Sequencing and de novo analysis of Crassostrea angulata (Fujian Oyster) from 8 different developing phases using 454 GSFLx

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Qin, Ji ^a   Huang, Zixia ^a   Chen, Jun ^a   Zou, Quan ^a   You, Weiwei ^a   Ke, Caihuan ^a  

^a XIAMEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ARTICLE; BREEDING; CHINA; CRASSOSTREA ANGULATA; DEVELOPMENTAL STAGE; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC RESOURCE; GENETIC VARIABILITY; METAMORPHOSIS; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; OYSTER; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

ANIMALS; CRASSOSTREA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS;

EID: 84865420461     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043653     Document Type: Article

References (37)

1. Bieler R, Mikkelsen PM, (2006) Bivalvia-a look at the branches. Zool J Linn Soc 148: 223-235.
2. Pedersen TM, Hansen JL, Josefson B, Hansen BW, (2008) Mortality through ontogeny of soft-bottom marine invertebrates with planktonic larvae. J Marine Syst 73: 185-207.
3. Hinman VF, O'Brien EK, Richards GS, Degnan BM, (2003) Expression of anterior Hox genes during larval development of the gastropod Haliotis asinina. Evol Dev 5: 508-521.
4. Jackson D, Leys SP, Hinman VF, Woods R, Lavin MF, et al. (2002) Ecological regulation of development: induction of marine invertebrate metamorphosis. Int J Dev Biol 46: 679-686.
5. Reyes-Bermudez A, DeSalvo MK, Voolstra CR, Sunagawa S, Szmant AM, et al. (2009) Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata. Mar Genom 2: 149-159.
6. FAO (2000) FAO Fisheries Department, Fishery Information, Data and Statistics Unit, FishStat Plus: Universal software for fishery statistical time series, Version 2.3.
7. Li Q, Wang QZ, Qi MJ, Ge JL, Cong RH, (2011) Development, characterization, and inheritance of 113 novel EST-SSR markers in the Pacific oyster (Crassostrea gigas). Genes Genom 33: 313-316.
8. Appleyard SA, Ward RD, (2006) Genetic diversity and effective population size in mass selection lines of Pacific oyster (Crassostrea gigas). Aquaculture 254: 148-159.
9. Evans S, Langdon C, (2006) Direct and indirect responses to selection on individual body weight in the Pacific oyster (Crassostrea gigas). Aquaculture 261: 546-555.
10. Guo X, (2004) Oyster breeding and the use of biotechnology. Bulletin of the Aquaculture Association of Canada 104: 26-33.
11. Dégremont L, Ernande B, Bédier E, Boudry P, (2007) Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas) I. Estimation of genetic parameters for survival and growth. Aquaculture 262: 41-53.
12. Sauvagea C, Pépina JF, Boudry P, Renault T, (2009) Ostreid herpes virus 1 infection in families of the Pacific oyster, Crassostrea gigas, during a summer mortality outbreak: differences in viral DNA detection and quantification using real-time PCR. Virus Res 142: 181-187.
13. Butt D, Raftos D, (2008) Phenoloxidase-associated cellular defense in the Sydney rock oyster, Saccostrea glomerata, provides resistance against QX disease infections. Dev Comp Immunol 32: 299-306.
14. Wang HY, Qian LM, Liu X, Zhang GF, Guo XM, (2010) Classification of a common cupped oyster from Southern China. J Shellfish Res 29: 857-866.
15. Fleury E, Huvet A, Lelong C, De Lorgeril J, Boulo V, et al. (2009) Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase. BMC genomics 10: 341.
16. Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, et al. (2010) Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns. PLoS one 5(1): e8875.
17. Feng B, Dong L, Niu D, Meng S, Zhang B, et at, (2010) Identification of immune genes of the Agamaki clam (Sinonovacula constricta) by sequencing and bioinformatic analysis of ESTs. Mar biotechnol 12: 282-291.
18. Clark MS, Thorne MA, Toullec JY, Meng Y, Guan LL, et al. (2010) Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome. PLos one 6(1): e15919.
19. Franchini P, Merwe M, Roodt-Wilding R, (2011) Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis. BMC Res Notes 4: 59.
20. Moroz LL, Edwards JR, Puthanveettil SV, Kohn AB, Ha T, (2006) Neuronal transcriptome of Aplysia: neuronal compartments and circuitry. Cell 127(7): 1453-1467.
21. 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(45): 613-624.
22. Hou R, Bao ZM, Wang S, Su HL, Li Y, et al. (2011) Transcriptome sequencing and de novo analysis for Yesso Scallop (Patinopecten yessoensis) using 454 GS FLX. Plos One 6(6): e21560.
23. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, (et al.)(2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10: 219.
24. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18): 3674-3676.
25. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server): W293-W297.
26. Clark MS, Thorne MA, Vieira FA, Cardoso JC, Power DM, et al. (2010) Peck LS: Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics 11: 362.
27. Milan M, Coppe A, Reinhardt R, Cancela LM, Leite RB, et al. (2011) Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics 12: 234.
28. Heyland A, Vue Z, Voolstra CR, Medina M, Moroz LL, (2011) Developmental transcriptome of Aplysia californica. J Exp Zool B Mol Dev Evol 316B(2): 113-134.
29. Fiedler TJ, Hudder A, McKay SJ, Shivkumar S, Capo TR, et al. (2010) The transcriptome of the early life history stages of the California Sea Hare Aplysia californica. Comp Biochem Physiol Genom Proteonomics 5(2): 165-170.
30. Huan P, Wang H, Liu B, (2012) Transcriptomic Analysis of the clam Meretrix meretrix on different larval stages. Mar Biotechnol 14(1): 69-78.
31. Coon SL, Bonar DB, (1987) Pharmacological evidence that alpha1-adrenoceptors mediate metamorphosis of the Pacific oyster, Crassostrea gigas. Neuroscience 23: 1169-1174.
32. Bonar DB, Coon SL, Walch M, Weiner RM, Fitt W, (1990) Control of oyster settlement and metamorphosis by endogenous and exogenous chemical cues. B Mar Sci 46(2): 484-498.
33. Gricourt L, Bonnec G, Boujard D, Mathieu M, Kellner K, (2003) Insulin-like system and growth regulation in the Pacific oyster Crassostrea gigas: hrIGF-1 effect on protein synthesis of mantle edge cells and expression of an homologous insulin receptor-related receptor. Gen Comp Endocr 134(1): 44-56.
34. Gricourt L, Mathieu M, Kellner K, (2006) An insulin-like system involved in the control of Pacific oyster Crassostrea gigas reproduction: hrIGF-1 effect on germinal cell proliferation and maturation associated with expression of an homologous insulin receptor-related receptor. Aquaculture 251(1): 85-98.
35. Serpentini A, Ghayor C, Poncet JM, Hebert V, Galera P, et al. (2000) Collagen study and regulation of the de novo synthesis by IGF-I in hemocytes from the gastropod mollusc, Haliotis tuberculata. J Exp Zool 287: 275-284.
36. Lebel J, Giard W, Favrel P, Boucaud-Camou B, (1996) Effects of different vertebrate growth factors on primary cultures of hemocytes of the gastropod mollusc, Haliotis tuberculata. Biol Cell 86: 67-72.
37. Gregory DJ, Waldbieser GC, Bosworth BG, (2004) Cloning and characterization of myogenic regulatory genes in three Ictalurid species. Anim Genet 35(6): 425-430.