Phylotranscriptomics of the carpel developmental toolkit - an evo-devo study towards understanding the origin of flowering plants

心皮（显花植物的雌性生殖器官）具有重要的经济意义，因为我们的大多数食物最终都来自心皮组织，它们是显花植物的定义性创新。心皮的进化起源是被子植物起源的一个基本的尚未解决的发展创新。令人惊讶的是，除了利用拟南芥产生的知识外，对心皮发育程序的起源和保护知之甚少。我们的研究将解决关键问题的起源和进化的基因相互作用网络控制心皮发育在不同的被子植物谱系。 例如，我们将确定是否基因有助于心皮发育起源于被子植物或早于被子植物的起源在祖先被子植物。如果是前者，我们将阐明被子植物特有的心皮发育基因是如何起源和进化的被子植物的历史和心皮发育基因网络如何在主要的被子植物谱系多样化。我们将通过对被子植物的姐妹类群裸子植物心皮和雌球花不同发育阶段的转录组进行比较分析，加深我们对心皮发育和进化的基本理解，包括被子植物Amborella dopoda（大多数基部被子植物），拟南芥（塔勒水芹，核心真双子叶模式生物）、加州石花菜（基部真双子叶植物）、水稻（稻，单子叶植物）、番茄（番茄，核心真双子叶植物）和裸子植物云杉（挪威云杉，针叶树）和奇异Welwitschia mirabilis（买麻藤目）。为了精确了解心皮发育过程中基因表达的时空动态，我们将采用激光捕获显微切割技术。将进行非标准的比较转录组分析，以确定一组核心基因用于心皮发育在大多数物种中以公正的方式。我们将在几个方面进行比较：（i）在不同的心皮发育阶段，（ii）叶和心皮组织之间，（iii）在被子植物和两种裸子植物中提取我们的候选基因，特别是从非模式植物生物。通过观察敲除和敲低表型的功能分析将对心皮起始和发育最重要的基因进行。这项工作将揭示新的，高度保守的心皮发育调节剂，是心皮的先决条件，因此被子植物的起源，这也可能被证明是有益的作物优化，从长远来看。

Carpels (female reproductive organs of flowering plants) are of major economic importance as most of our food is ultimately derived from carpel tissue and they are a defining innovation for flowering plants. The evolutionary origin of the carpel is a fundamental yet unresolved developmental innovation contributing to the origin of angiosperms. Amazingly, little is known about the origin and conservation of the developmental program of the carpel besides the knowledge generated by utilizing Arabidopsis thaliana. Our research would address critical questions about the origin and evolution of gene interaction network controlling carpel development in diverse angiosperm lineages. For example, we will determine whether genes contributing to carpel development originated with the angiosperms or predated the origin of angiosperms in the ancestral angiosperm. If the former, we will elucidate how angiosperm-specific carpel development genes originated and evolved over angiosperm history and how the carpel developmental gene network has diversified across major angiosperm lineages. We will deepen our fundamental understanding of carpel development and evolution through comparative analysis of transcriptomes from carpels and female cones of gymnosperms, the sister group to angiosperms across different developmental stages in a wide range of phylogenetically informative and economically important species including the angiosperms Amborella trichopoda (most basal angiosperm), Arabidopsis thaliana (thale cress, core eudicot model organism), Eschscholzia californica (basal eudicot), Oryza sativa (rice, monocot), Solanum lycopersicum (tomato, core eudicot), and the gymnosperms Picea abies (Norway spruce, conifer), and Welwitschia mirabilis (gnetales). In order to gain a precise understanding of the spatial and temporal dynamics of gene expression in carpel development, we will employ Laser Capture Microdissection. Non-standard comparative transcriptome analysis will be performed to identify a set of core genes utilized for carpel development in the majority of species in an unbiased way. We will compare in several dimensions: (i) across different carpel developmental stages, (ii) between leaf and carpel tissue, (iii) across angiosperms and two gymnosperms to extract our candidate genes specifically from non-model plant organisms. Functional analyses by observing knock-out and knock-down phenotypes will be performed on genes implicated as most important for carpel initiation and development. This work will reveal novel, highly conserved carpel development regulators that were the prerequisite for the carpel, and thus angiosperm origin and which might also prove useful for crop optimization in the long run.