Open AccessComparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools
Author(s) -
Li Yang,
Chia Jer Ming,
Bartfai Richard,
Christoffels Alan,
Yue Gen Hua,
Ding Ke,
Ho Mei Yin,
Hill James A.,
Stupka Elia,
Orban Laszlo
Publication year - 2004
Publication title -
comparative and functional genomics
Language(s) - English
Resource type - Journals
eISSN - 1532-6268
pISSN - 1531-6912
DOI - 10.1002/cfg.418
Subject(s) - zebrafish , gonad , biology , ovary , transcriptome , complementary dna , expressed sequence tag , gene , danio , cdna library , development of the gonads , genetics , gene expression , computational biology , anatomy
Abstract 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. Copyright © 2004 John Wiley & Sons, Ltd.