Klebsome: Klebsormidiophyceaen genome diversity and adaptations to terrestrial environments

我们的星球被陆地植物覆盖。所有这些生物多样性都是从藻类进化而来的，在一个单一的事件中，植物开始征服土地，永远改变了我们星球的面貌。主要的植物基因组学研究已经建立了一个强大的框架来理解这种奇异性：绿色谱系被深深地分为绿藻和链藻。链霉菌包括陆生植物和链霉菌藻类。在这些链霉菌藻类中，Zygnematophyceae其次是Coleochaetophyceae被认为是最接近陆地植物的藻类亲戚。然而，可以说最有弹性的土地殖民者在链藻藻类是Klebsormidiophyceae，它与陆地植物有着7亿多年前的共同祖先。我假设，尽管它们的系统发育距离，klebsormidiophyceaen弹性是建立在一个遗传底盘，是保守的陆地植物和它们的藻类亲属之间的7亿年的链藻进化。Klebsormidium nitens是第一个进行核基因组测序的链霉菌。它被发现携带着数量惊人的陆地植物遗传基因，但当时没有其他链藻藻类的基因组来解释这些结果。现在，我们有几乎所有主要的链藻藻类的基因组覆盖。然而，Klebsormidium仍然突出了经典归因于陆地植物的通路和信号级联的连续性，特别是鉴于其与陆地植物的差异超过7亿年。克雷伯氏菌科在陆地环境中的普遍存在可能是写在它们的基因中的，可能是那些与陆地植物共享的基因。在这个项目中，我们将建立在我和我的团队在不同链藻藻类的功能基因组学方面积累的经验基础上。我们将测试的假设，一个强大的遗传骨干响应途径的环境因素，如苯丙烷类生物合成基因，是共享的所有克雷伯氏菌科和潜在的突触形态的克雷伯氏菌科和Phragmoplastophyta。我们将：（1）通过进行克雷伯氏菌纲的首次系统性基因组调查，建立克雷伯氏菌纲的基因组框架;（2）对克雷伯氏菌纲的四个基因组进行测序，以促进性状进化的稳健推断;（3）生成受陆地胁迫物挑战的多种克雷伯氏菌纲的全局基因表达数据，以建立所有四种克雷伯氏菌纲共有的细粒度响应谱;（4）利用功能基因组数据比较和重新定义突触形态。通过整合强大的基因组骨架与基因表达谱和重要的候选基因家族的分析，我们将定义突出的（a）分支Klebsormidiophyceae和（B）的应激响应编码能力，与陆地植物数据相结合，重建它们的共同祖先，存在于7亿多年前。

Our planet is covered by land plants. All of this biodiversity evolved from algae in a singular event that set the conquest of land by plants in motion, forever changing the face of our planet. Major phylogenomic efforts have established a robust framework for understanding this singularity: The green lineage is deeply split into the chlorophytes and the streptophytes. The streptophytes encompass the land plants and the streptophyte algae. Among these streptophyte algae, the Zygnematophyceae followed by the Coleochaetophyceae were pinpointed as closest algal relatives to land plants. However, the arguably most resilient land colonizers among streptophyte algae are the Klebsormidiophyceae, which shared a common ancestor with land plants more than 700 million years ago. I hypothesize that, despite their phylogenetic distance, klebsormidiophyceaen resilience is built on a genetic chassis that is conserved between land plants and their algal relatives—across 700 million years of streptophyte evolution. Klebsormidium nitens was the first streptophyte alga to have its nuclear genome sequenced. It was found to bear a surprising number of land plant heritage genes—but at the time there were no other genomes of streptophyte algae to contextualize these results. Now, we have genome coverage of almost all major groups of streptophyte algae. Yet, Klebsormidium still stands out regarding the contiguity of pathways and signaling cascades classically ascribed to land plants—especially in light of its more than 700 million years divergence from land plants. The ubiquity of Klebsormidiophyceae in terrestrial environments is likely written in their genes—potentially those shared with land plants. In this project, we will build upon the experience my team and I have garnered in functional genomics on diverse streptophyte algae. We will test the hypothesis that a robust genetic backbone for response pathways to environmental factors, such as the phenylpropanoid biosynthesis genes, is shared by all Klebsormidiophyceae—and a potential synapomorphy of Klebsormidiophyceae and Phragmoplastophyta. We will: (1) establish a phylogenomic framework for Klebsormidiophyceae by performing the first systematic phylogenomic survey of the class Klebsormidiophyceae; (2) sequence four genomes of Klebsormidiophyceae to facilitate robust inference of trait evolution; (3) generate global gene expression data of diverse Klebsormidiophyceae challenged by terrestrial stressors to establish a fine-grained response profile that is common to all four Klebsormidiophyceae; (4) compare and redefine synapomorphies using the functional genomic data. By integrating the robust genomic backbone with gene expression profiles and analyses of important candidate gene families, we will define the stress responsive coding capacity salient to (a) the clade Klebsormidiophyceae and (b), contextualized with land plant data, reconstruct their common ancestor that existed more than 700 million years ago.