An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Reading, Benjamin J ^a   Chapman, Robert W ^b   Schaff, Jennifer E ^a   Scholl, Elizabeth H ^a   Opperman, Charles H ^a   Sullivan, Craig V ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b SOUTH CAROLINA DEPARTMENT OF NATURAL RESOURCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DANIO RERIO; MORONE; MORONE SAXATILIS; MORONIDAE;

COMPLEMENTARY DNA; TRANSCRIPTOME;

ANIMAL; ARTICLE; BASS; CHEMISTRY; CYTOLOGY; DNA SEQUENCE; ESTUARY; EXPRESSED SEQUENCE TAG; FEMALE; FISHERY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; OOCYTE; OOCYTE DEVELOPMENT; OVARY; ZEBRA FISH;

ANIMALS; BASS; DATABASES, GENETIC; DNA, COMPLEMENTARY; ESTUARIES; EXPRESSED SEQUENCE TAGS; FEMALE; FISHERIES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; OOCYTES; OOGENESIS; OVARY; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; ZEBRAFISH;

EID: 84857130843     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-111     Document Type: Article

References (70)

1. Selective breeding for the hybrid striped bass (Morone chrysops, Rafinesque x M. saxatilis, Walbaum) industry: status and perspectives. Garber AF, Sullivan CV, Aquacult Res 2006 37 319 338
2. A case history of effective fishery management: Chesapeake Bay striped bass. Richards RA, Rago PJ, N Am J Fish Manage 1999 19 356 375 (Pubitemid 29405219)
3. Isolation and characterization of 149 novel microsatellite DNA markers for striped bass, Morone saxatilis, and cross-species amplification in white bass, M. chrysops, and their hybrid. Couch CR, Garber AF, Rexroad CE III, Abrams JM, Stannard JA, Westerman ME, Sullivan CV, Mol Ecol Notes 2006 6 667 669 (Pubitemid 44252570)
4. Identification and characterization of microsatellites for striped bass from repeat-enriched libraries. Rexroad CE III, Vallejo R, Coulibaly I, Westerman ME, Sullivan CV, Conserv Genet 2006 7 971 982 (Pubitemid 44736874)
5. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus). Liu S, Rexroad CE III, Couch CR, Cordes J, Reece K, Sullivan CV, Mar Biotechnol doi: 10.1007/s10126-011-9407-2
6. Endocrine manipulations of spawning in cultured fish: from hormones to genes. Zohar Y, Mylonas CC, Aquaculture 2001 197 99 136 (Pubitemid 32442666)
7. Functional genomics and proteomic approaches for the study of gamete formation and viability in farmed finfish. Cerd J, Bobe J, Babin PJ, Admon A, Lubzens E, Rev Fish Sci 2008 16 Suppl 1 54 70
8. Egg and sperm quality in fish. Bobe J, Labbé C, Gen Comp Endocrinol 2010 165 535 548
9. RNA-Seq: a revolutionary tool for transcriptomics. Wang Z, Gerstein M, Snyder M, Nat Rev Genet 2009 10 57 63
10. High-throughput functional annotation and data mining with the Blast2GO suite. Götz S, García-Gámez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talán M, Dopazo J, Conesa A, Nucleic Acids Res 2008 36 3420 3435 (Pubitemid 351859009)
11. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, Nat Methods 2008 5 621 628 (Pubitemid 351911867)
12. Protein identification by tandem mass spectrometry and sequence database searching. Nesvizhskii AI, Methods in Molecular Biology New York: Springer, Matthiesen R, 2007 87 119
13. A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. von Schalburg KR, Rise ML, Brown GD, Davidson WS, Koop BF, Biol Reprod 2005 72 687 699 (Pubitemid 40279848)
14. Identification of new participants in the rainbow trout (Oncorhynchus mykiss) oocyte maturation and ovulation process using cDNA microarrays. Bobe J, Montfort J, Nguyen T, Fostier A, Reprod Biol Endocrinol 2006 4 39
15. In silico identification and molecular characterization of genes predominantly expressed in the fish oocyte. Bobe J, Nguyen T, Mahé S, Monget P, BMC Genomics 2008 9 499
16. Comparative transcriptomic analysis of follicle-enclosed oocyte maturational and developmental competence acquisition in two non-mammalian vertebrates. Gohin M, Bobe J, Chesnel F, BMC Genomics 2010 11 18
17. Identification of differentially expressed genes during primary and early secondary oocyte growth in coho salmon. Luckenbach JA, Iliev DB, Goetz FW, Swanson P, Oncorhynchus kisutch. Reprod Biol Endocrinol 2008 6 2
18. Profile analysis of expressed sequence tags derived from ovary of tilapia, Oreochromis mossambicus. Chu S-L, Weng C-F, Hsiao C-D, Hwang P-P, Chen Y-C, Ho J-M, Lee S-J, Aquacult 2006 251 537 548 (Pubitemid 43138798)
19. Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality. Mommens M, Fernandes JMO, Bizuayehu TT, Bolla SL, Johnston IA, Babiak I, BMC Res Notes 2010 3 138
20. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform. Cerd J, Mercadé J, Lozano JJ, Manchado M, Tingaud-Sequeira A, Astola A, Infante C, Halm S, Vĩas J, Castellana B, Asensio E, Cãavate P, Martínez-Rodríguez G, Piferrer F, Planas JV, Prat F, Yúfera M, Durany O, Subirada F, Rosell E, Maes T, BMC Genomics 2008 9 508
21. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. Leong JS, Jantzen SG, von Schalburg KR, Cooper GA, Messmer AM, Liao NY, Munro S, Moore R, Holt RA, Jones SJM, Davidson WS, Koop BF, BMC Genomics 2010 11 279
22. Using global genome approaches to address problems in cod mariculture. Goetz FW, McCauley L, Goetz GW, Norberg B, ICES J Mar Sci 2006 63 393 399 (Pubitemid 43265944)
23. Sequencing breakthroughs for genomic ecology and evolutionary biology. Hudson ME, Mol Ecol Resour 2008 8 3 17 (Pubitemid 350231221)
24. Rapid transcriptome sequencing for a nonmodel organism using 454 pyrosequencing. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH, Mol Ecol 2008 17 1636 1647 (Pubitemid 351441703)
25. Wasp brain gene expression supports an evolutionary link between maternal behavior and eusociality. Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, Willoughby DA, Simons JF, Egholm M, Hunt JH, Hudson ME, Robinson GE, Science 2007 318 441 444 (Pubitemid 47614527)
26. A hitchhiker's guide to expressed sequence tag (EST) analysis. Nagaraj SH, Gasser RB, Ranganathan S, Brief Bioinform 2006 8 6 21
27. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. Sreenivasan R, Cai M, Bartfai R, Wang X, Christoffels A, Orban L, PLoS ONE 2008 3 1791
28. Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools. Li Y, Chia JM, Bartfai R, Christoffels A, Yue GH, Ding K, Ho MY, Hill JA, Stupka E, Orban L, Comp Funct Genomics 2004 5 403 418 (Pubitemid 39206857)
29. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, Lee SC, Xu M, Liu F, Ruan H, Eun A, He Y, Ma W, Wang W, Wen Z, Peng J, Genome Res 2003 13 455 466 (Pubitemid 36395403)
30. WU-GSC EST Group: An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson SL, Genome Res 2001 11 1594 1602 (Pubitemid 32894686)
31. The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Habermann B, Oegema J, Sunyaev S, Shevchenko A, Mol Cell Proteomics 2004 3 238 249 (Pubitemid 38714279)
32. Striped Bass Transcriptome Sequence Contigs Database. Reading BJ, Sullivan CV, Chapman RW, http://www.animalgenome.org/aquaculture/database/
33. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF, Genome Res 2004 14 478 490 (Pubitemid 38380403)
34. The expression of three abundance classes of messenger RNA in mouse tissues. Hastie ND, Bishop JO, Cell 1976 9 761 774
35. A gene atlas of the mouse and human protein-encoding transcriptomes. Su AI, Wiltshire T, Batalov B, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB, Proc Natl Acad Sci USA 2004 101 6062 6067 (Pubitemid 38520528)
36. Comparative proteomics of the developing fish (zebrafish and gilthead seabream) oocytes. Ziv T, Gattegno T, Chapovetsky V, Wolf H, Barnea E, Lubzens E, Admon A, Comp Biochem Physiol Part D Genomics Proteomics 2008 3 12 35 (Pubitemid 351250858)
37. Zebrafish ovarian follicle transcriptome. Knoll-Gellida A, Babin PJ, The Fish Oocyte: From Basic Studies to Biotechnological Applications New York: Springer, Babin PJ, Cerd J, Lubzens E, 2007 77 97
38. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals. Knoll-Gellida A, André M, Gattegno T, Forgue J, Admon A, Babin PJ, BMC Genomics 2006 7 46
39. Characterization of the ovarian transcriptome through the use of differential analysis of gene expression methodologies. Hennebold JD, Hum Reprod Update 2004 10 227 239 (Pubitemid 38744868)
40. A mammalian oocyte-specific linker histone gene H1oo: homology with the genes for the oocyte-specific cleavage stage histone (CS-H1) of sea urchin and the B4/H1M histone of the frog. Tanaka M, Hennebold JD, Macfarlane J, Adashi EY, Development 2001 128 655 664 (Pubitemid 32229243)
41. Cellular and subcellular localization of stathmin during oocyte and preimplantation embryo development. Koppel J, Rehák P, Baran V, Veselá J, Hlinka D, Manceau V, Sobel A, Mol Reprod Dev 1999 53 306 317 (Pubitemid 29247330)
42. Oolemmal proteomics-identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane. Calvert ME, Digilio LC, Herr JC, Coonrod SA, Reprod Biol Endocrinol 2003 1 27
43. In silico gene expression analysis-an overview. Murray D, Doran P, MacMathuna P, Moss AC, Mol Cancer 2007 6 50
44. Cloning and characterization of a novel oocyte-specific gene zorg in zebrafish. Dai L, Ma W, Li J, Xu Y, Li W, Zhao Y, Deng F, Theriogenology 2009 71 441 449 (Pubitemid 50279869)
45. Regulation of the oocyte-to-zygote transition. Stitzel ML, Seydoux G, Science 2007 316 407 408 (Pubitemid 46651482)
46. Cyclin B in fish oocytes: its cDNA and amino acid sequences, appearance during maturation, and induction of p34 cdc2 activation. Hirai T, Yamashita M, Yoshikuni M, Lou YH, Nagahama Y, Mol Reprod Dev 1992 33 131 140
47. 17,20-dihydroxy-4-pregnen-3-one, a maturation inducing hormone in fish oocytes: mechanisms of synthesis and action. Nagahama Y, Steroids 1997 62 190 196 (Pubitemid 27067004)
48. On cyclins, oocytes, and eggs. Taieb F, Thibier C, Jessus C, Mol Reprod Dev 1997 48 397 411 (Pubitemid 27413554)
49. Molecular characterization and expression profiles of cyclin B1, B2 and Cdc2 kinase during oogenesis and spermatogenesis in rainbow trout (Oncorhynchus mykiss). Qiu G, Ramachandra RK, Rexroad CE III, Yao J, Anim Reprod Sci 2008 105 209 225 (Pubitemid 351324034)
50. Human cyclin K, a novel polymerase II-associated cyclin possessing both carboxy-terminal domain kinase and cdk-activating kinase activity. Edwards MC, Wong C, Elledge SJ, Mol Cell Biol 1998 18 4291 4300 (Pubitemid 28287952)
51. Securin' M-phase entry. Solomon MJ, Burton JL, Nat Cell Biol 2008 10 381 383
52. Novel expression of importin homologue in marine teleost, Pagrus major. Gen K, Yamaguchi S, Okuzawa K, Kagawa H, Alam MS, Comp Biochem Physiol B Biochem Mol Biol 2008 151 420 427
53. Geminin, an inhibitor of DNA replication, is degraded during mitosis. McGarry TJ, Kirschner MW, Cell 1998 93 1043 1053 (Pubitemid 28280797)
54. Histone H2A has a novel variant in fish oocytes. Wu N, Yue H, Chen B, Gui JF, Biol Reprod 2009 81 275 283
55. Comparison of human solute carriers. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A, Protein Sci 2010 19 412 428
56. The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteins. Hediger M, Romero MF, Peng J, Rolfs A, Takanaga H, Bruford EA, Pflugers Arch 2004 447 465 468 (Pubitemid 38241432)
57. The HUGO Gene Nomenclature Committee (HGNC). Povey S, Lovering R, Bruford E, Wright M, Lush M, Wain H, Hum Genet 2001 109 678 680 (Pubitemid 34051423)
58. Marine fish egg hydration is aquaporin-mediated. Fabra M, Raldúa D, Power DM, Deen PM, Cerd J, Science 2005 307 545 (Pubitemid 40165672)
59. Vitellogenesis in Fishes. Reading BJ, Sullivan CV, Encyclopedia of Fish Physiology: From Genome to Environment Maryland Heights: Academic Press, Inc., Farrell AP, Stevens ED, Cech JJ Jr, Richards JG, 2011 257
60. Induced maturation and spawning of domestic and wild striped bass Morone saxatilis (Walbaum), broodstock with implanted GnRH analogue and injected hCG. Hodson RG, Sullivan CV, Aquacult Res 1993 24 389 398
61. Artificial spawning and fry production of striped bass and hybrids. Rees RA, Harrell RM, Culture and Propagation of Striped Bass and its Hybrids Bethesda: American Fisheries Society, Harrell RM, Kerby JH, Minton RV, 1990 43 72
62. Changes in gonadal hormones during oocyte development in the striped bass, Morone saxatilis. Berlinsky DL, Specker JL, Fish Physiol Biochem 1991 9 51 62
63. Purification, characterization and immunoassay of striped bass (Morone saxatilis) vitellogenin. Tao Y, Hara A, Hodson RG, Woods LC III, Sullivan CV, Fish Physiol Biochem 1993 12 31 46
64. Cyto-histological examination of post-vitellogenesis and final oocyte maturation in captive-reared striped bass. Mylonas CC, Woods LC III, Zohar Y, J Fish Biol 1997 50 34 49 (Pubitemid 27155403)
65. Genome sequencing in microfabricated high-density picolitre reactors. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM, Nature 2005 437 376 80 (Pubitemid 41613494)
66. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 403 410
67. Gene Ontology: tool for the unification of biology. Ashburner M, Ball K, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G, Nat Genet 2000 25 25 29 (Pubitemid 30257031)
68. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Conesa A, Götz S, Int J Plant Genomics 2008 2008 619832
69. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Conesa A, Götz S, García-Gámez JM, Terol J, Talán M, Robles M, Bioinformatics 2005 21 3674 3676 (Pubitemid 41264107)
70. Utilization of digital differential display to identify novel targets of Oct3/4. Tokuzawa Y, Maruyama M, Yamanaka S, Methods Mol Biol 2006 329 223 231