emboj.2011.162
) / EMBO J. by N Kourtis (2011) -
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)
(
10.1073/pnas.1100652108
) / Proc. Natl Acad. Sci. USA by EF Lee (2011) -
Bender, C. E. et al. Mitochondrial pathway of apoptosis is ancestral in metazoans. Proc. Natl Acad. Sci. USA 109, 4904–4909 (2012)
(
10.1073/pnas.1120680109
) / Proc. Natl Acad. Sci. USA by CE Bender (2012) - Galtsoff, P. S. The American oyster Crassostrea virginica Gmelin. Fishery Bull. 64, 1–480 (United States Govt Printing Office, 1964) / Crassostrea virginica by PS Galtsoff (1964)
-
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)
(
10.1128/MCB.17.9.5317
) / Mol. Cell. Biol. by DD Mosser (1997) -
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)
(
10.1098/rstb.1984.0036
) / Phil. Trans. R. Soc. Lond. B by S Weiner (1984) -
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)
(
10.1016/j.cbpb.2009.07.011
) / Comp. Biochem. Physiol. B Biochem. Mol. Biol. by T Furuhashi (2009) -
Mount, A. S., Wheeler, A. P., Paradkar, R. P. & Snider, D. Hemocyte-mediated shell mineralization in the eastern oyster. Science 304, 297–300 (2004)
(
10.1126/science.1090506
) / Science by AS Mount (2004) -
Stark, M. et al. Macroscopic fibers self-assembled from recombinant miniature spider silk proteins. Biomacromolecules 8, 1695–1701 (2007)
(
10.1021/bm070049y
) / Biomacromolecules by M Stark (2007) -
Lemmon, C. A., Chen, C. S. & Romer, L. H. Cell traction forces direct fibronectin matrix assembly. Biophys. J. 96, 729–738 (2009)
(
10.1016/j.bpj.2008.10.009
) / Biophys. J. by CA Lemmon (2009) -
Keller, S., Sanderson, M. P., Stoeck, A. & Altevogt, P. Exosomes: from biogenesis and secretion to biological function. Immunol. Lett. 107, 102–108 (2006)
(
10.1016/j.imlet.2006.09.005
) / Immunol. Lett. by S Keller (2006) -
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)
(
10.1093/nar/gkr828
) / Nucleic Acids Res. by S Mathivanan (2012) - Mount, A. S., Gohad, N. V., Hansen, D. C., Mueller, K. & Johnstone, M. B. Deposition of nanocrystalline calcite on surfaces by a tissue and cellular biomineralization. US patent 2010/0150982 A1. (2010)
-
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)
(
10.1111/j.1574-6976.2008.00105.x
) / FEMS Microbiol. Rev. by E Sauvage (2008) -
Nagai, K., Yano, M., Morimoto, K. & Miyamoto, H. Tyrosinase localization in mollusc shells. Comp. Biochem. Physiol. B 146, 207–214 (2007)
(
10.1016/j.cbpb.2006.10.105
) / Comp. Biochem. Physiol. B by K Nagai (2007) -
Chang, T. S. An updated review of tyrosinase inhibitors. Int. J. Mol. Sci. 10, 2440–2475 (2009)
(
10.3390/ijms10062440
) / Int. J. Mol. Sci. by TS Chang (2009) - Waite, J. H. in The Mollusca Vol. I (eds Hochachka, P. & Wilbur, K. M. ) Ch. 11, 467–504 (Academic, 1983) / The Mollusca by JH Waite (1983)
-
Zhang, G. et al. Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030 (2012)
(
10.5524/100030
)
Dates
Type | When |
---|---|
Created | 12 years, 11 months ago (Sept. 19, 2012, 6:37 a.m.) |
Deposited | 2 years, 3 months ago (May 18, 2023, 2:03 p.m.) |
Indexed | 4 hours, 15 minutes ago (Sept. 6, 2025, 3:51 p.m.) |
Issued | 12 years, 11 months ago (Sept. 19, 2012) |
Published | 12 years, 11 months ago (Sept. 19, 2012) |
Published Online | 12 years, 11 months ago (Sept. 19, 2012) |
Published Print | 12 years, 11 months ago (Oct. 1, 2012) |
@article{Zhang_2012, title={The oyster genome reveals stress adaptation and complexity of shell formation}, volume={490}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature11413}, DOI={10.1038/nature11413}, number={7418}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Zhang, Guofan and Fang, Xiaodong and Guo, Ximing and Li, Li and Luo, Ruibang and Xu, Fei and Yang, Pengcheng and Zhang, Linlin and Wang, Xiaotong and Qi, Haigang and Xiong, Zhiqiang and Que, Huayong and Xie, Yinlong and Holland, Peter W. H. and Paps, Jordi and Zhu, Yabing and Wu, Fucun and Chen, Yuanxin and Wang, Jiafeng and Peng, Chunfang and Meng, Jie and Yang, Lan and Liu, Jun and Wen, Bo and Zhang, Na and Huang, Zhiyong and Zhu, Qihui and Feng, Yue and Mount, Andrew and Hedgecock, Dennis and Xu, Zhe and Liu, Yunjie and Domazet-Lošo, Tomislav and Du, Yishuai and Sun, Xiaoqing and Zhang, Shoudu and Liu, Binghang and Cheng, Peizhou and Jiang, Xuanting and Li, Juan and Fan, Dingding and Wang, Wei and Fu, Wenjing and Wang, Tong and Wang, Bo and Zhang, Jibiao and Peng, Zhiyu and Li, Yingxiang and Li, Na and Wang, Jinpeng and Chen, Maoshan and He, Yan and Tan, Fengji and Song, Xiaorui and Zheng, Qiumei and Huang, Ronglian and Yang, Hailong and Du, Xuedi and Chen, Li and Yang, Mei and Gaffney, Patrick M. and Wang, Shan and Luo, Longhai and She, Zhicai and Ming, Yao and Huang, Wen and Zhang, Shu and Huang, Baoyu and Zhang, Yong and Qu, Tao and Ni, Peixiang and Miao, Guoying and Wang, Junyi and Wang, Qiang and Steinberg, Christian E. W. and Wang, Haiyan and Li, Ning and Qian, Lumin and Zhang, Guojie and Li, Yingrui and Yang, Huanming and Liu, Xiao and Wang, Jian and Yin, Ye and Wang, Jun}, year={2012}, month=sep, pages={49–54} }