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: 1541511
• 负责人: Laura Katz
• 金额: $ 57.9万
• 依托单位: Smith College
• 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=1541511&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.

真核生物的生物多样性大多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和进化生物学。这项研究将推进我们的知识，一个主要的进化组（分支）的微生物真核生物，包括层藻，Alveolata和Rhizaria，（SAR）。SAR是最近通过进化分析确定的多种显微真核生物的主要分支，并且其他数据有力地支持SAR作为独立的进化谱系。这一发现迫使人们重新评估几种真核生物特征的进化，最引人注目的是光合作用。在合成孔径雷达中，有许多不同的谱系，但遗传数据很少，而且只集中在少数几个谱系：顶复门（如疟疾寄生虫）、菌类（如寄生水霉菌）和硅藻（如生态上重要的浮游植物）。该项目建议增加具有遗传数据的搜索和救援物种的数量，并大规模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，以提供关于微生物真核生物多样性的综合资源。尽管它们在全球生态中具有重要意义，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（转录组，草案基因组，单细胞扩增基因组），主要集中在捕捉SAR内的多样性。这些数据集将公开提供，大大增加了我们对这些生物进化的了解。应用已建立的生物基因组学和新兴的相似性网络方法将能够进行多层次的分析，为这些生物的进化分析提供新的信息。这将包括：1）使用靶向环境18 S调查结合高通量FlowCam成像的多样性发现; 2）高通量转录组测序;和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遗传镶嵌，在SAR内的早期进化的基础。除了增加来自SAR进化枝不同成员的基因组规模资源外，拟议的工作将生成图像数据层，并将其与EOL中文献中的其他图像整合。本科生，研究生和博士后研究员将接受尖端技术的培训，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树的高中课程。

项目成果

Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis

• DOI: 10.1093/jhered/esaa060
• 发表时间: 2021-01-01
• 期刊: JOURNAL OF HEREDITY
• 影响因子: 3.1
• 作者: Collens, Adena B.;Katz, Laura A.
• 通讯作者: Katz, Laura A.