Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis

Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcript ion units. We therefore undertook a survey of the repertoire of genes expre ssed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis E STs computationally collapsed into 1560 cDNA set used for further analysis. OF those, 11% correspond to named genes, and 33% provide biological eviden ce for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST Frequency a nd microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furt hermore, >80% of the genes expressed in the testis showed onefold overexpre ssion relative to ovaries, or gonadectomized flies. Additionally, >3% showe d more than threefold overexpression at p <0.05. Surprisingly, 22% of the g enes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequenc ing additional cDNA libraries From defined tissues, such as testis, will be important tools For refined annotation of the Drosophila genome. Additiona lly, these data suggest that the number of genes in Drosophila will signifi cantly exceed the conservative estimate of 13,601.