Genomic approachs to studying plant evolution, function and phylogeny

我的研究计划的重点是发现陆地植物是如何相互关联的（植物生殖;生命之树），并使用这些信息，沿着新测序的植物基因组，以了解主要植物生活史转变的后果。拟议的工作包括为包括本科生研究人员在内的不同学生提供基因组方法的新培训机会。我们研究的主要转变包括：（一）植物光合作用的损失，从土壤真菌获得糖和其他营养物质（真菌异养），而不是使用阳光（光合作用），（二）驯化的“小”作物在安第斯山脉，和（三）食肉植物的起源，捕食昆虫的基本元素在其沼泽栖息地失踪。我们还推断在其他群体的利益，包括Hydatellaceae的aprogenies。我们将探索系统发育推断的挑战性方面，包括非光合植物基因组中进化速率的提升。基因组测序技术已经足够先进，可以使用全基因组测序方法相对容易地对植物基因组（叶绿体、线粒体和最近的核基因组）进行测序。我们将对几种感兴趣的植物进行此操作。一个主要的任务是，然后组装，注释和研究基因组的生物学有趣的问题，例如，以确定是否有扩展或删除的基因和基因家族有关的主要功能转变，并测试在保留的基因的自然选择的变化。植物基因组可以与亲缘植物进行比较，以更好地理解这些变化（例如，作物与其作物野生亲戚;食肉植物与非食肉亲戚）。类似的比较基因组学方法使我们能够发现和表征与转变相关的平行（趋同）进化（例如与光合作用损失相关的基因丢失和基因组减少）。我们还将使用目标富集方法来提取大量的核基因，使我们能够更好地估计基因树中的物种遗传。我们将在几个地理学研究中使用这种方法，包括安第斯山的块茎作物奥卢科，和一种食肉植物，三尖杉。这种方法可用于在研究中包括降解的DNA（例如，从植物标本）。最后，我们将建立一个实验系统，以更好地了解光合作用的进化损失。将对两种部分真菌异养的兰花物种进行遮荫实验，它们可以在没有阳光的情况下生长，依靠与各种土壤真菌的伙伴关系。还将测量真菌伴侣（=根微生物组）和表达的异养程度（通过定量稳定同位素评估）的可能变化。将对植物转录组（根和芽组织中表达的基因）进行测序，并在处理之间进行比较，并与部分异养的野生亲缘植物进行比较，直至光合作用完全丧失。

The focus of my research program is to discover how land plants are related to each other (plant phylogeny; tree of life), and to use this information, along with newly sequenced plant genomes, to understand the consequences of major plant life-history shifts. The proposed work includes new training opportunities in genomic methods for diverse students, including undergraduate researchers. The major transitions we study include: (i) the loss of photosynthesis in plants that obtain sugars and other nutrients from soil fungi (mycoheterotrophy), instead of using sunlight (photosynthesis), (ii) domestication of 'minor' crops in the Andes, and (iii) the origin of a carnivorous plant which preys on insects for essential elements missing in its boggy habitats. We also infer phylogenies in other groups of interest, including Hydatellaceae. We will explore challenging aspects of phylogenetic inference, including elevation of evolutionary rates in the genomes of non-photosynthetic plants. Genome sequencing technology has advanced enough to sequence plant genomes (chloroplast, mitochondrial and recently the nuclear genome) with relative ease using whole genome sequencing approaches. We will do this for several plants of interest. A major task is to then assemble, annotate and study the genomes with respect to biologically interesting questions, for example to determine if there is expansion or deletion of genes and gene families related to major functional shifts, and to test for changes in natural selection in retained genes. Plant genomes can be compared to relatives to better understand these changes (e.g., crops to their crop wild relatives; carnivorous plants to non-carnivorous relatives). Similar comparative genomic approaches allow us to discover and characterize parallel (convergent) evolution related to the shift (e.g. gene loss and genome reduction related to the loss of photosynthesis). We will also use target-enrichment approaches to pull out large sets of nuclear genes, allowing us to better estimate species phylogenies from gene trees. We will use that approach in several phylogeographic studies, including the Andean tuber crop olluco, and a carnivorous plant, Triantha occidentalis. This approach can be used to include degraded DNAs in the study (e.g., from herbarium specimens). Finally, we will set up an experimental system to better understand the evolutionary loss of photosynthesis. Shading experiments will be done for two partially mycoheterotrophic orchid species, which can grow facultatively without sunlight, by relying on partnerships with various soil fungi. Possible shifts in fungal partners (= root microbiomes) and in the degree of expressed heterotrophy (assessed by quantifying stable isotopes) will also be measured. Plant transcriptomes (the expressed genes in root and shoot tissues) will be sequenced and compared across treatments, and to wild relatives with partial heterotrophy through to full loss of photosynthesis.