Sex-biased expression occurs in one-third of genes. (A) On average, 9995 genes are observed in each stage, 7214 genes are shared between all stages, and 12,490 genes are expressed in one or more stages. (B) 85.7% of genes exhibit greater than fourfold difference in expression between maximum and minimum expression time points. (C) The distribution of coefficient of variation calculated for each gene identifies genes whose expression is highly consistent across development. (D) Technical replicates of pupa RNA-seq exhibit nearly perfect correlation (R = 0.99). (E) Females and early embryos exhibit a high degree of correlation (R = 0.80). (F) 5251 exhibit fourfold difference in expression level between males and females: 1088 genes up-regulated in females are consistent with their expression in early embryos (red), suggesting their importance in embryonic development, 3486 genes are up-regulated in males (blue). (G) Genes without a known ortholog are abundantly expressed in males, many of which have known male-specific functions including seminal fluid proteins and male-specific transcripts. (H) Many genes on unassembled heterochromatin (chrU) exhibit male-specific expression. (I) Genomic PCR results suggest CG40968, CG40583, CG40992, and CG41561 are linked to chromosome Y.
