Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates [ATAC-Seq]. Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates [ATAC-Seq]

Evolutionary history of deuterostomes has remained unsolved and is intimately related to how chordates originated. Within the clade of deuterostomes, hemichordates and echinoderms (together called Ambulacraria) are sister groups of chordates; comparative studies among the three are insightful for understanding deuterostome evolution. Indirect-developing hemichordates, such as Ptychodera flava, develop into planktonic larvae, which are morphologically similar to echinoderm larvae, before metamorphosing into the adult body plan that retains an anteroposterior polarity homologous to that of chordates. Therefore, deciphering developmental programmes of indirect-developing hemichordates may provide a key for understanding the evolution of deuterostomes and chordate origins. Here, we characterise transcriptomes and chromatin accessibility across multiple developmental stages of P. flava and uncover biphasic developmental programmes controlled by different sets of transcription factors and their corresponding cis-regulatory elements. Transcriptome age and network analyses reveal that the gastrula transcriptome is relatively ancient and highly connected. By comparing developmental transcriptomes of hemichordate, sea urchin and amphioxus, a high conservation of gene expression during gastrulation is identified and extended to neurula stages of amphioxus, in addition to the highly similar larval transcriptomes among the three species. Moreover, P. flava possesses conserved interactions of transcription factors required for the development of echinoderm endomesoderm and chordate axial mesoderm. These results suggest a deuterostome phylotypic stage during gastrulation (corresponding to amphioxus gastrulation and neurulation) controlled by gene regulatory networks with conserved cis-regulatory interactions, and support the hypothesis that the deuterostome ancestor is an indirect-developer. Overall design: ATACseq experiments in different developmental stages in Ptychodera flava

后口动物（deuterostomes）的演化历史至今尚未厘清，且与脊索动物（chordates）的起源问题密切相关。在后口动物演化支中，半索动物（hemichordates）与棘皮动物（echinoderms）合称步带动物（Ambulacraria），二者为脊索动物的姊妹群；对这三类类群开展比较研究，有助于解析后口动物的演化历程。间接发育型半索动物（如黄鳃羽鳃蠕虫 *Ptychodera flava*）的幼体为浮游幼虫，形态与棘皮动物幼虫相似，经变态发育后形成成体躯体构型，该构型保留了与脊索动物同源的前后轴极性。因此，解析间接发育型半索动物的发育程序，可为理解后口动物演化与脊索动物起源问题提供关键线索。本研究对*Ptychodera flava*多个发育阶段的转录组与染色质可及性进行了表征，并揭示了由不同转录因子（transcription factors）及其对应顺式调控元件（cis-regulatory elements）调控的双相发育程序。转录组年龄与调控网络分析显示，原肠胚期转录组相对古老且调控连接度极高。通过比较半索动物、海胆（sea urchin）与文昌鱼（amphioxus）的发育转录组，本研究不仅发现三类物种的幼虫转录组高度相似，还证实原肠胚期的基因表达模式具有高度保守性，且该保守性延伸至文昌鱼的神经胚期。此外，*Ptychodera flava*保留了棘皮动物内中胚层与脊索动物轴中胚层发育所需的保守转录因子互作网络。上述结果表明，后口动物存在一个受保守顺式调控互作的基因调控网络控制的原肠胚期系统发育型阶段（对应文昌鱼的原肠胚与神经胚阶段），且支持“后口动物祖先为间接发育类群”的假说。实验设计：对*Ptychodera flava*不同发育阶段开展转座酶可及性测序（ATAC-seq）实验。