Gene duplications have been broadly implicated in the generation of 
testis-specific genes. To perform a comprehensive analysis of paralogous 
testis-biased genes, we characterized the testes transcriptome of Drosophila 
melanogaster by comparing gene expression in testes vs. ovaries, heads, and 
gonadectomized males. A number of the identified 399 testis-biased genes code 
for the known components of mature sperm. Among the detected 69 genes 
downregulated in testes, a large fraction is required for viability. By 
analyzing paralogs of testis-biased genes, we identified "co-regulated" 
paralogous pairs in which both genes are testis biased, "anti-regulated" pairs 
in which one paralog is testis biased and the other downregulated in testes, and 
"neutral" pairs in which one paralog is testis biased and the other 
constitutively expressed. The numbers of identified co-regulated and 
anti-regulated pairs were higher than expected by chance. Testis-biased genes 
included in these pairs show decreased frequency of lethal mutations, suggesting 
their specific role in male reproduction. These genes also show exceptionally 
high interspecific variability of expression in comparison between D. 
melanogaster and the closely related D. simulans. Further, interspecific changes 
in testis bias of expression are generally correlated within the co-regulated 
pairs and are anti-correlated within the anti-regulated pairs, suggesting 
coordinated regulation within both types of paralogous gene pairs.