A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: evidence for masculinization of the transcriptome

Abstract

Background: In many taxa, males and females are very distinct phenotypically, and these differences often reflect divergent selective pressures acting on the sexes. Phenotypic sexual dimorphism almost certainly reflects differing patterns of gene expression between the sexes, and microarray studies have documented widespread sexually dimorphic gene expression. Although the evolutionary significance of sexual dimorphism in gene expression remains unresolved, these studies have led to the formulation of a hypothesis that male-driven evolution has resulted in the masculinization of animal transcriptomes. Here we use a microarray assessment of sex- and gonad-biased gene expression to test this hypothesis in zebrafish.

Results: By using zebrafish Affymetrix microarrays to compare gene expression patterns in male and female somatic and gonadal tissues, we identified a large number of genes (5899) demonstrating differences in transcript abundance between male and female Danio rerio. Under conservative statistical significance criteria, all sex-biases in gene expression were due to differences between testes and ovaries. Male-enriched genes were more abundant than female-enriched genes, and expression bias for male-enriched genes was greater in magnitude than that for female-enriched genes. We also identified a large number of genes demonstrating elevated transcript abundance in testes and ovaries relative to male body and female body, respectively.

Conclusion: Overall our results support the hypothesis that male-biased evolutionary pressures have resulted in male-biased patterns of gene expression. Interestingly, our results seem to be at odds with a handful of other microarray-based studies of sex-specific gene expression patterns in zebrafish. However, ours was the only study designed to address this specific hypothesis, and major methodological differences among studies could explain the discrepancies. Regardless, all of these studies agree that transcriptomic sex differences in D. rerio are widespread despite the apparent absence of heterogamety. These differences likely make important contributions to phenotypic sexual dimorphism in adult zebrafish; thus, from an evolutionary standpoint, the precise roles of sex-specific selection and sexual conflict in the evolution of sexually dimorphic gene expression are very important. The results of our study and others like it set the stage for further work aimed at directly addressing this exciting issue in comparative genomics.

Figure 1

Expression bias for male-enriched genes is greater than expression bias for female-enriched genes. Histogram showing the distributions of fold change values for female-enriched (red) and male-enriched (blue) genes. Recall that our differential expression criteria revealed 2512 female-enriched and 3387 male-enriched genes. Each observation represented in this graph is a mean across four fold change values, corresponding to the four different absolute expression analyses. Arrows at x-axis termini represent distribution tails, which are not shown. These tails (approximately 200 observations each) were omitted for ease of graphical representation, and their absence does not affect the interpretation of the histogram. Comparison of the two distributions reveals that male-enriched genes are more frequent at higher fold change intervals, relative to female-enriched genes, and a Mann-Whitney U test formally confirms higher fold change values for male-enriched genes (p < 0.001).

Figure 2

Overlap of sex- and gonad-biased gene expression. Male (left) and female (right) Venn diagrams, demonstrating the proportion of genes that fall into both sex- and gonad-biased expression categories. These numbers are based on a "strict consensus" FDR = 0.05, and no fold change threshold. Roughly 33% of male-enriched genes are also significantly testis-upregulated, whereas approximately 22% of female-enriched genes are also significantly ovary-upregulated.