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: 1541529
• 负责人: Charles Delwiche
• 金额: $ 60.44万
• 依托单位: University of Maryland, College Park
• 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 2022-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1541529&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（具有独特细胞核的生物）的大多数生物多样性以微观物种的形式存在，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。微生物真核生物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，也影响了我们如何从最广泛的意义上解释细胞生物学和进化生物学。这项研究将促进我们对微生物真核生物的主要进化群（进化枝）的认识，包括层胞菌、肺泡菌和根瘤菌（SAR）。SAR是多种微观真核生物的一个主要分支，最近被进化分析发现，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一些真核生物特征的进化，最著名的是光合作用。在SAR内有许多不同的谱系，但遗传数据很少，而且只集中在少数谱系：顶复合体（如疟疾寄生虫）、菌（如寄生水霉菌）和硅藻（如生态重要的浮游植物）。本项目拟增加具有遗传数据的SAR物种数量，并大规模增加每个物种的遗传数据收集量。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，但在公共数据库中，只有不到50%的SAR进化支具有单个基因组。这里提出的工作将增加至少250个新的基因组尺度数据集（转录组，草图基因组，单细胞扩增基因组），主要集中在捕获SAR内的多样性。这些数据集将公开提供，大大增加我们对这些生物进化的理解。既有的系统基因组学方法和新兴的相似性网络方法的应用将使多层次的分析成为可能，这将为这些生物的进化分析提供新的信息。这将包括：1)利用有针对性的环境18S调查结合高通量FlowCam成像进行多样性发现；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构成SAR早期进化基础的遗传嵌合。除了来自SAR分支不同成员的基因组规模资源的增加之外，拟议的工作将生成图像数据层，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，并将为教师提供显微镜培训研讨会。该项目将从代表性不足的群体中招募学生，并开发一门关于微生物生命之树的高中课程，从而增加参与者的多样性。