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

GoLife：合作研究：将多样化的微生物进化枝 Stramenopila Alveolata Rhizaria (SAR) 引入现代基因组背景

• 批准号: 1541510
• 负责人: Christopher Lane
• 金额: $ 133.85万
• 依托单位: University of Rhode Island
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2021-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1541510&HistoricalAwards=false
• 关键词: GoLife; Collaborative; Research; Bringing; diverse

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.

真核生物（具有不同细胞核的生物体）的大部分生物多样性都是微观物种的形式，与其他真核生物（植物、动物和真菌）相比，在形态特征、物种间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相对缺乏，不仅影响我们对地球上所​​有生物多样性的理解，而且影响我们如何从最广泛的意义上解释细胞和进化生物学。这项研究将增进我们对微生物真核生物主要进化群体（进化枝）的了解，该进化群体包括原生藻菌、泡藻菌和根菌（SAR）。 SAR 是多种微观真核生物的一个主要分支，最近通过进化分析确定，并且其他数据有力地支持 SAR 作为一个独立的进化谱系。这一发现迫使人们重新评估几种真核生物特征的进化，尤其是光合作用。 SAR 内有许多不同的谱系，但遗传数据很少，并且仅集中在几个谱系中：顶复纲（例如疟疾寄生虫）、菌类（例如寄生虫水霉菌）和硅藻（例如生态上重要的浮游植物）。该项目提议增加具有遗传数据的SAR物种数量，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体将被成像，并将被整合到生命百科全书（EOL）中，以提供有关微生物真核生物多样性的综合资源。尽管它们具有全球生态重要性，但公共数据库中只有不到 50% 的 SAR 进化枝由单个基因组代表。这里提出的工作将添加至少 250 个新颖的基因组规模数据集（转录组、基因组草案、单细胞扩增基因组），主要侧重于捕捉 SAR 内的多样性。这些数据集将公开，从而大大增加我们对这些生物体进化的理解。已建立的系统发育学和新兴相似性网络方法的应用将实现多层分析，为这些生物体的进化分析提供新信息。这将包括：1) 使用有针对性的环境 18S 调查结合高通量 FlowCam 成像来发现多样性； 2）高通量转录组测序； 3）不可培养类群的单细胞基因组学。系统发育分析将捕获 SAR 早期进化背后的遗传镶嵌。除了来自 SAR 进化枝不同成员的基因组规模资源的增加之外，拟议的工作还将生成图像数据层并将其与 EOL 文献中的其他图像集成。本科生、研究生和博士后将接受尖端技术培训，并将举办显微镜教师培训研讨会。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，并开发关于微生物生命树的高中课程。