EST analysis on the gonad development related organs and microarray screen for differentially expressed genes in mature ovary and testis of Scylla paramamosain

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 6, Issue 2, 2011, Pages 150-157

  Zou, Zhihua ^a   Zhang, Ziping ^a,b   Wang, Yilei ^a   Han, Kunhuang ^a   Fu, Mingjun ^a   Lin, Peng ^a   Xiwei, Jia ^a  

^a JIMEI UNIVERSITY   (China)

^b Texas State University   (United States)

Author keywords

Crab; Gene expression; Microarray; Normalized cDNA library; Ovary; Testis

Indexed keywords

CATHEPSIN; RIBOSOME PROTEIN; RIBOSOME PROTEIN L24; THIOREDOXIN PEROXIDASE; UBIQUITIN CONJUGATING ENZYME E2; UNCLASSIFIED DRUG; VITELLOGENIN;

ARTICLE; CRAB; GENE EXPRESSION; MICROARRAY ANALYSIS; NONHUMAN; OVARY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCYLLA PARAMAMOSAIN; TESTIS;

DECAPODA (CRUSTACEA); SCYLLA PARAMAMOSAIN;

EID: 79956351563     PISSN: 1744117X     EISSN: 18780407     Source Type: Journal    
DOI: 10.1016/j.cbd.2010.12.003     Document Type: Article

References (64)

1. Arner, E.S., Holmgren, A., 2000. Physiological functions of thioredoxin and thioredoxin reductase. Eur. J. Biochem. 267, 6102-6109.
2. Bujo, H., Hermann, M., Kaderli, M.O., Jacobsen, L., Sugawara, S., Nimpf, J., Yamamoto, T., Schneider, W.J., 1994. Chicken oocyte growth is mediated by an eight ligand binding repeat member of the LDL receptor family. EMBO J. 13, 51-65.
3. Bustin, S.A., Benes, V., Nolan, T., Pfaffl, M.W., 2005. Quantitative real-time RT-PCR-a perspective. J. Mol. Endocrinol. 34, 597-601.
4. Castrillon, D.H., Quade, B.J., Wang, T.Y., Quigley, C., Crum, C.P., 2000. The human VASA gene is specifically expressed in the germ cell lineage. Proc. Natl Acad. Sci. USA 97, 9585-9590.
5. Chae, H.Z., Kim, I.H., Kim, K., Rhee, S.G., 1993. Cloning, sequencing, and mutation of thiol-specific antioxidant gene of Saccharomyces cerevisiae. J. Biol. Chem. 268, 16815-16821.
6. Chaves-Pozo, E., Zou, J., Secombes, C.J., Cuesta, A., Tafalla, C., 2010. The rainbow trout (Oncorhynchus mykiss) interferon response in the ovary. Mol. Immunol. 47, 1757-1764.
7. Chen, H., Tzeng, C., 2006. Applications of microarray in reproductive medicine. Chang Gung Med. J. 29, 15.
8. Coblentz, F.E., Towle, D.W., Shafer, T.H., 2006. Expressed sequence tags from normalized cDNA libraries prepared from gill and hypodermal tissues of the blue crab, Callinectes sapidus. Comp. Biochem. Physiol. Part D Genomics Proteomics 1, 200-208.
9. Dailey, L., Basilico, C., 2001. Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes. J. Cell. Physiol. 186, 315-328.
10. de Lorgeril, J., Saulnier, D., Janech, M.G., Gueguen, Y., Bachere, E., 2005. Identification of genes that are differentially expressed in hemocytes of the Pacific blue shrimp (Litopenaeus stylirostris) surviving an infection with Vibrio penaeicida. Physiol. Genomics 21, 174-183. (Pubitemid 40898477)
11. DeRisi, J., Penland, L., Brown, P.O., Bittner, M.L., Meltzer, P.S., Ray, M., Chen, Y., Su, Y.A., Trent, J.M., 1996. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457-460.
12. Ellis, J.R., Burke, J.M., 2007. EST-SSRs as a resource for population genetic analyses. Heredity 99, 125-132. (Pubitemid 47123480)
13. Evans, A.C.O., Forde, N., O'Gorman, G.M., Zielak, A.E., Lonergan, P., Fair, T., 2008. Use of microarray technology to profile gene expression patterns important for reproduction in cattle. Reprod. Domest. Anim. 43, 359-367.
14. Ewing, B., Green, P., 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194.
15. Ewing, B., Hillier, L.D., Wendl, M.C., Green, P., 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185.
16. Gavin, A.J., Scheetz, T.E., Roberts, C.A., O'Leary, B., Braun, T.A., Sheffield, V.C., Soares, M.B., Robinson, J.P., Casavant, T.L., 2002. Pooled library tissue tags for EST-based gene discovery. Bioinformatics 18, 1162-1166.
17. Gross, P.S., Bartlett, T.C., Browdy, C.L., Chapman, R.W., Warr, G.W., 2001. Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific White Shrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus. Dev. Comp. Immunol. 25, 565-577.
18. Gusev, O., Ikeda, H., Okochi, T., Lee, J.M., Hatakeyama, M., Kobayashi, C., Agata, K., Yamada, H., Saigusa, M., 2004. Purification and cDNA cloning of the ovigerous-hair stripping substance (OHSS) contained in the hatch water of an estuarine crab Sesarma haematocheir. J. Exp. Biol. 207, 621-632.
19. Habermann, B., Bebin, A.G., Herklotz, S., Volkmer, M., Eckelt, K., Pehlke, K., Epperlein, H., Schackert, H., Wiebe, G., Tanaka, E., 2004. An Ambystoma mexicanum EST sequencing project: analysis of 17, 352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries. Genome Biol. 5, R67.
20. Huang, X., Madan, A., 1999. CAP3: a DNA sequence assembly program. Genome Res. 9, 868-877. (Pubitemid 29488446)
21. Huang, H.Y., Ye, H.H., Li, S.J., Wang, G.Z., 2003. Role of mandibular organ in stimulating ovarian maturation in mud crab, Scylla serrata: an in vitro study. Xiamen Da Xue Xue Bao Zi Ran Ke Xue Ban 22, 295-298.
22. Jiang, H., Cai, Y.M., Chen, L.Q., Zhang, X.W., Hu, S.N., Wang, Q., 2009. Functional annotation and analysis of expressed sequence tags from the hepatopancreas of mitten crab. Mar. Biotechnol. 11, 317-326.
23. Jiang, H., Ren, F., Sun, J., He, L., Li, W., Xie, Y., Wang, Q., 2010. Molecular cloning and gene expression analysis of the leptin receptor in the Chinese mitten crab Eriocheir sinensis. PLoS ONE 5, e11175.
24. Kanehisa, M., Goto, S., 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30. (Pubitemid 30047706)
25. Karoonuthaisiri, N., Sittikankeaw, K., Preechaphol, R., Kalachikov, S., Wongsurawat, T., Uawisetwathana, U., Russo, J.J., Ju, J., Klinbunga, S., Kirtikara, K., 2009. ReproArrayGTS: a cDNA microarray for identification of reproduction-related genes in the giant tiger shrimp Penaeus monodon and characterization of a novel nuclear autoantigenic sperm protein (NASP) gene. Comp. Biochem. Physiol. Part D Genomics Proteomics 4, 90-99.
26. Kim, K., Kim, I.H., Lee, K.Y., Rhee, S.G., Stadtman, E.R., 1988. The isolation and purification of a specific "protector" protein which inhibits enzyme inactivation by a thiol/Fe (III)/O2 mixed-function oxidation system. J. Biol. Chem. 263, 4704-4711.
27. Kim, I.H., Kim, K., Rhee, S.G., 1989. Induction of an antioxidant protein of Saccharomyces cerevisiae by O2, Fe3+, or 2-mercaptoethanol. Proc. Natl Acad. Sci. USA 86, 6018-6022.
28. Kohno, S., Katsu, Y., Urushitani, H., Ohta, Y., Iguchi, T., Guillette Jr., L.J., 2009. Potential contributions of heat shock proteins to temperature-dependent sex determination in the American alligator. Sex. Dev. 4, 73-87.
29. Kuballa, A.V., Elizur, A., 2008. Differential expression profiling of components associated with exoskeletal hardening in crustaceans. BMC Genomics 9, 575.
30. Li, A., Sadasivam, M., Ding, J.L., 2003. Receptor-ligand interaction between vitellogenin receptor (VtgR) and vitellogenin (Vtg), implications on low density lipoprotein receptor and apolipoprotein B/E. J. Biol. Chem. 278, 2799-2806.
31. Ma, C.Y., Guo, Y.J., Zhou, K.Y., 2010. Identification and characteristics of a novel gene, EJO1, in the Chinese mitten crab (Eriocheir japonica sinensis) ovary. Mol. Biol. Rep. 37, 2587-2592.
32. Macnae, W., 1969. A general account of the fauna and flora of mangrove swamps and forests in the Indo-West-Pacific region. Adv. Mar. Biol. 6, 73-103.
33. Noce, T., Okamoto-Ito, S., Tsunekawa, N., 2001. Vasa homolog genes in mammalian germ cell development. Cell Struct. Funct. 26, 131-136.
34. O'Leary, N.A., Trent, H.F., Robalino, J., Peck, M.E.T., McKillen, D.J., Gross, P.S., 2006. Analysis of multiple tissue-specific cDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei. Integr. Comp. Biol. 46, 931-939.
35. Overton, J.L., Macintosh, D.J., Thorpe, R.S., 1997. Multivariate analysis of the mud crab Scylla serrata (Brachyura: Portunidae) from four locations in Southeast Asia. Mar. Biol. 128, 55-62.
36. Perez, F., Ortiz, J., Zhinaula, M., Gonzabay, C., Calderon, J., Volckaert, F.A.M.I., 2005. Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar. Biotechnol. 7, 554-569.
37. Preechaphol, R., Leelatanawit, R., Sittikankeaw, K., Klinbunga, S., Khamnamtong, B., Puanglarp, N., Menasveta, P., 2007. Expressed sequence tag analysis for identification and characterization of sex-related genes in the giant tiger shrimp Penaeus monodon. J. Biochem. Mol. Biol. 40, 501-510.
38. Qiu, G.F., Liu, P., 2009. On the role of Cdc2 kinase during meiotic maturation of oocyte in the Chinese mitten crab, Eriocheir sinensis. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 152, 243-248.
39. Qiu, G.F., Yamano, K., Unuma, T., 2005. Cathepsin C transcripts are differentially expressed in the final stages of oocyte maturation in kuruma prawn Marsupenaeus japonicus. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 140, 171-181.
40. Qiu, L., Jiang, S., Huang, J., Wang, W., Zhang, D., Wu, Q., Yang, K., 2008. Molecular cloning and mRNA expression of cathepsin C gene in black tiger shrimp (Penaeus monodon). Comp. Biochem. Physiol. A Mol. Integr. Physiol. 150, 320-325.
41. Raz, E., 2000. The function and regulation of vasa-like genes in germ-cell development. Genome Biol. 1, REVIEWS1017.
42. Shagin, D.A., Rebrikov, D.V., Kozhemyako, V.B., Altshuler, I.M., Shcheglov, A.S., Zhulidov, P.A., Bogdanova, E.A., Staroverov, D.B., Rasskazov, V.A., Lukyanov, S., 2002. A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res. 12, 1935-1942. (Pubitemid 35469943)
43. Shen, B.L., Zhang, Z.P., Wang, Y.L., Wang, G.Z., Chen, Y., Lin, P., Wang, S.H., Zou, Z.H., 2009. Differential expression of ubiquitin-conjugating enzyme E2r in the developing ovary and testis of penaeid shrimp Marsupenaeus japonicus. Mol. Biol. Rep. 36, 1149-1157.
44. Small, C.M., Carney, G.E., Mo, Q., Vannucci, M., Jones, A.G., 2009. A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: evidence for masculinization of the transcriptome. BMC Genomics 10, 579.
45. Smith, T.P.L., Grosse, W.M., Freking, B.A., Roberts, A.J., Stone, R.T., Casas, E., Wray, J.E., White, J., Cho, J., Fahrenkrug, S.C., 2001. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res. 11, 626-630. (Pubitemid 32331560)
46. Smyth, G.K., Speed, T., 2003. Normalization of cDNA microarray data. Methods 31, 265-273. (Pubitemid 37338763)
47. Stillman, J.H., Teranishi, K.S., Tagmount, A., Lindquist, E.A., Brokstein, P.B., 2006. Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes. Integr. Comp. Biol. 46, 919-929.
48. Sugama, K., Hutapea, J.H., 1999. Genetic characterization in the mud crab Scylla (Brachyura: Portunidae). In: Keenan, C.P., Blackshaw, A. (Eds.), Mud Crab Aquaculture and Biology, vol. 78. ACIAR Proceedings, Brisbane, pp. 43-47.
49. Tassanakajon, A., Klinbunga, S., Paunglarp, N., Rimphanitchayakit, V., Udomkit, A., Jitrapakdee, S., Sritunyalucksana, K., Phongdara, A., Pongsomboon, S., Supungul, P., 2006. Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database. Gene 384, 104-112. (Pubitemid 44738332)
50. Tatusov, R.L., Koonin, E.V., Lipman, D.J., 1997. A genomic perspective on protein families. Science 278, 631-637. (Pubitemid 27464953)
51. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., 2003. The COG database: an updated version includes eukaryotes. BMC Bioinform. 4, 41.
52. Thiel, T., Michalek, W., Varshney, R., Graner, A., 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411-422.
53. van de Wetering, M., Oosterwegel, M., van Norren, K., Clevers, H., 1993. Sox-4, an Sry-like HMG box protein, is a transcriptional activator in lymphocytes. EMBO J. 12, 3847-3854. (Pubitemid 23282761)
54. Wang, Y.L., Dai, J., Yao, Y.L., Zhang, Z.P., 2004. Screen on sex-differential DNA fragments in mud crab Scylla serrata using AFLP. J Fisher Sci China 11, 286-290.
55. Wang, G.Z., Li, S.J., Zeng, C.S., Lin, S.J., Kong, X.H., Ai, C.X., Lin, Q.W., 2005. Status of biological studies and aquaculture development of the mud crab, Scylla serrata, in China. Aquacult. Int. 13, 459-468.
56. Wonglapsuwan, M., Miyazaki, T., Loongyai, W., Chotigeat, W., 2010. Characterization and biological activity of the ribosomal protein L10a of the white shrimp: Fenneropenaeus merguiensis De Man during vitellogenesis. Mar. Biotechnol. 12, 230-240.
57. Wu, L.T., Chu, K.H., 2010. Characterization of an ovary-specific glutathione peroxidase from the shrimp Metapenaeus ensis and its role in crustacean reproduction. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 155, 26-33.
58. Yamano, K., Unuma, T., 2006. Expressed sequence tags from eyestalk of kuruma prawn, Marsupenaeus japonicus. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 143, 155-161.
59. Ye, H.H., Li, S.J., Huang, H.Y., Wang, G.Z., 2002. Study on the relation between Y-organ and ovarian development of the mud crab, Scylla serrata. Xiamen Da Xue Xue Bao Zi Ran Ke Xue Ban 41, 791-795.
60. Ye, H.H., Li, S.J., Huang, H.Y., Wang, G.Z., Lin, Q.W., 2003. Histological studies on the development of androgenic gland in mud crab, Scylla serrata. J Fishery Scif China 10, 376-381.
61. Yokota, N., Harada, Y., Sawada, H., 2010. Identification of testis-specific ubiquitin-conjugating enzyme in the ascidian Ciona intestinalis. Mol. Reprod. Dev. 77, 640-647.
62. Zhang, E.F., Qiu, G.F., 2010. A novel Dmrt gene is specifically expressed in the testis of Chinese mitten crab, Eriocheir sinensis. Dev. Genes Evol. 220, 151-159.
63. Zhang, Z.P., Wang, Y.L., Jiang, Y.H., Lin, P., Jia, X.W., Zou, Z.H., 2007. Ribosomal protein L24 is differentially expressed in ovary and testis of the marine shrimp Marsupenaeus japonicus. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 147, 466-474.
64. Zhang, Z.P., Shen, B.L., Wang, Y.L., Chen, Y., Wang, G.Z., Lin, P., Zou, Z.H., 2010. Molecular cloning of proliferating cell nuclear antigen and its differential expression analysis in the developing ovary and testis of penaeid shrimp Marsupenaeus japonicus. DNA Cell Biol. 29, 163-170.