TABLE 2.

Genes used in the analysis of six species of the melanogaster group

Gene classification	No. of genes used
Sex tissue expressed	A total of 5156 genes classified on the basis of their site of expression using the EST database (UniGene, supplemental Table 1 at http://www.genetics.org/supplemental/; 1400 head-specific, 397 ovary-specific, 1102 testis-specific, 372 ovary-related, 922 testis-related, 246 sex-tissue-shared, and 717 genes expressed in all three tissues). A total of 889 genes did not match any tissue category.
Seminal fluid proteins	A stringently selected set of 25 SFP genes (supplemental Table 1 at http://www.genetics.org/supplemental/) were analyzed (see materialsandmethods).
Female reproductive tract proteins	Divided into 246 genes with extracellular localization signals, which are more likely to interact directly with male SFPs and sperm proteins, and 433 genes without a predicted secretion signal sequence and/or predicted transmembrane helices (see materialsandmethods). A total of 8 genes were characterized in SFPs and FRTPs.
Gametogenesis	Identified on the basis of Gene Ontology searches via TermLink (FlyBase).
Spermatogenesis	Seventy-three genes involved in the development and/or maturation of sperm.
Oogenesis	A total of 226 genes involved in the development of eggs. Among the 73 and 226 genes, 21 genes are found to be involved in both spermatogenesis and oogenesis.
SRR genes	A total of 2505 genes are classified as SRR genes (testis-specific and ovary-specific genes, genes expressed in both testis and ovary, SFPs, FRTPs, and genes characterized in gametogenesis). A total of 2298 genes were found in only one category (testis/ovary/testis&ovary, SFP/FRTP, gametogenesis), 198 genes in at least two categories, and 8 in the three different categories (testis/ovary/ testis&ovary, SFP/FRTP and gametogenesis, supplemental Table 2 at http://www.genetics.org/supplemental/).