GoLife: Collaborative Research: Bringing the diverse microbial clade Stramenopila + Alveolata + Rhizaria (SAR) into a modern genomic context

真核生物(具有不同核的生物体)中的大多数生物多样性是以微小物种的形式存在的，与其他真核生物(植物、动物和真菌)相比，在形态特征、物种之间的进化关系和遗传变异方面的研究较少。关于微生物真核生物的信息的相对缺乏不仅影响了我们对地球上所有生物多样性的理解，也影响了我们从最广泛的意义上解释细胞和进化生物学的方式。这项研究将促进我们对微生物真核生物的一个主要进化类群(支系)的了解，这些微生物真核生物包括斯特拉莫尼拉、肺泡和根霉(SAR)。合成孔径雷达是最近被进化分析和更多的数据有力地支持了合成孔径雷达作为一个独立进化谱系的不同微观真核生物的一个主要分支。这一发现迫使人们重新评估几个真核生物特征的进化，其中最引人注目的是光合作用。在SAR内有许多不同的谱系，但遗传数据很少见，只集中在几个谱系中：尖端复合体(例如疟疾寄生虫)、真菌(例如寄生虫、水霉)和硅藻(例如具有生态重要性的浮游植物)。该项目建议增加具有遗传数据的SAR物种的数量，并大幅增加每个物种收集的遗传数据量。用于基因组数据的生物将被成像，并将被整合到生命百科全书(EOL)中，以提供关于微生物真核生物多样性的全面资源。尽管它们具有全球生态重要性，但在公共数据库中，只有不到50%的SAR分支由单个基因组代表。这里提出的工作将增加至少250个新的基因组规模的数据集(转录本、草稿基因组、单细胞扩增基因组)，主要侧重于捕获SAR内的多样性。这些数据集将公之于众，大大增加了我们对这些生物进化的了解。已建立的系统基因组学方法和新出现的相似性网络方法的应用将使多层次分析成为可能，这将为这些生物的进化分析提供新的信息。这将包括：1)使用定向环境18S调查结合高通量FlowCam成像来发现多样性；2)高通量转录测序；以及3)不可培养分类群的单细胞基因组学。系统发育分析将捕捉构成SAR早期进化的遗传马赛克。除了来自SAR分支不同成员的基因组规模资源的增加外，拟议的工作还将生成图像数据层，并将这些数据层与EOL上的文献中的其他图像整合在一起。本科生、研究生和博士后研究员将接受尖端技术培训，并将为显微镜教师培训提供研讨会。该项目将通过从代表性不足的群体中招募学生来增加参与者的多样性，并制定关于微生物生命之树的高中课程。

Most of the biological diversity in eukaryotes (organisms with distinct nuclei) is in the form of microscopic species and, when compared to other eukaryotes (plants, animals and fungi), is less well-studied in terms of morphological characterisitics, evolutionary relationships among species, and genetic variation. This relative lack of information on microbial eukaryotes not only has consequences for our understanding of all biodiversity on Earth, but also how we interpret cellular and evolutionary biology in the broadest sense. This research will advance our knowledge of a major evolutionary group (clade) of microbial eukaryotes that comprise the Stramenopila, Alveolata and Rhizaria, (SAR). SAR is a major clade of diverse microscopic eukaryotes that was recently identified by evolutionary analyses and additional data have robustly supported SAR as an independent evolutionary lineage. This discovery is forcing a re-evaluation of the evolution of several eukaryotic traits, most notably photosynthesis. Within SAR there are many diverse lineages but genetic data are rare and concentrated in only a few lineages: Apicomplexa (e.g. malarial parasites), omycetes (e.g. parasite water molds) and diatoms (e.g. ecologically important phytoplankton). This project proposes to increase the number of SAR species with genetic data as well as massively increase the amount of genetic data collected per species. Organisms used for genomic data will be imaged and will be integrated to the Encyclopedia of Life (EOL) to provide a comprehensive resource on microbial eukaryotic diversity.Despite their global ecological importance, fewer than 50% of all SAR clades are represented by even a single genome in public databases. The work proposed here would add at least 250 novel genomic-scale datasets (transcriptomes, draft genomes, single-cell amplified genomes), focused primarily on capturing diversity within SAR. These datasets will be made publicly available, substantially increasing our understanding of the evolution of these organisms. The application of both established phylogenomic and emerging similarity network methods will enable a multi-layered analysis that will provide new information for evolutionary analyses of these organisms. This will include: 1) diversity discovery using targeted environmental 18S surveys coupled with high-throughput FlowCam imaging; 2) high-throughput transcriptomic sequencing; and 3) single cell genomics of unculturable taxa. Phylogenetic analyses will capture the genetic mosaics that underlie the early evolution within SAR. Beyond the increase in genome scale resources from diverse members of the SAR clade, the proposed work will generate image data layers and integrate these with other images from the literature in EOL. Undergraduates, graduate students and postdoctoral fellows will be trained in cutting edge techniques and will provide a workshop for teacher training in microscopy. This project will increase diversity of participants by recruiting students from underrepresented groups and develop of a high school curriculum on the microbial tree of life.