Deuterostomes are one major group of bilaterians composed by hemichordates and echinoderms (collectively called Ambulacraria) and chordates. Comparative studies between these groups can provide valuable insights into the nature of the last common ancestor of deuterostomes and that of bilaterians. Indirect development of hemichordates, with larval phases similar to echinoderms and an adult body plan with an anteroposterior polarity like chordates and other bilaterians, makes them a suitable model for studying the molecular basis of development among deuterostomes. However, a comprehensive, quantitative catalogue of gene expression and chromatin dynamics in hemichordates is still lacking. In this study, we analysed the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordate Ptychodera flava. We observed that P. flava development is underpinned by a biphasic transcriptional program probably controlled by distinct genetic networks. Comparisons with other bilaterian species revealed similar transcriptional and regulatory dynamics during hemichordate gastrulation, cephalochordate neurulation and elongation stages of annelids. By means of regulatory networks analysis and functional validations by transgenesis experiments in echinoderms, we propose that gastrulation is the stage of highest molecular resemblance in deuterostomes and that much of the molecular basis of deuterostome development was probably present in the bilaterian last common ancestor.

Deuterostomes 是由半脊索动物和棘皮动物（统称为 Ambulacraria）和脊索动物组成的一个主要双侧动物群。这些群体之间的比较研究可以为了解后口动物和双侧动物的最后一个共同祖先的性质提供有价值的见解。半脊索动物的间接发育，幼虫期类似于棘皮动物，成体计划像脊索动物和其他双侧动物一样具有前后极性，使它们成为研究后口动物发育分子基础的合适模型。然而，仍然缺乏半脊索动物中基因表达和染色质动力学的全面、定量目录。在这项研究中，我们分析了间接发育的半脊索动物 Ptychodera flava 多个发育阶段的转录组和染色质可及性。我们观察到 P. flava 的发育以双相转录程序为基础，可能由不同的遗传网络控制。与其他双侧物种的比较揭示了半脊索动物原肠胚形成、头索动物神经形成和环节动物伸长阶段相似的转录和调节动力学。通过棘皮动物转基因实验的调控网络分析和功能验证，我们提出原肠胚形成是后口中分子相似性最高的阶段，并且后口发育的大部分分子基础可能存在于双侧最后一个共同祖先中。