Evolutionary landscapes of zygotic genome activation across animals

During early animal embryogenesis, control over gene expression transitions from maternally deposited products to newly transcribed zygotic RNA. This process, termed zygotic genome activation (ZGA), is universal and essential but remains poorly characterized beyond a handful of model species 1. Here, we generated a comprehensive transcriptomic atlas of early embryogenesis from 61 animal species, spanning 13 phyla. By applying a unified computational framework, we systematically inferred the timing of ZGA across species. We uncover a large variation in ZGA timing, but find that a proxy for nuclear-to-cytoplasmic (N/C) ratio robustly predicts the onset of genome activation. Comparative analyses of the properties of zygotic genes showed that they are shorter and with fewer introns, enriched in functions related to RNA processing and gene expression, and phylogenetically younger than maternal genes. Altogether, our findings suggest that ZGA is universally timed by the stoichiometry between DNA content and specific maternally deposited factors, and this activation involves a highly flexible transcriptomic program that follows a deeply conserved molecular logic.