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

陆地植物是在一个单一的进化事件中由链藻进化而来的。细致的系统基因组学分析现在已经一致地恢复了Zygnematophyceae作为最接近陆地植物的藻类姐妹谱系。最近，在密切的连续研究中，已经获得了Zygnematophycidae的四个代表性物种的基因组（其中三个是Zygnematophycidae）。虽然这是一个重大的进步，但我们对这些基因组中功能基因空间的探索，目前仅限于纯粹的同源性。在本项目中，我们将利用强大的系统发育框架，该框架已将Zygnematophyceae作为与陆地植物最接近的藻类亲戚，以及最近在共表达网络方法中这些生物基因组数据的激增，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性枢纽基因（节点）在链藻中具有深层同源性，特别是在Zygnematophyceae中；这是信号基因(i)生长素，（ii）乙烯，（iii）茉莉酸，水杨酸和n -羟基果酸，（iv）非生物胁迫和(v)生物相互作用的情况，如对MAMPs的反应或共生或致病真菌的存在。利用共表达网络，我们将探测这些中心基因之间的连线（边缘）。我们将验证核心植物特异性功能是围绕同源共调节基因群的保守中心构建的假设。共表达网络允许我们使用基于同源性的推断作为关联内疚方法的信标，探索基因邻域，将基于同源性的已知与未知联系起来。我们在此建议生成所需的转录组数据来构建这样的网络。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植物关键功能的深层进化根源建立一个框架。在meta分析中，我们将检验这样一个假设，即同源基因（节点）的共表达（边）将这些关键植物功能的最小框架串在一起，这些关键植物功能被推定为(i) Zygnematophyceae共享，并在（ii）陆生植物中建立。从这个最小的框架中，基因的协同作用决定了陆地植物最后共同祖先的植物功能。

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.