Phylotranscriptomic profiling of the Arabidopsis life cycle, organogenesis, and the cell cycle

发育沙漏模型是发育生物学中的经典概念之一。在动物中，来自同一门的不同类群的胚胎在早期阶段表现不同，在胚胎发生中期收敛到相似的形式，并在胚胎发育的后期再次分化。这个形态发生系列被称为发育沙漏，是基于卡尔·恩斯特·冯·贝尔从19世纪初的观察。最近对几种动物物种的研究表明，全球基因表达谱也遵循沙漏模式，为发育沙漏模型提供了令人信服的分子支持。虽然植物也进化了胚胎发生，但发育沙漏的概念在植物界还没有得到解决。通过结合系统发育学和转录组学（系统转录组学），我们最近可以证明拟南芥胚胎发生的系统转录沙漏模式的存在，这表明了一种控制跨王国全球基因表达谱的基本机制。基于植物和动物发育的根本差异，我们假设发育沙漏模式可能并不局限于胚胎发生，而可能是发育过程的普遍特征。利用植物发育的主要后胚胎性质（与大多数动物相比）提供了实验机会，以评估在几个重要的发育过程中系统转录组模式的普遍存在。在这个跨学科的项目中，我们试图在三个不同的时空层面上解决这个假设。利用拟南芥模型系统，我们计划进行系统转录组学研究(i)完整植物的生命周期，（ii）从早期分生组织活动到成熟分化器官的器官发生，以及（iii）细胞周期。基于新兴的系统转录组模式，我们的目标是确定模式塑造基因和控制其活动的假定顺式调控模块。总之，我们的目标是生成对植物群落普遍感兴趣的数据集，并向理解观察到的系统转录组学模式迈出第一步。

The developmental hourglass model is one of the classic concepts in developmental biology. In animals, embryos from various taxa from a common phylum appear different in early stages, converge to a similar form during mid embryogenesis, and again diverge in later stages of embryo development. This morphogenetic series is known as the developmental hourglass and is based on observations by Karl Ernst von Baer from the early 19th century. Recent studies in several animal species showed that global gene expression profiles also followed an hourglass pattern, providing convincing molecular support for the developmental hourglass model. Although plants also evolved embryogenesis, the developmental hourglass concept had not been addressed in the plant kingdom. By combining phylogenetics and transcriptomics (phylotranscriptomics), we could recently demonstrate the existence of a phylotranscriptomic hourglass pattern for Arabidopsis embryogenesis, suggesting a fundamental mechanism controling global gene expression profiles across kingdoms.Based on fundamental differences in plant and animal development, we hypothesize that the developmental hourglass pattern might not be restricted to embryogenesis, but might be a general characteristic of developmental processes. Exploiting the predominantly post-embryonic nature of plant development (in contrast to most animals) offers experimental opportunities to assess the general existence of phylotranscriptomic patterns in several important developmental processes. In this interdisciplinary project, we seek to address this hypothesis on three different spatio-temporal levels. Using the Arabidopsis model system we plan to perform phylotranscriptomic studies of (i) the life cycle of complete plants, (ii) organogenesis from early meristematic activities to the mature differentiated organ, and (iii) the cell cycle. Based on the emerging phylotranscriptomic patterns, we aim to identify pattern-shaping genes and putative cis-regulatory modules controling their activities. Together, our objective is to generate data sets that are of general interest for the plant community and take a first step toward understanding the observed phylotranscriptomic patterns.