show Abstracthide AbstractComplete metamorphosis of holometabolous insects is a complex biological process characterized by profound morphological, physiological, and transcriptional changes. To reveal the temporal dynamics of gene expression during this critical developmental transition, a detailed analysis of the developmental transcriptomes of two Drosophila species, Drosophila melanogaster and Drosophila virilis, was conducted. We confirm partial recapitulation of the embryonic transcriptional program in pupae, but instead of the traditional hourglass model, which posits maximal conservation at mid-embryonic stages, at different stages of pupae we observe a more complicated pattern of alternating low and high diversity, resembling an inverted hourglass, or "spindle". This observation challenges the notion of a singular conserved phylotypic period during holometabola ontogeny and underscores the complexity of developmental processes during complete metamorphosis. Notably, recently formed genes (specific to insects) exhibit pronounced expression peaks during mid-pupal development, underscoring their potential role in developmental transitions. Overall design: The dataset includes RNA sequencing samples from wild-type Drosophila melanogaster (Oregon-R) and Drosophila virilis (Strain 9), representing the subgenera Sophophora and Drosophila. Collections included phylotypic embryonic stage, larvae, stages P1 to P5, intermediate, and late pupal stages, as well as five-day-old adult males. All samples were gathered in three biological replicates.