Gene discovery from an ovary cDNA library of oriental river prawn Macrobrachium nipponense by ESTs annotation

Ping Wu1, Dan Qi2, Liqiao Chen1, Hao Zhang1, Xiaowei Zhang2, Jian Guang Qin3, Songnian Hu2
1College of Life Science, East China Normal University, Shanghai 200062, PR China
2Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
3School of Biological Sciences, Flinders University of South Australia, Adelaide, SA 5001, Australia

Tài liệu tham khảo

Adams, 1991, Complementary DNA sequencing: expressed sequence tags and human genome project, Science, 252, 1651, 10.1126/science.2047873 Aflalo, 2007, Characterization of a vasa-like gene from the Pacific white shrimp Litopenaeus vannamei and its expression during oogenesis, Mol. Reprod. Dev., 74, 172, 10.1002/mrd.20622 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Aoki, 2003, Molecular cloning and characterization of cathepsin B from the hepatopancreas of northern shrimp Pandalus borealis, Comp. Biochem. Phys. B, 134, 681, 10.1016/S1096-4959(03)00023-X Avarre, 2003, Relationship between vitellogenin and vitellin in a marine shrimp (Penaeus semisulcatus) and molecular characterization of vitellogenin complementary DNAs, Biol. Reprod., 69, 355, 10.1095/biolreprod.102.011627 Beninger, 2003, Demonstration of nutrient pathway from the digestive system to oocytes in the gonad intestinal loop of the scallop Pecten maximus L, Biol. Bull., 205, 83, 10.2307/1543448 Bond, 1987, Intracellular proteases, Annu. Rev. Biochem., 56, 333, 10.1146/annurev.bi.56.070187.002001 Chen, 1998, Purification and characterization of vitellin from the freshwater giant prawn, Macrobrachium rosenbergii, Zool. Stud., 37, 126 Chenna, 2003, Multiple sequence alignment with the clustal series of programs, Nucleic Acids Res., 31, 3497, 10.1093/nar/gkg500 Cho, 1999, Mosquito cathepsin B-like protease involved in embryonic degradation of vitellin is produced as a latent extraovarian precursor, J. Biol. Chem., 274, 13311, 10.1074/jbc.274.19.13311 Chu, 2006, Profile analysis of expressed sequence tags derived from the ovary of tilapia, Oreochromis mossambicus, Aquaculture, 251, 537, 10.1016/j.aquaculture.2005.05.040 Chuang, 2007, Cloning and expression analysis of heat shock cognate 70 gene promoter in tiger shrimp (Penaeus monodon), Gene, 405, 10, 10.1016/j.gene.2007.08.016 Clark, 1990, Jelly layer formation in Penaeoidean shrimp eggs, Biol. Bull., 178, 295, 10.2307/1541831 Dong, 2007, Discovery of genes involved in defense/immunity functions in a haemocytes cDNA library from Fenneropenaeus chinensis by ESTs annotation, Aquaculture, 272, 208, 10.1016/j.aquaculture.2007.07.217 Durand, 2004, Crassostrea gigas ferritin: cDNA sequence analysis for two heavy chain type subunits and protein purification, Gene, 338, 187, 10.1016/j.gene.2004.04.027 Dyrlov Bendtsen, 2004, Improved prediction of signalpeptides: SignalP 3.0, J. Mol. Biol., 340, 783, 10.1016/j.jmb.2004.05.028 Ewing, 1998, Base-calling of automated sequencer traces using phred II Error probabilities, Genome Res., 8, 186, 10.1101/gr.8.3.186 Ewing, 1998, Base-calling of automated sequencer traces using phred I Accuracy assessment, Genome Res., 8, 175, 10.1101/gr.8.3.175 Finn, 2008, The Pfam protein families database: nucleic acids research, vol. 36, D281 Fu, 2007, The technology of non-pollution farming of Macrobrachium nipponense, J. Sci. Fish. Farm., 12 Fu, 2004, Artificial interspecific hybridization between Macrobrachium species, Aquaculture, 232, 215, 10.1016/j.aquaculture.2003.08.002 Gao, 2006, Study on site of vitellogenin in synthesis in the freshwater prawn Macrobrachium nipponense, Biotechnol. Bull. Suppl., 438 Glotzer, 1991, Cyclin is degraded by the ubiquitin pathway, Nature, 349, 132, 10.1038/349132a0 Gross, 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, 10.1016/S0145-305X(01)00018-0 Gubler, 1983, A simple and very efficient method for generating cDNA libraries, Gene, 25, 263, 10.1016/0378-1119(83)90230-5 Han, 1994, Immunocytochemical identification of the site of vitellogenin synthesis in the freshwater prawn Macrobrachium nipponense, Fish. Sci., 60, 149, 10.2331/fishsci.60.149 Harris, 2004, The Gene Ontology (GO) database and informatics resource, Nucleic Acids Res., 32, 258, 10.1093/nar/gkh036 Hsieh, 2006, Molecular cloning and tissue distribution of ferritin in Pacific white shrimp (Litopenaeus vannamei), Fish Shellfish Immunol., 21, 279, 10.1016/j.fsi.2005.12.003 http://beta.uniprot.org/. http://www.ebi.uniprot.org/index.shtml. http://www.phrap.org. Hu, 2004, Shrimp cathepsin L encoded by an intronless gene has predominant expression in hepatopancreas, and occurs in the nucleus of oocyte, Comp. Biochem. Phys. B, 137, 21, 10.1016/j.cbpc.2003.09.010 Huang, 1999, CAP3: a DNA sequence assembly program, Genome Res., 9, 868, 10.1101/gr.9.9.868 Huang, 2003, Two types of new ferritin cDNA sequences from Xenopus laevis germinal vesicle oocytes, DNA Sequence, 14, 211, 10.1080/1042517031000098810 Irion, 1999, Developmental and cell biological functions of the Drosophila DEAD-box protein abstrakt, Curr. Biol., 9, 1, 10.1016/S0960-9822(00)80082-2 Jasmani, 2004, Localization of vitellogenin mRNA expression and vitellogenin uptake during ovarian maturation in the giant freshwater prawn Macrobrachium rosenbergii, J. Exp. Zool. Part A, 301, 334, 10.1002/jez.a.20044 Kanehisa, 2000, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27 Khayat, 2001, Molecular characterization and high expression during oocyte development of a shrimp ovarian cortical rod protein homologous to insect intestinal peritrophins, Biol. Reprod., 64, 1090, 10.1095/biolreprod64.4.1090 Kim, 2007, Molecular cloning and characterization of cortical rod protein in the giant freshwater prawn Macrobrachium rosenbergii, a species not forming cortical rod structures in the oocytes, Comp. Biochem. Physiol. B, 148, 184, 10.1016/j.cbpb.2007.05.008 Klinbunga, 2006, Genetic diversity of the giant tiger shrimp (Penaeus monodon) in Thailand revealed by PCR-SSCP of polymorphic EST-derived markers, Biochem. Genet., 44, 222, 10.1007/s10528-006-9027-0 Le Boulay, 1998, Cathepsin L gene organization in crustaceans, Gene, 218, 77, 10.1016/S0378-1119(98)00385-0 Lee, 1999, Hepatopancreas is the likely organ of vitellogenin synthesis in the freshwater prawn, Macrobrachium rosenbergii, J. Exp. Zool., 284, 798, 10.1002/(SICI)1097-010X(19991201)284:7<798::AID-JEZ10>3.0.CO;2-C Lehnert, 1999, Tissue-specific expressed sequence tags from the black tiger shrimp Penaeus monodon, Mar. Biotechnol., 1, 465, 10.1007/PL00011803 Liu, 2004, Molecular cloning and expression of two HSP70 genes in the prawn, Macrobrachium rosenbergii, Cell Stress Chaperones, 9, 313, 10.1379/CSC-40R.1 Lo, 2004, Cloning and molecular characterization of heat shock cognate 70 from tiger shrimp (Penaeus monodon), Cell Stress Chaperones, 9, 332, 10.1379/CSC-47R.1 Lo, 2007, Molecular coordinated regulation of gene expression during ovarian development in the penaeid shrimp, Mar. Biotechnol., 9, 459, 10.1007/s10126-007-9006-4 Loongyai, 2007, Isolation and functional characterization of a new shrimp ovarian peritrophin with antimicrobial activity from Fenneropenaeus merguiensis, Mar. Biotechnol., 9, 624, 10.1007/s10126-007-9019-z Matsubara, 1993, cDNA analyses in the human genome project, Gene, 135, 265, 10.1016/0378-1119(93)90076-F Matsumoto, 1993, Haploid specific activations of protamine 1 and hsc70t genes in mouse spermatogenesis, Biochim. Biophys. Acta., 1174, 274, 10.1016/0167-4781(93)90196-K McGrath, 1999, The lysosomal cysteine proteases, Annu. Rev. Biophys. Biomol. Struct., 28, 181, 10.1146/annurev.biophys.28.1.181 Melecha, 1992, Sex-ratio and sex-determination in progeny from crosses of surgically sex-reversed freshwater prawns, Macrobrachium rosenbergii, Aquaculture, 105, 201, 10.1016/0044-8486(92)90087-2 Moriya, 2007, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Res., 35, 182, 10.1093/nar/gkm321 Nakkrasae, 2007, A vasa-like gene in the giant freshwater prawn, Macrobrachium rosenbergii, Mol. Reprod. Dev., 74, 835, 10.1002/mrd.20680 Ono, 2003, Regulation of actin filament dynamics by actin depolymerizing factor/cofilin and actin-interacting protein 1: new blades for twisted filaments, Biochemistry, 42, 13363, 10.1021/bi034600x Pham, 2008, Cofilin/ADF is required for retinal elongation and morphogenesis of the Drosophila rhabdomere, Dev. Biol., 318, 82, 10.1016/j.ydbio.2008.03.006 Phiriyangkul, 2006, Molecular characterization of a cDNA encoding vitellogenin in the banana shrimp, Penaeus (Litopenaeus) merguiensis and sites of vitellogenin mRNA expression, Mol. Reprod. Dev., 73, 410, 10.1002/mrd.20424 Preechaphol, 2005, Isolation and characterization of differentially expressed genes in ovaries of the giant tiger shrimp Preechaphol, 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, 10.5483/BMBRep.2007.40.4.501 Qiu, 2005, Three forms of cyclin B transcripts in the ovary of the kuruma prawn Marsupenaeus japonicus: their molecular characterizations and expression profiles during oogenesis, Comp. Biochem. Physiol. B, 141, 186, 10.1016/j.cbpc.2005.03.003 Qiu, 2007, Molecular cloning and characterization of a cyclin B gene on the ovarian maturation stage of black tiger shrimp (Penaeus monodon), Mol. Biol. Rep., 10.1007/s11033-006-9052-4 Ravid, 1999, Lipid accumulation in the ovaries of a marine shrimp Penaeus semisulcatus (De Haan), J. Exp. Biol., 202, 1819, 10.1242/jeb.202.13.1819 Rojtinnakorn, 2002, Gene expression in haemocytes of kuruma prawn, Penaeus japonicus, in response to infection with WSSV by EST approach, Fish Shellfish Immunol., 13, 69, 10.1006/fsim.2001.0382 Schmid, 1992, D-E-A-D protein family of putative RNA helicases, Mol. Microbiol., 6, 283, 10.1111/j.1365-2958.1992.tb01470.x Sellars, 2007, A PL10 vasa-Like gene in the kuruma shrimp, Marsupenaeus japonicus, expressed during development and in adult gonad, Mar. Biotechnol., 9, 377, 10.1007/s10126-007-6118-9 Shafer, 2006, Identifying exoskeleton proteins in the blue crab from an expressed sequence tag (EST) library, Integr. Comp. Biol., 46, 978, 10.1093/icb/icl022 Shen, 2004, Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs, Prog. Nat. Sci., 1, 47, 10.1080/10020070412331343131 Sirotkin, 2006, The role of protein kinase A and cyclin-dependent (CDC2) kinase in the control of basal and IGF-II-induced proliferation and secretory activity of chicken ovarian cells, Anim. Reprod. Sci., 92, 169, 10.1016/j.anireprosci.2005.05.018 Stillman, 2006, Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes, Integr. Comp. Biol., 46, 919, 10.1093/icb/icl007 Styhler, 1998, Vasa is required for GURKEN accumulation in the oocyte, and is involved in oocyte differentiation and germline cyst development, Development, 125, 1569, 10.1242/dev.125.9.1569 Supungul, 2004, Antimicrobial peptides discovered in the black tiger shrimp Penaeus monodon using the EST approach, Dis. Aquat. Org., 61, 123, 10.3354/dao061123 Tassanakajon, 2006, Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database, Gene, 384, 104, 10.1016/j.gene.2006.07.012 Tiu, 2006, Equal contribution of hepatopancreas and ovary to the production of vitellogenin (PmVg1) transcripts in the tiger shrimp, Penaeus monodon, Aquaculture, 254, 666, 10.1016/j.aquaculture.2005.11.001 Towle, 2006, Gene discovery in Carcinus maenas and Homarus americanus via expressed sequence tags, Integr. Comp. Biol., 46, 912, 10.1093/icb/icl002 Troys, 2008, Ins and outs of ADF/cofilin activity and regulation, Eur. J. Cell. Biol., 4, 1 Tsang, 2003, Organization of the shrimp vitellogenin gene: evidence of multiple genes and tissue specific expression by the ovary and hepatopancreas, Gene, 303, 99, 10.1016/S0378-1119(02)01139-3 Tseng, 2002, Hepatopancreas and ovary are sites of vitellogenin synthesis as determined from partial cDNA encoding of vitellogenin in the marine shrimp, Penaeus vannamei, Invertebr. Reprod. Dev., 42, 137, 10.1080/07924259.2002.9652770 Turk, 2000, Lysosomal cysteine proteases: more than scavengers, Biochim. Biophys. Acta, 1477, 98, 10.1016/S0167-4838(99)00263-0 Vega-Núñez, 1999, Dynamic restricted expression of the chaperone Hsc70 in early chick development, Mech. Dev., 82, 199, 10.1016/S0925-4773(99)00015-5 Vernet, 1995, Processing of the papain precursor. The ionization state of a conserved amino acid motif within the Pro region participates in the regulation of intramolecular processing, J. Biol. Chem., 270, 10838, 10.1074/jbc.270.18.10838 Wouters, 2001, Lipid composition and vitamin content of wild female Litopenaeus vannamei in different stages of sexual maturation, Aquaculture, 198, 307, 10.1016/S0044-8486(01)00522-1 Yamaguchi, 1998, Chicken chromobox proteins: cDNA cloning of CHCB1,-2,-3 and their relation to W-heterochromatin, Exp. Cell. Res., 242, 303, 10.1006/excr.1997.4082 Yamamoto, 1994, Molecular cloning and sequencing of cDNA that encodes cysteine proteinase in the eggs of the silkmoth, Bombyx mori, J. Biochem., 116, 1330, 10.1093/oxfordjournals.jbchem.a124683 Yamashita, 2004, Characterization of multiple members of the HSP70 family in platyfish culture cells: molecular evolution of stress protein HSP70 in vertebrates, Gene, 336, 207, 10.1016/j.gene.2004.04.023 Yang, 2000, Determination of amino acid sequence and site of mRNA expression of four vitellins in the giant freshwater prawn, Macrobrachium rosenbergii, J. Exp. Zool., 287, 413, 10.1002/1097-010X(20001101)287:6<413::AID-JEZ2>3.0.CO;2-V Zhang, 2006, Cloning, expression and identification of ferritin from Chinese shrimp, Fenneropenaeus chinensis, J. Biotechnol., 125, 173, 10.1016/j.jbiotec.2006.03.010 Zhou, 2008, Gene expression of ferritin in tissue of the Pacific white shrimp, Litopenaeus vannamei after exposure to pH stress, Aquaculture, 275, 356, 10.1016/j.aquaculture.2007.12.005