Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidian species to symmetrically document the dynamics of ZGA. We identify two coordinated ZGA waves represent early developmental and housekeeping gene reactivation, respectively. Single-cell RNA sequencing reveals that the major expression wave exhibits spatial heterogeneity and significantly correlates with cell fate. Moreover, allele-specific expression occurs in a species- rather than parent-related manner, demonstrating the divergence of cis-regulatory elements between the two species. These findings provide insights into ZGA in chordates.

合子基因组激活（ZGA）是后生动物早期胚胎发生中的一个普遍过程，此时静止的合子核启动全局转录。然而，与大规模基因组激活和等位基因特异性表达（ASE）相关的机制仍不清楚。在这里，我们开发了两种深度分化（120 Mya）海鞘物种的杂交体，以对称地记录 ZGA 的动态。我们确定了两个协调的 ZGA 波，分别代表早期发育和管家基因重新激活。单细胞 RNA 测序表明，主要表达波表现出空间异质性，并与细胞命运显着相关。此外，等位基因特异性表达以物种而非亲本相关的方式发生，证明了两个物种之间顺式调控元件的差异。这些发现为脊索动物中的 ZGA 提供了见解。