Developmental milestones punctuate gene expression in the Caenorhabditis embryo

The complex process by which a metazoan develops from a single cell to a multi-cellular differentiated organism is typically organized by biologists into stages. For example, in the chordate embryo, the gastrula, the neurula and the tail-bud constitute characteristic processes. A debate runs through the history of embryology questioning whether such stages hint at the modularity of embryonic development1-3, or rather, that stages exist in the mind of the biologist, and not in the larva4 or embryo. It thus remains unclear which position accurately reflects the nature of development on a molecular, gene regulatory level. Here we demonstrate that development of five Caenorhabditis species proceeds through multiple distinct stages in which the transcriptome is resistant to differences in species-specific developmental timings. By comparing the complete protein-coding transcriptomes of individually staged embryos across ten morphological markers, we found that time-invariant stages occur throughout development, including a stage we identify as the nematode phylotypic stage. Between such stages, embryos follow transitory states characterized by an acceleration of transcriptional activity. Therefore, on a molecular level, development cannot be viewed as a single process continuously proceeding through time, but rather as a succession of discontinuous stages, or milestones. Comparing the nematode developmental transcriptome with that of the chordate we report on the macro evolution of a milestone by duplication and diversification. This modular view of development by milestones will allow for a more complete understanding of how the functional organization of the embryo has influenced the evolution of animal morphology and diversity.后生动物（metazoan）从单细胞发育为多细胞分化有机体的复杂过程，通常被生物学家划分为若干阶段。例如在脊索动物胚胎中，原肠胚（gastrula）、神经胚（neurula）与尾芽（tail-bud）均为典型的发育进程。胚胎学史上始终存在一场持久争论：这类发育阶段究竟暗示了胚胎发育的模块化（modularity）本质，抑或这些阶段仅存在于生物学家的认知框架中，而非幼虫或胚胎本身的固有属性[1-3,4]。因此，在分子与基因调控层面，哪种观点更准确地反映了发育的本质，目前仍无定论。本研究证实，5种隐杆线虫属（Caenorhabditis）的发育过程会历经多个截然不同的阶段，这些阶段的转录组（transcriptome）不受物种特异性发育时序差异的影响。通过比对基于10种形态学标记（morphological markers）单独分期的胚胎的完整编码蛋白转录组，我们发现整个发育过程中均存在时间不变阶段（time-invariant stages），其中包括我们鉴定出的线虫系统发生阶段（phylotypic stage）。在这些阶段之间，胚胎会经历以转录活性增强为特征的过渡状态。因此，从分子层面来看，发育并非一个随时间持续推进的单一过程，而是一系列不连续的阶段或里程碑。通过比对线虫与脊索动物的发育转录组，我们揭示了里程碑阶段通过基因复制与功能分化实现的宏观进化（macro evolution）过程。这种基于里程碑阶段的发育模块化视角，将帮助我们更全面地理解胚胎的功能组织如何影响动物形态与多样性的演化。