Comparative genomic and phylogenetic approaches for investigating plant diversity and evolution

我的研究计划的重点是发现陆地植物是如何相互关联的，并利用这些信息来理解植物生命树上的主要生活史变化。我们提议的工作的第一个组成部分使用以基因组为重点的方法来重建广泛的植物类群的系统发育关系。我们将应用这一知识来了解失去光合作用能力的植物谱系中发生了什么。光合作用是植物利用来自太阳的能量从二氧化碳和水中生产葡萄糖的过程。被称为共生异养植物的非光合作用植物在不同的植物群中已经收敛地进化了大约50次。它们依靠土壤真菌伙伴提供固定碳和其他营养物质。我们建议研究真菌异养生物的所有三种植物基因组是如何受到这种重大营养转变的影响的。我们将对植物细胞中发现的两种细胞器基因组--叶绿体和线粒体--进行详细研究。由于叶绿体(作为绿色植物的叶绿体)的主要作用是进行光合作用，预计随着专性异养的进化，叶绿体基因组特别容易被修改和降解。我们将通过对多个真菌异养植物群的叶绿体基因组进行测序，测试和改进光合作用丧失后这个基因组如何退化的模型，使我们能够筛选基因丢失和保留的收敛模式。光合作用丧失对植物线粒体基因组的影响还不是很清楚，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有重点的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，我们将使用测试来检测在经历重大生活史转变的谱系中的放松选择的实例，例如真菌异质营养的起源。例如，如果环境在重大变化之前就已经作用于基因的子集，那么选择强度变化的时间可能早于显著的生活史变化。我们将通过观察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，以及沉水水生植物(返回水中的陆地植物)和食肉植物中主要质体蛋白复合体(NAD(P)H脱氢酶)的收敛损失。拟议的工作包括为包括本科生研究人员在内的学生提供新的基因组方法培训机会。

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.