Amphimedon queenslandica high resolution developmental transcriptomic time-course. Amphimedon queenslandica

Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 124 single embryo samples.

经典胚胎学研究表明，脊椎动物在胚胎发育中期会呈现相似的形态学特征。这一“phylotypic stage（胚型阶段）”近期得到了转录组分析的支持，相关分析还在线虫动物与节肢动物中检测到了类似的发育阶段。这三个类群的保守性发育阶段促使我们提出疑问：是否所有动物都会因动物发育的祖先演化约束而经历一个通用的确定性发育阶段？既往研究提示，HOX基因或许构成了这类“zootypic stage（动物型阶段）”，但该假说性阶段迄今尚未得到系统性分析。我们对10个分属不同动物门的物种开展了胚胎发育分析，涵盖环节动物、扁形动物、线虫动物、缓步动物、果蝇、海胆、斑马鱼、海葵、海绵以及栉水母。针对每个物种，我们在约100个不同发育阶段采集了胚胎转录组，并对其基因表达谱进行了分析。我们发现，所有物种的基因表达均呈现动态变化，且以阶段特异性的模式进行组织。值得注意的是，从蛋白质结构域组成来看，动物胚胎发育中的合子表达存在两个核心模块：其一与细胞增殖相关，其二则与细胞分化相关。这两个模块之间的转换涉及zootype（动物型）的诱导；除含同源框的基因外，该过程还涉及Wnt信号通路、Notch信号通路以及叉头框结构域转录因子。我们的研究成果对动物发育的普遍性进行了系统性表征，并明确了胚胎发育的约束位点与可塑性位点。实验整体设计：共包含124个单胚胎样本。