Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex-the hermaphrodite-and there are a relatively large number of genes that remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression and co-expression analyses, we identified transcription factors required for differentiation of male genital structures, semen proteins, and candidates for components of synapse function. Comparison with other prediction tools suggests that our dataset can expand gene predictions. The results validate the dataset as a rich resource for future gene discovery in C. elegans.