Comparative genomic and phylogenetic approaches for investigating plant diversity and evolution

我的研究项目的重点是发现陆地植物是如何相互关联的，并利用这些信息来了解植物生命树的主要生命史转变。我们提出的工作的第一个组成部分使用基因组为重点的方法来重建系统发育关系的广泛的植物群体。我们将应用这些知识来了解失去光合作用能力的植物谱系中发生了什么（植物利用太阳能从二氧化碳和水产生葡萄糖的过程）。感兴趣的非光合植物，称为真菌异养生物，在不同的植物群中进化了大约50次。它们依靠土壤真菌伙伴来获得固定碳和其他养分。我们建议研究所有三种植物基因组的真菌异养菌是如何影响这一重大的营养转变。我们将对植物细胞中发现的两种细胞器基因组进行详细的研究，质体和质体。预计质体基因组特别容易响应专性异养的进化而发生修饰和降解，因为质体的主要作用（如绿色植物的叶绿体）是进行光合作用。我们将测试和完善模型，这个基因组如何降解后光合作用的损失，通过测序质体基因组从多个mycoheterotrophic植物组，使我们能够筛选基因丢失和保留的收敛模式。光合作用损失对植物线粒体基因组的影响还不太清楚，也将通过寻找这种细胞器基因组中的收敛变化模式来解决。我们还将使用核基因组的聚焦转录组研究来观察核编码的细胞器基因中基因表达的变化。最后，我们将采用测试来检测放松选择的情况下，经历重大的生活史转变，如起源的mycoheterotrophy的血统。例如，选择强度变化的时间可能早于明显的生活史变化，如果环境在主要变化之前已经作用于基因的子集。我们将通过研究多种类型的生活史转变的影响来解决这个问题，包括真菌异养，以及沉水植物（陆地植物返回水中）和食肉植物中主要质体蛋白复合物（NAD（P）H脱氢酶）的趋同损失。拟议的工作包括为学生，包括本科生研究人员提供基因组方法的新培训机会。

The focus of my research program is to discover how land plants are related to each other, and to use this information to understand major life-history shifts across the plant tree of life. The first component of our proposed work uses genome-focused approaches to reconstruct phylogenetic relationships for a broad range of plant groups. We will apply this knowledge to understand what happens in plant lineages that have lost the ability to photosynthesize (the process by which plants use energy from the sun to produce glucose from carbon dioxide and water). The non-photosynthetic plants of interest, called mycoheterotrophs, have evolved convergently around 50 times in different plant groups. They rely on soil fungal partners for their fixed carbon and other nutrients. We propose to examine how all three plant genomes of mycoheterotrophs are affected by this major nutritional shift. We will perform detailed studies of the two organellar genomes found in plant cells, the plastid and mitochondrion. The plastid genome is expected to be especially prone to modification and degradation in response to the evolution of obligate heterotrophy, as the plastid's primary role (as the chloroplast of green plants) is to perform photosynthesis. We will test and refine models for how this genome degrades following the loss of photosynthesis, by sequencing plastid genomes from multiple mycoheterotrophic plant groups, allowing us to screen for convergent patterns of gene loss and retention. The effect of photosynthesis loss on the plant mitochondrial genome is much less well understand, and will also be addressed by looking for convergent patterns of change in this organellar genome. We will also use focused transcriptome studies of the nuclear genome to look at shifts in gene expression in nuclear-encoded organellar genes. Finally, we will employ tests to detect instances of relaxed selection in lineages undergoing major life-history shifts, such as the origin of mycoheterotrophy. For example, the timing of shifts in selection intensity may predate a noticeable life-history change, if the environment is already acting on subsets of genes prior to the major shift. We will address this by looking at the effects of multiple types of life-history shifts, including mycoheterotrophy, in addition to convergent losses of a major plastid protein complex (NAD(P)H dehydrogenase) in submerged aquatic plants (land plants that returned to the water) and carnivorous plants. The proposed work includes new training opportunities in genomic methods for students, including undergraduate researchers.