Deciphering the evolutionary mechanisms shaping the regulatory circuitry underlying the novel brooding organ in syngnathids (pipefishes & seahorses) using cutting-edge single-cell multiomics

破译形成海龙鱼（海龙）新型育雏器官背后的调节电路的进化机制

• 批准号: 517907115
• 负责人: Dr. Ralf Schneider
• 金额: --
• 依托单位: Zoologisches Institut
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/517907115?language=en
• 关键词: Deciphering; evolutionary; mechanisms; shaping; regulatory

The diversity of life reflects the multifaceted adaptations organisms evolved to adjust to an everchanging environment. New phenotypic traits can evolve due to gradual change to already existing traits (making them “homolog”), or they can arise as entirely new characteristics without any phenotypic precursor. Such “de novo” traits may still show homology on the level of gene regulation though (“deep homology”): novel traits may coopt regulatory circuitry of other preexisting traits, which can accelerate the evolution of novelty and complexity. Syngnathids (pipefish and seahorse) show such a novel trait: male pregnancy via specialized brooding organs. Across species, brooding organs may be simple (in the pipefish Nerophis ophidion the brooding organ merely serves to attach the eggs to the father’s belly, where they remain exposed to seawater), complex (in the seahorse Hippocampus erectus the brooding organ on the fish’s tail forms a pouch-like structure that holds the eggs in a regulated micro-environment shielded from seawater), or of intermediate complexity (in the pipefishes Syngnathus typhle and Doryrhamphus excisus). This project aims to investigate the molecular and evolutionary mechanisms underlying brooding organs to further our understanding of how evolutionary novel structures can arise. For this purpose, tissue samples of the four aforementioned syngnathids will be collected across brooding organ development. In three sub-projects (i.) the organs’ morphological developments will be comparatively described via histology and immunohistology, (ii.) the brooding organs’ transcriptome-wide gene expression patterns will be comparatively analyses across developmental stages, and (iii.) robust regulatory gene networks will be generated via single-cell multiomics, integrating RNA-seq and ATAC-seq from the same individual cells, of selected individuals. Subsequently, morphological characteristics will be associated to gene expression characteristics, cell types will be identified per developmental stage and species, trait-specific gene regulatory networks will be identified, and upstream transcription regulators orchestrating these gene regulatory networks determined. By comparative analyses of networks among brooding organ stages and between species, unique genes/regulatory elements and regulatory interactions can be identified. These analyses will reveal, for instance, if convergent brooding organ phenotypes evolved via parallel regulatory evolution and if the development of more complex phenotypes indeed recapitulates its evolution on a regulatory level, as suggested by morphological observations. Thus, this study will provide valuable insights into the developmental biology, molecular basis and evolutionary mechanisms underlying the syngnathids’ novel brooding organs and discuss more broadly the evolutionary mechanism underlying the evolution of novel traits, ranging from de novo evolution to deep homology.

生命的多样性反映了生物体为适应不断变化的环境而进化出的多方面适应能力。新的表型性状可以由于已经存在的性状的逐渐变化而进化（使它们成为“同源物”），或者它们可以作为完全新的特征出现而没有任何表型前体。然而，这种“从头”性状可能仍然在基因调控水平上显示出同源性（“深度同源性”）：新性状可能会占用其他先前存在的性状的调控电路，这可以加速新奇和复杂性的进化。海龙科（海龙和海马）显示了这样一个新的特征：雄性通过专门的育雏器官怀孕。在所有物种中，育雏器官可能很简单，（在海龙Nerophis ophidion中，育雏器官仅用于将卵附着在父亲的腹部，在那里它们仍然暴露在海水中），复杂（海马的尾部的育雏器官形成了一个囊状结构，将卵保存在一个受监管的微环境中，与海水隔离），或中等复杂性的（在海龙属和锯吻海龙属中）。本项目旨在研究育雏器官的分子和进化机制，以进一步了解进化的新结构如何产生。为此，将在育雏器官发育过程中收集上述四种海龙的组织样本。在三个分项目中（一）通过组织学和免疫组织学比较描述器官的形态发育，（ii.）将在发育阶段对育雏器官的全转录组基因表达模式进行比较分析，以及（iii.）通过单细胞多组学，整合来自选定个体的相同个体细胞的RNA-seq和ATAC-seq，将产生稳健的调控基因网络。随后，形态特征将与基因表达特征相关联，细胞类型将根据发育阶段和物种进行鉴定，将鉴定性状特异性基因调控网络，并确定协调这些基因调控网络的上游转录调控因子。通过比较分析育雏器官阶段和物种之间的网络，可以确定独特的基因/调控元件和调控相互作用。这些分析将揭示，例如，如果收敛的育雏器官表型通过平行的监管演变，如果更复杂的表型的发展确实概括了其演变的监管水平，如形态学观察所示。因此，本研究将提供有价值的见解的发育生物学，分子基础和进化机制背后的海龙类的新的育雏器官和更广泛地讨论新的特征的进化机制，从从头进化到深同源性。