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

陆地植物是在一个独特的进化事件中从链藻进化而来的。藻类基因组分析现在一致地恢复了双星藻科作为最接近陆地植物的藻类姐妹谱系。最近，在紧密的连续性，四个基因组的代表性物种从Zygnematophyceae（其中三个是Zygnematophyceae）已成为可用。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同源性。在这个项目中，我们将利用强大的系统发育框架，征求了最接近的藻类亲属的藻类陆生植物和最近激增的基因组数据，这些生物体的共表达网络的方法来了解功能模块的起源。比较基因组学已经表明，决定性的枢纽基因（节点）的基因调控网络突出的定义功能的陆地植物有深刻的同源链藻藻类-特别是在接合藻;对于（i）生长素，（ii）乙烯，（iii）茉莉酮酸酯、水杨酸酯和N-羟基哌啶酸，（iv）非生物胁迫和（v）生物相互作用的信号基因，例如对MAMPs的反应或共生或致病真菌的存在。使用共表达网络，我们将探测这些枢纽基因之间的连线（边缘）。我们将测试的假设，核心植物特异性功能是建立在保守的枢纽的orthopathic组的共调节基因。共表达网络使我们能够使用基于同源性的推断作为信标，通过关联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，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，我们将测试的假设，共表达（边缘）的直向基因（节点）串在一起的最小框架，这些关键植物功能pueros共享（i）Zygnematophyceae和建立在（ii）陆地植物。从这个最小的框架，基因的协调行动，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.