Logo of compfungenJournal's HomeManuscript SubmissionAims and ScopeAuthor GuidelinesEditorial BoardHome
Comp Funct Genomics. 2004 Jul; 5(5): 403–418.
PMCID: PMC2447462

Comparative Analysis of the Testis and Ovary Transcriptomes in Zebrafish by Combining Experimental and Computational Tools


Studies on the zebrafish model have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the zebrafish is still limited. Here we provide an analysis on the gene sets expressed in the adult zebrafish testis and ovary in an attempt to identify genes with potential role in (zebra)fish gonad development and function. We produced 10 533 expressed sequence tags (ESTs) from zebrafish testis or ovary and downloaded an additional 23 642 gonad-derived sequences from the zebrafish EST database. We clustered these sequences together with over 13 000 kidney-derived zebrafish ESTs to study partial transcriptomes for these three organs. We searched for genes with gonad-specific expression by screening macroarrays containing at least 2600 unique cDNA inserts with testis-, ovary- and kidney-derived cDNA probes. Clones hybridizing to only one of the two gonad probes were selected, and subsequently screened with computational tools to identify 72 genes with potentially testis-specific and 97 genes with potentially ovary-specific expression, respectively. PCR-amplification confirmed gonad-specificity for 21 of the 45 clones tested (all without known function). Our study, which involves over 47 000 EST sequences and specialized cDNA arrays, is the first analysis of adult organ transcriptomes of zebrafish at such a scale. The study of genes expressed in adult zebrafish testis and ovary will provide useful information on regulation of gene expression in teleost gonads and might also contribute to our understanding of the development and differentiation of reproductive organs in vertebrates.

Full Text

The Full Text of this article is available as a PDF (498K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. [PMC free article] [PubMed]
  • Andrews J, Bouffard GG, Cheadle C, Lü J, Becker KG, Oliver B. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res. 2000 Dec;10(12):2030–2043. [PMC free article] [PubMed]
  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25–29. [PMC free article] [PubMed]
  • Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, Mitchell AL, Moulton G, Nordle A, Paine K, Taylor P, et al. PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 2003 Jan 1;31(1):400–402. [PMC free article] [PubMed]
  • Bateman Alex, Birney Ewan, Cerruti Lorenzo, Durbin Richard, Etwiller Laurence, Eddy Sean R, Griffiths-Jones Sam, Howe Kevin L, Marshall Mhairi, Sonnhammer Erik L L. The Pfam protein families database. Nucleic Acids Res. 2002 Jan 1;30(1):276–280. [PMC free article] [PubMed]
  • Bleil JD, Wassarman PM. Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae possessing receptor activity for sperm. Cell. 1980 Jul;20(3):873–882. [PubMed]
  • Bleil JD, Wassarman PM. Structure and function of the zona pellucida: identification and characterization of the proteins of the mouse oocyte's zona pellucida. Dev Biol. 1980 Apr;76(1):185–202. [PubMed]
  • Bleil JD, Wassarman PM. Sperm-egg interactions in the mouse: sequence of events and induction of the acrosome reaction by a zona pellucida glycoprotein. Dev Biol. 1983 Feb;95(2):317–324. [PubMed]
  • Boeckmann Brigitte, Bairoch Amos, Apweiler Rolf, Blatter Marie-Claude, Estreicher Anne, Gasteiger Elisabeth, Martin Maria J, Michoud Karine, O'Donovan Claire, Phan Isabelle, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003 Jan 1;31(1):365–370. [PMC free article] [PubMed]
  • Bonaldo MF, Lennon G, Soares MB. Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 1996 Sep;6(9):791–806. [PubMed]
  • Bono Hidemasa, Yagi Ken, Kasukawa Takeya, Nikaido Itoshi, Tominaga Naoko, Miki Rika, Mizuno Yosuke, Tomaru Yasuhiro, Goto Hitoshi, Nitanda Hiroyuki, et al. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. 2003 Jun;13(6B):1318–1323. [PMC free article] [PubMed]
  • Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W. STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res. 2001 Jan 1;29(1):234–238. [PMC free article] [PubMed]
  • Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson SL, Group tW An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Genome Res. 2001 Sep;11(9):1594–1602. [PMC free article] [PubMed]
  • Coimbra Roney S, Weil Dominique, Brottier Phillipe, Blanchard Stéphane, Levi Michael, Hardelin Jean-Pierre, Weissenbach Jean, Petit Christine. A subtracted cDNA library from the zebrafish (Danio rerio) embryonic inner ear. Genome Res. 2002 Jun;12(6):1007–1011. [PMC free article] [PubMed]
  • Cooke Howard J, Saunders Philippa T K. Mouse models of male infertility. Nat Rev Genet. 2002 Oct;3(10):790–801. [PubMed]
  • De Kretser DM, Baker HW. Infertility in men: recent advances and continuing controversies. J Clin Endocrinol Metab. 1999 Oct;84(10):3443–3450. [PubMed]
  • Del Giacco L, Diani S, Cotelli F. Identification and spatial distribution of the mRNA encoding an egg envelope component of the Cyprinid zebrafish, Danio rerio, homologous to the mammalian ZP3 (ZPC). Dev Genes Evol. 2000 Jan;210(1):41–46. [PubMed]
  • Geisler R, Rauch GJ, Baier H, van Bebber F, Bross L, Dekens MP, Finger K, Fricke C, Gates MA, Geiger H, et al. A radiation hybrid map of the zebrafish genome. Nat Genet. 1999 Sep;23(1):86–89. [PubMed]
  • Hauri H, Appenzeller C, Kuhn F, Nufer O. Lectins and traffic in the secretory pathway. FEBS Lett. 2000 Jun 30;476(1-2):32–37. [PubMed]
  • Hillier LD, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S, Dietrich N, DuBuque T, Favello A, Gish W, et al. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 1996 Sep;6(9):807–828. [PubMed]
  • Hosono M, Ishikawa K, Mineki R, Murayama K, Numata C, Ogawa Y, Takayanagi Y, Nitta K. Tandem repeat structure of rhamnose-binding lectin from catfish (Silurus asotus) eggs. Biochim Biophys Acta. 1999 Nov 16;1472(3):668–675. [PubMed]
  • Hsiao Chung-Der, Tsai Huai-Jen. Transgenic zebrafish with fluorescent germ cell: a useful tool to visualize germ cell proliferation and juvenile hermaphroditism in vivo. Dev Biol. 2003 Oct 15;262(2):313–323. [PubMed]
  • Hukriede N, Fisher D, Epstein J, Joly L, Tellis P, Zhou Y, Barbazuk B, Cox K, Fenton-Noriega L, Hersey C, et al. The LN54 radiation hybrid map of zebrafish expressed sequences. Genome Res. 2001 Dec;11(12):2127–2132. [PMC free article] [PubMed]
  • Jakobsson PJ, Thorén S, Morgenstern R, Samuelsson B. Identification of human prostaglandin E synthase: a microsomal, glutathione-dependent, inducible enzyme, constituting a potential novel drug target. Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7220–7225. [PMC free article] [PubMed]
  • Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):218–223. [PMC free article] [PubMed]
  • Kanamori Akira, Naruse Kiyoshi, Mitani Hiroshi, Shima Akihiro, Hori Hiroshi. Genomic organization of ZP domain containing egg envelope genes in medaka (Oryzias latipes). Gene. 2003 Feb 13;305(1):35–45. [PubMed]
  • Kilpatrick David C. Animal lectins: a historical introduction and overview. Biochim Biophys Acta. 2002 Sep 19;1572(2-3):187–197. [PubMed]
  • Kleene KC. A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells. Mech Dev. 2001 Aug;106(1-2):3–23. [PubMed]
  • Knapik EW, Goodman A, Ekker M, Chevrette M, Delgado J, Neuhauss S, Shimoda N, Driever W, Fishman MC, Jacob HJ. A microsatellite genetic linkage map for zebrafish (Danio rerio). Nat Genet. 1998 Apr;18(4):338–343. [PubMed]
  • Lilford R, Jones AM, Bishop DT, Thornton J, Mueller R. Case-control study of whether subfertility in men is familial. BMJ. 1994 Sep 3;309(6954):570–573. [PMC free article] [PubMed]
  • Lo Jane, Lee Sorcheng, Xu Min, Liu Feng, Ruan Hua, Eun Alvin, He Yawen, Ma Weiping, Wang Weefuen, Wen Zilong, et al. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res. 2003 Mar;13(3):455–466. [PMC free article] [PubMed]
  • Loris Remy. Principles of structures of animal and plant lectins. Biochim Biophys Acta. 2002 Sep 19;1572(2-3):198–208. [PubMed]
  • Maduro Maria Rosa, Lamb Dolores J. Understanding new genetics of male infertility. J Urol. 2002 Nov;168(5):2197–2205. [PubMed]
  • Matzuk Martin M, Lamb Dolores J. Genetic dissection of mammalian fertility pathways. Nat Cell Biol. 2002 Oct;4 (Suppl):s41–s49. [PubMed]
  • Miller RT, Christoffels AG, Gopalakrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA. A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res. 1999 Nov;9(11):1143–1155. [PMC free article] [PubMed]
  • Dias Neto E, Correa RG, Verjovski-Almeida S, Briones MR, Nagai MA, da Silva W, Jr, Zago MA, Bordin S, Costa FF, Goldman GH, et al. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3491–3496. [PMC free article] [PubMed]
  • Dias Neto E, Harrop R, Correa-Oliveira R, Wilson RA, Pena SD, Simpson AJ. Minilibraries constructed from cDNA generated by arbitrarily primed RT-PCR: an alternative to normalized libraries for the generation of ESTs from nanogram quantities of mRNA. Gene. 1997 Feb 20;186(1):135–142. [PubMed]
  • Onichtchouk Daria, Aduroja Kristin, Belting Heinz-Georg, Gnügge Lara, Driever Wolfgang. Transgene driving GFP expression from the promoter of the zona pellucida gene zpc is expressed in oocytes and provides an early marker for gonad differentiation in zebrafish. Dev Dyn. 2003 Nov;228(3):393–404. [PubMed]
  • Ozeki Y, Yokota Y, Kato KH, Titani K, Matsui T. Developmental expression of D-galactoside-binding lectin in sea urchin (Anthocidaris crassispina) eggs. Exp Cell Res. 1995 Feb;216(2):318–324. [PubMed]
  • Pijnacker LP, Ferwerda MA. Zebrafish chromosome banding. Genome. 1995 Oct;38(5):1052–1055. [PubMed]
  • Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, et al. A global profile of germline gene expression in C. elegans. Mol Cell. 2000 Sep;6(3):605–616. [PubMed]
  • Schummer M, Ng WV, Bumgarner RE, Nelson PS, Schummer B, Bednarski DW, Hassell L, Baldwin RL, Karlan BY, Hood L. Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas. Gene. 1999 Oct 1;238(2):375–385. [PubMed]
  • Sigrist Christian J A, Cerutti Lorenzo, Hulo Nicolas, Gattiker Alexandre, Falquet Laurent, Pagni Marco, Bairoch Amos, Bucher Philipp. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 2002 Sep;3(3):265–274. [PubMed]
  • Sola L, Gornung E. Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. Genetica. 2001;111(1-3):397–412. [PubMed]
  • Spargo Scott C, Hope Rory M. Evolution and nomenclature of the zona pellucida gene family. Biol Reprod. 2003 Feb;68(2):358–362. [PubMed]
  • Tateno H, Ogawa T, Muramoto K, Kamiya H, Hirai T, Saneyoshi M. A novel rhamnose-binding lectin family from eggs of steelhead trout (Oncorhynchus mykiss) with different structures and tissue distribution. Biosci Biotechnol Biochem. 2001 Jun;65(6):1328–1338. [PubMed]
  • Tateno Hiroaki, Ogawa Tomohisa, Muramoto Koji, Kamiya Hisao, Saneyoshi Mineo. Distribution and molecular evolution of rhamnose-binding lectins in Salmonidae: isolation and characterization of two lectins from white-spotted Charr (Salvelinus leucomaenis) eggs. Biosci Biotechnol Biochem. 2002 Jun;66(6):1356–1365. [PubMed]
  • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. [PMC free article] [PubMed]
  • Ton C, Hwang DM, Dempsey AA, Tang HC, Yoon J, Lim M, Mably JD, Fishman MC, Liew CC. Identification, characterization, and mapping of expressed sequence tags from an embryonic zebrafish heart cDNA library. Genome Res. 2000 Dec;10(12):1915–1927. [PMC free article] [PubMed]
  • Ton Christopher, Stamatiou Dimitri, Dzau Victor J, Liew Choong-Chin. Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development. Biochem Biophys Res Commun. 2002 Sep 6;296(5):1134–1142. [PubMed]
  • Uchida Daisuke, Yamashita Michiaki, Kitano Takeshi, Iguchi Taisen. Oocyte apoptosis during the transition from ovary-like tissue to testes during sex differentiation of juvenile zebrafish. J Exp Biol. 2002 Mar;205(Pt 6):711–718. [PubMed]
  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995 Nov 11;23(21):4407–4414. [PMC free article] [PubMed]
  • Wakimoto BT. Doubling the rewards: testis ESTs for Drosophila gene discovery and spermatogenesis expression profile analysis. Genome Res. 2000 Dec;10(12):1841–1842. [PubMed]
  • Wassarman P, Chen J, Cohen N, Litscher E, Liu C, Qi H, Williams Z. Structure and function of the mammalian egg zona pellucida. J Exp Zool. 1999 Oct 15;285(3):251–258. [PubMed]
  • Woods IG, Kelly PD, Chu F, Ngo-Hazelett P, Yan YL, Huang H, Postlethwait JH, Talbot WS. A comparative map of the zebrafish genome. Genome Res. 2000 Dec;10(12):1903–1914. [PMC free article] [PubMed]
  • Wu Xuemei, Viveiros Maria M, Eppig John J, Bai Yuchen, Fitzpatrick Susan L, Matzuk Martin M. Zygote arrest 1 (Zar1) is a novel maternal-effect gene critical for the oocyte-to-embryo transition. Nat Genet. 2003 Feb;33(2):187–191. [PubMed]
  • Yasumasu S, Wardrip NJ, Zenner BD, Lee YM, Smith AJ, Hedrick JL. Fertilisation in fish: a cortical alveolar lectin and its potential role in the block to polyspermy. Zygote. 2000;8 (Suppl 1):S66–S66. [PubMed]
  • Zeng Sheng, Gong Zhiyuan. Expressed sequence tag analysis of expression profiles of zebrafish testis and ovary. Gene. 2002 Jul 10;294(1-2):45–53. [PubMed]

Articles from Comparative and Functional Genomics are provided here courtesy of Hindawi Publishing Corporation


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...