SHOAL: Signaling Hubs in the clOsest Algal relatives of Land plants

陆地植物是从链藻进化而来的，这是一次独特的进化事件。细致的系统基因组分析现在一致地恢复了Zygnematophyceae作为与陆地植物最接近的藻类姐妹谱系。最近，已经有四个有代表性的种的基因组相继问世(其中三个是尺蛾科)。虽然这是一项重大的进步，但我们对这些基因组中功能基因空间的探索，目前仅限于同源性。在这个项目中，我们将利用强大的系统发育框架，将Zygnematophyceae作为与陆地植物最近的藻类近亲，以及最近在共表达网络方法中这些生物的基因组数据激增，以了解功能模块的起源。比较基因组学表明，决定陆地植物特征的基因调控网络的决定中枢基因(节点)在链藻中有很深的同源性，特别是在Zygnematophyceae中；(I)生长素、(Ii)乙烯、(Iii)茉莉酸、水杨酸和N-羟基吡啶甲酸、(Iv)非生物胁迫和(V)生物相互作用，例如对MAMPs的反应或共生或致病真菌的存在。利用共表达网络，我们将探测这些中枢基因之间的导线(边缘)。我们将检验这样的假设，即核心的植物特有功能是围绕共同调节基因的同源基因组的保守枢纽构建的。共表达网络允许我们使用基于同源性的推断作为灯塔，通过内疚-联想的方法来探索基因邻域，以将基于同源性的已知与未知联系起来。我们在这里建议生成构建这样的网络所需的转录组数据。在陆地植物模型系统中建立的功能模块的基础上并与之进行比较，我们将剖析这些网络以预测陆地植物的标志性功能。我们的数据将为研究关键植物功能的深层进化根源建立一个框架。在荟萃分析中，我们将检验这样一个假设，即直源基因(节点)的共同表达(边)将这些关键植物功能的最小框架串在一起，这些关键功能假定由(I)Zygnematophyceae共享，并在(Ii)陆地植物中建立。从这个最小的框架出发，支持陆地植物最后一个共同祖先定义植物功能的基因的协同作用演变而来。

Land plants evolved from streptophyte algae in a singular evolutionary event. Meticulous phylogenomic analyses have now consistently recovered the Zygnematophyceae as the closest algal sister lineage to land plants. Recently, and in close succession, four genomes of representative species from the Zygnematophyceae (three of those are Zygnematophycidae) have become available. While this is a significant advance, our exploration of the functional gene space in these genomes is, for now, limited to mere homology. In this project, we will make use of the robust phylogenetic framework that has solicited the Zygnematophyceae as the closest algal relatives to land plants and the recent surge in genome data for these organisms in a co-expression network approach to understand the origin of functional modules. Comparative genomics have shown that decisive hub genes (nodes) of gene regulatory networks salient to defining features of land plants have deep homologs in streptophyte algae — and especially in the Zygnematophyceae; this is the case for signaling genes for (i) auxin, (ii) ethylene, (iii) jasmonate, salicylate and N-hydroxy pipecolic acid, (iv) abiotic stresses and (v) biotic interactions, such as the response to MAMPs or the presence of symbiotic or pathogenic fungi. Using co-expression networks, we will probe the wires (edges) between these hub genes. We will test the hypothesis that core plant-specific functions are built around conserved hubs of orthologous groups of co-regulated genes. Co-expression networks allow us to use the homology-based inferences as beacons for a guilt-by-association approach to explore gene neighborhoods for linking homology-based knowns with unknowns. We here propose to generate the required transcriptome data to construct such networks. Building on and comparisons to functional modules established in land plant model systems, we will dissect these networks for predicted hallmark functions of land plants. Our data will establish a framework for studying the deep evolutionary roots of key plant function. In a meta-analysis, we will test the hypothesis that co-expression (edges) of orthologous genes (nodes) strings together a minimal framework for these key plant functions putatively shared by (i) Zygnematophyceae and established in (ii) land plants. From this minimal framework, the concerted action of genes underpinning defining plant functions of the last common ancestor of land plants evolved.