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

心皮（开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，它们是开花植物的决定性创新。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育创新。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存知之甚少。我们的研究将解决在不同被子植物谱系中控制心皮发育的基因相互作用网络的起源和进化的关键问题。例如，我们将确定影响心皮发育的基因是否起源于被子植物，还是早于被子植物祖先的被子植物起源。如果是前一种，我们将阐明被子植物特异性心皮发育基因在被子植物历史上是如何起源和进化的，以及心皮发育基因网络如何在主要被子植物谱系中多样化。我们将通过比较分析裸子植物的心皮和雌球果的转录组加深我们对心皮发育和进化的基本理解，裸子植物是被子植物的姐妹类群，在不同的发育阶段，包括被子植物Amborella trichopoda（最基础的被子植物），拟南芥（thale crew，核心的ediicot模式生物），加州青果（基生植物）、水稻（单子叶植物）、番茄茄（番茄，核心植物）和裸子植物云杉（挪威云杉，针叶树）和奇异威氏（银杏）。为了准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解剖技术。将进行非标准比较转录组分析，以公正的方式确定大多数物种中用于心皮发育的一组核心基因。我们将在几个方面进行比较：(i)在不同心皮发育阶段，（ii）在叶片和心皮组织之间，（iii）在被子植物和两种裸子植物之间进行比较，以从非模式植物生物中提取我们的候选基因。通过观察敲除和敲除表型，将对心皮形成和发育最重要的基因进行功能分析。这项工作将揭示新的、高度保守的心皮发育调控因子，这些调控因子是心皮形成和被子植物起源的先决条件，从长远来看也可能对作物优化有用。

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.