Toward deciphering the phylotranscriptomic hourglass in plant embryogenesis

胚胎发生是复杂多细胞生命的重要发育过程。胚胎发生的一个基本模式，发育沙漏，可以追溯到19世纪早期卡尔·恩斯特·冯·贝尔对脊椎动物的开创性研究。发育沙漏描述了一种看似普遍的模式，即来自不同分类群的动物胚胎在早期阶段出现不同，在胚胎发生中期收敛到相似的形式，并在后期再次分化。这种形态模式最近得到了分子的支持，证明中期胚胎发生在转录组水平上也最大限度地保守。有趣的是，这种经典的形态沙漏模式从未在植物谱系中被报道过，而植物谱系是进化胚胎发生的第二个领域。然而，通过结合系统发育和转录信息，我们最近能够证明在模式植物拟南芥的胚胎发生过程中存在系统转录沙漏。由于植物和动物最后的共同祖先是单细胞的，这强烈表明转录组沙漏的趋同进化是一个基本的发育特征，控制着进化年轻或快速进化的基因在各个王国的表达。虽然我们推测这种机制可能是复杂多细胞生命的时空组织和分化所必需的，但我们还不了解沙漏模式的分子起源。在本研究中，我们的目的是研究沙漏型系统转录组模式是否也存在于其他植物物种中，或者它是否仅为模式植物拟南芥所特有。我们将通过生成RNA-seq数据集来解决这个问题，这些数据集涵盖了拟南芥和另外两个物种的胚胎发生，这两个物种是近亲芸苔科的风疹油菜和远亲苔藓的小壶藓。我们将把这些转录数据与各种进化、系统基因组学和序列信息结合起来，揭示影响这三个物种系统转录模式的因素。通过应用信息理论的方法，我们期望开始了解沙漏或其他可能的植物胚胎发生模式的分子起源和进化。

Embryogenesis is an essential developmental processes that enables complex multicellular life. A fundamental pattern of embryogenesis, the developmental hourglass, dates back to pioneering work by Karl Ernst von Baer on vertebrates in the early 19th century. The developmental hourglass describes a seemingly universal pattern that animal embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphological pattern has recently received molecular support by demonstrating that mid-embryogenesis is also maximally conserved on the transcriptomic level.Interestingly, the classic morphological hourglass pattern had never been reported for the plant lineage, the second kingdom that evolved embryogenesis. However, by combining phylogenetic and transcriptional information we were recently able to demonstrate the existence of a phylotranscriptomic hourglass during embryogenesis of the model plant Arabidopsis thaliana. As the last common ancestor of plants and animals was unicellular, this strongly suggested convergent evolution of the transcriptomic hourglass as a fundamental developmental profile controlling the expression of evolutionarily young or rapidly evolving genes across kingdoms. While we speculate that such a mechanism may be required for enabling spatio-temporal organization and differentiation of complex multicellular life in general, we do not yet understand the molecular origin responsible for the hourglass pattern. In this proposal, we aim to investigate whether the phylotranscriptomic hourglass pattern also exists in other plant species or whether it is specific for the model plant A. thaliana. We will address this question by generating RNA-seq data sets that cover embryogenesis in A. thaliana and two additional species, the closely related Brassicaceae Capsella rubella and the distantly related moss Physcomitrella patens. We will combine these transcriptional data with various evolutionary, phylogenomic, and sequence information to unravel factors that shape phylotranscriptomic patterns in these three species. By applying information theoretic approaches, we expect to begin to understand the molecular origin and evolution of the hourglass or possible other patterns in plant embryogenesis.