Transcriptome analysis of orange-spotted grouper (Epinephelus coioides) spleen in response to Singapore grouper iridovirus

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Huang, Youhua ^a   Huang, Xiaohong ^a   Yan, Yang ^a   Cai, Jia ^a   Ouyang, Zhengliang ^a   Cui, Huachun ^b   Wang, Peiran ^b   Qin, Qiwei ^a  

^a SOUTH CHINA SEA INSTITUTE OF OCEANOLOGY   (China)

^b SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE; COMPLEMENTARY DNA; CYTOKINE; CYTOKINE RECEPTOR; INTERFERON; MITOGEN ACTIVATED PROTEIN KINASE; RETINOIC ACID INDUCIBLE PROTEIN I; TOLL LIKE RECEPTOR; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

APOPTOSIS; ARTICLE; BIOGENESIS; CELL METABOLISM; CONTROLLED STUDY; DNA LIBRARY; EPINEPHELUS COIOIDES; EXPRESSED SEQUENCE TAG; FISH; GENE EXPRESSION; GENETIC ANALYSIS; IRIDOVIRUS; NONHUMAN; ONTOGENY; PYROSEQUENCING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSOME; SIGNAL TRANSDUCTION; SINGAPORE GROUPER IRIDOVIRUS; SPLEEN; TRANSCRIPTOME ANALYSIS; VIRUS INFECTION; ANIMAL; ANIMAL DISEASE; DNA SEQUENCE; DNA VIRUS INFECTION; FISH DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; METABOLISM; PATHOGENICITY; PERCIFORMES; VIROLOGY;

BETANODAVIRUS; EPINEPHELUS COIOIDES; IRIDOVIRUS; SINGAPORE GROUPER IRIDOVIRUS; VERTEBRATA;

ANIMALS; DNA VIRUS INFECTIONS; EXPRESSED SEQUENCE TAGS; FISH DISEASES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; IRIDOVIRUS; PERCIFORMES; SEQUENCE ANALYSIS, DNA; SPLEEN; TRANSCRIPTOME;

EID: 81055126942     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-556     Document Type: Article

References (58)

1. Zhou L, Gui JF. Molecular mechanisms underlying sex change in hermaphroditic groupers. Fish Physiol Biochem 2010, 36:181-193. 10.1007/s10695-008-9219-0, 20467860.
2. Marino G, Azzurro E, Massari A, Finoia MG, Mandich A. Reproduction in the dusky grouper from the southern Mediterranean. J Fish Biol 2001, 58:908-927.
3. Walker PJ, Winton JR. Emerging viral diseases of fish and shrimp. Vet Res 2010, 41:51. 10.1051/vetres/2010022, 2878170, 20409453.
4. Whittington RJ, Becker JA, Dennis MM. Iridovirus infections in finfish - critical review with emphasis on ranaviruses. J Fish Dis 2010, 33:95-122. 10.1111/j.1365-2761.2009.01110.x, 20050967.
5. Qin QW, Shi C, Gin KY, Lam TJ. Antigenic characterization of a marine fish iridovirus from grouper, Epinephelus spp. J Virol Methods 2002, 106:89-96. 10.1016/S0166-0934(02)00139-8, 12367733.
6. Chao CB, Chen CY, Lai YY, Lin CS, Huang HT. Histological, ultrastructural, and in situ hybridization study on enlarged cells in grouper Epinephelus hybrids infected by grouper iridovirus in Taiwan (TGIV). Dis Aquat Organ 2004, 58:127-142.
7. Kai YH, Su HM, Tai KT, Chi SC. Vaccination of grouper broodfish (Epinephelus tukula) reduces the risk of vertical transmission by nervous necrosis virus. Vaccine 2010, 28:996-1001. 10.1016/j.vaccine.2009.10.132, 19954763.
8. Lü L, Zhou SY, Chen C, Weng SP, Chan SM, He JG. Complete genome sequence analysis of an iridovirus isolated from the orange-spotted grouper, Epinephelus coioides. Virology 2005, 339:81-100. 10.1016/j.virol.2005.05.021, 15964605.
9. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17:1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
10. Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 2009, 10:399. 10.1186/1471-2164-10-399, 2748093, 19709400.
11. Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 2010, 11:564. 10.1186/1471-2164-11-564, 3091713, 20942956.
12. Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 2010, 11:384. 10.1186/1471-2164-11-384, 2897810, 20565788.
13. Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007, 17:69-73. 1716268, 17095711.
14. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:33-36. 10.1093/nar/28.1.33, 102395, 10592175.
15. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
16. Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 2009, 10:135-151. 10.1146/annurev-genom-082908-145957, 19715439.
17. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature 2011, 471:473-479. 10.1038/nature09715, 3075879, 21179090.
18. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453:1239-1243. 10.1038/nature07002, 18488015.
19. Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 2010, 11:681. 10.1186/1471-2164-11-681, 3053591, 21122097.
20. Fehniger TA, Wylie T, Germino E, Leong JW, Magrini VJ, Koul S, Keppel CR, Schneider SE, Koboldt DC, Sullivan RP, Heinz ME, Crosby SD, Nagarajan R, Ramsingh G, Link DC, Ley TJ, Mardis ER. Next-generation sequencing identifies the natural killer cell microRNA transcriptome. Genome Res 2010, 20:1590-1604. 10.1101/gr.107995.110, 2963822, 20935160.
21. Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP. The developmental dynamics of the maize leaf transcriptome. Nat Genet 2010, 42:1060-1067. 10.1038/ng.703, 21037569.
22. Jin JY, Zhou L, Wang Y, Li Z, Zhao JG, Zhang QY, Gui JF. Antibacterial and Antiviral Roles of a Fish β-Defensin Expressed Both in Pituitary and Testis. PLoS One 2010, 5:e12883. 10.1371/journal.pone.0012883, 3004800, 21188147.
23. Zhou JG, Wei JG, Xu D, Cui HC, Yan Y, Ou-Yang ZL, Huang XH, Huang YH, Qin QW. Molecular cloning and characterization of two novel hepcidins from orange-spotted grouper, Epinephelus coioides. Fish Shellfish Immunol 2011, 30:559-568. 10.1016/j.fsi.2010.11.021, 21145974.
24. Cui H, Yan Y, Wei J, Hou Z, Huang Y, Huang X, Qin Q. Cloning, characterization, and expression analysis of orange-spotted grouper (Epinephelus coioides) ILF2 gene (EcILF2). Fish Shellfish Immunol 2011, 30:378-388. 10.1016/j.fsi.2010.11.015, 21109006.
25. Dong H, Zeng L, Duan D, Zhang H, Wang Y, Li W, Lin H. Growth hormone and two forms of insulin-like growth factors I in the giant grouper (Epinephelus lanceolatus): molecular cloning and characterization of tissue distribution. Fish Physiol Biochem 2010, 36:201-212. 10.1007/s10695-008-9231-4, 20467861.
26. Shi Y, Zhang Y, Li S, Liu Q, Lu D, Liu M, Meng Z, Cheng CH, Liu X, Lin H. Molecular identification of the Kiss2/Kiss1ra system and its potential function during 17alpha-methyltestosterone-induced sex reversal in the orange-spotted grouper, Epinephelus coioides. Biol Reprod 2010, 83:63-74. 10.1095/biolreprod.109.080044, 20375257.
27. Xia W, Zhou L, Yao B, Li CJ, Gui JF. Differential and spermatogenic cell-specific expression of DMRT1 during sex reversal in protogynous hermaphroditic groupers. Mol Cell Endocrinol 2007, 263:156-172. 10.1016/j.mce.2006.09.014, 17092636.
28. Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O'Donovan C, Apweiler R. The role SWISS-PROT and TrEMBL play in the genome research environment. J Biotechnol 2000, 78:221-234. 10.1016/S0168-1656(00)00198-X, 10751683.
29. Ye J, McGinnis S, Madden TL. BLAST: improvements for better sequence analysis. Nucleic Acids Res 2006, 34:W6-9. 10.1093/nar/gkl164, 1538791, 16845079.
30. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 2009, 37:D205-210. 10.1093/nar/gkn845, 2686570, 18984618.
31. Xing Z, Cardona CJ, Anunciacion J, Adams S, Dao N. Roles of the ERK MAPK in the regulation of proinflammatory and apoptotic responses in chicken macrophages infected with H9N2 avian influenza virus. J Gen Virol 2010, 91:343-351. 10.1099/vir.0.015578-0, 19864500.
32. Regan AD, Cohen RD, Whittaker GR. Activation of p38 MAPK by feline infectious peritonitis virus regulates pro-inflammatory cytokine production in primary blood-derived feline mononuclear cells. Virology 2009, 384:135-143. 10.1016/j.virol.2008.11.006, 19058829.
33. Holloway G, Coulson BS. Rotavirus activates JNK and p38 signaling pathways in intestinal cells, leading to AP-1-driven transcriptional responses and enhanced virus replication. J Virol 2006, 80:10624-10633. 10.1128/JVI.00390-06, 1641755, 16928761.
34. Huang XH, Huang YH, Ouyang ZL, Xu LX, Yan Y, Cui HC, Han X, Qin QW. Singapore grouper iridovirus, a large DNA virus, induces nonapoptotic cell death by a cell type dependent fashion and evokes ERK signaling. Apoptosis 2011, 16:831-845. 10.1007/s10495-011-0616-y, 21656148.
35. Huang XH, Huang YH, Ouyang ZL, Cai J, Yan Y, Qin QW. Roles of Stress-Activated Protein Kinases in the replication of Singapore grouper iridovirus and regulation of the inflammatory responses in grouper cells. J Gen Virol 92:1292-1301.
36. Jiang D, Weidner JM, Qing M, Pan XB, Guo H, Xu C, Zhang X, Birk A, Chang J, Shi PY, Block TM, Guo JT. Identification of five interferon-induced cellular proteins that inhibit west nile virus and dengue virus infections. J Virol 2010, 84:8332-8341. 10.1128/JVI.02199-09, 2916517, 20534863.
37. Wang X, Hinson ER, Cresswell P. The interferon-inducible protein viperin inhibits influenza virus release by perturbing lipid rafts. Cell Host Microbe 2007, 2:96-105. 10.1016/j.chom.2007.06.009, 18005724.
38. Li Y, Li C, Xue P, Zhong B, Mao AP, Ran Y, Chen H, Wang YY, Yang F, Shu HB. ISG56 is a negative-feedback regulator of virus-triggered signaling and cellular antiviral response. Proc Natl Acad Sci USA 2009, 106:7945-7950. 10.1073/pnas.0900818106, 2683125, 19416887.
39. Shi Y, Zhu XP, Yin JK, Zhang QY, Gui JF. Identification and characterization of interferon regulatory factor-1 from orange-spotted grouper (Epinephelus coioides). Mol Biol Rep 2010, 37:1483-1493. 10.1007/s11033-009-9544-0, 19444647.
40. Cui H, Yan Y, Wei J, Huang X, Huang Y, Ouyang Z, Qin Q. Identification and functional characterization of an interferon regulatory factor 7-like (IRF7-like) gene from orange-spotted grouper, Epinephelus coioides. Dev Comp Immunol 2011, 35:672-684. 10.1016/j.dci.2011.01.021, 21295068.
41. Lenschow DJ, Lai C, Frias-Staheli N, Giannakopoulos NV, Lutz A, Wolff T, Osiak A, Levine B, Schmidt RE, García-Sastre A, Leib DA, Pekosz A, Knobeloch KP, Horak I, Virgin HW. IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses. Proc Natl Acad Sci USA 2007, 104:1371-1376. 10.1073/pnas.0607038104, 1783119, 17227866.
42. Okumura A, Lu G, Pitha-Rowe I, Pitha PM. Innate antiviral response targets HIV-1 release by the induction of ubiquitin-like protein ISG15. Proc Natl Acad Sci USA 2006, 103:1440-1445. 10.1073/pnas.0510518103, 1360585, 16434471.
43. Nicholl MJ, Robinson LH, Preston CM. Activation of cellular interferon-responsive genes after infection of human cells with herpes simplex virus type 1. J Gen Virol 2000, 81:2215-2218.
44. Broering R, Zhang X, Kottilil S, Trippler M, Jiang M, Lu M, Gerken G, Schlaak JF. The interferon stimulated gene 15 functions as a proviral factor for the hepatitis C virus and as a regulator of the IFN response. Gut 2010, 59:1111-1119. 10.1136/gut.2009.195545, 20639253.
45. Tan J, Qiao W, Wang J, Xu F, Li Y, Zhou J, Chen Q, Geng Y. IFP35 is involved in the antiviral function of interferon by association with the viral tas transactivator of bovine foamy virus. J Virol 2008, 82:4275-4283. 10.1128/JVI.02249-07, 2293045, 18305040.
46. Song WJ, Qin QW, Qiu J, Huang CH, Wang F, Hew CL. Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis. J Virol 2004, 78:12576-12590. 10.1128/JVI.78.22.12576-12590.2004, 525058, 15507645.
47. Lin PW, Huang YJ, John JA, Chang YN, Yuan CH, Chen WY, Yeh CH, Shen ST, Lin FP, Tsui WH, Chang CY. Iridovirus Bcl-2 protein inhibits apoptosis in the early stage of viral infection. Apoptosis 2008, 13:165-176. 10.1007/s10495-007-0152-y, 17955372.
48. Huang XH, Huang YH, Gong J, Yan Y, Qin QW. Identification and characterization of a putative lipopolysaccharide-induced TNF-alpha factor (LITAF) homolog from Singapore grouper iridovirus. Biochem Biophys Res Commun 2008, 373:140-145. 10.1016/j.bbrc.2008.06.003, 18554501.
49. Viswanathan K, Früh K, DeFilippis V. Viral hijacking of the host ubiquitin system to evade interferon responses. Curr Opin Microbiol 2010, 13:517-523. 10.1016/j.mib.2010.05.012, 2939720, 20699190.
50. Alcami A. Viral mimicry of cytokines, chemokines and their receptors. Nat Rev Immunol 2003, 3:36-50. 10.1038/nri980, 12511874.
51. Ploegh HL. Viral strategies of immune evasion. Science 1998, 280:248-253. 10.1126/science.280.5361.248, 9535648.
52. Yeh CH, Chen YS, Wu MS, Chen CW, Yuan CH, Pan KW, Chang YN, Chuang NN, Chang CY. Differential display of grouper iridovirus-infected grouper cells by immunostaining. Biochem Biophys Res Commun 2008, 372:674-680. 10.1016/j.bbrc.2008.05.126, 18519026.
53. Chen LM, Tran BN, Lin Q, Lim TK, Wang F, Hew CL. iTRAQ analysis of Singapore grouper iridovirus infection in a grouper embryonic cell line. J Gen Virol 2008, 89:2869-2876. 10.1099/vir.0.2008/003681-0, 18931085.
54. Xu D, Wei J, Cui H, Gong J, Yan Y, Lai R, Qin Q. Differential profiles of gene expression in grouper Epinephelus coioides, infected with Singapore grouper iridovirus, revealed by suppression subtractive hybridization and DNA microarray. J Fish Biol 2010, 77:341-360. 10.1111/j.1095-8649.2010.02676.x, 20646160.
55. Chou HH, Holmes MH. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104. 10.1093/bioinformatics/17.12.1093, 11751217.
56. Huang X, Madan A. CAP3:A DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
57. Leu JH, Chang CC, Wu JL, Hsu CW, Hirono I, Aoki T, Juan HF, Lo CF, Kou GH, Huang HC. Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon. BMC Genomics 2007, 8:120. 10.1186/1471-2164-8-120, 1888707, 17506900.
58. Zhang Z, Wang Y, Wang S, Liu J, Warren W, Mitreva M, Walter RB. Transcriptome analysis of female and male Xiphophorus maculatus Jp 163 A. PLoS One 2011, 6:e18379. 10.1371/journal.pone.0018379, 3071723, 21483681.