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.

真核生物中的大多数生物学多样性（具有独特核的生物）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，物种之间的进化关系和遗传变异方面，植物，动物，动物和真菌的形式较少。这种相对缺乏有关微生物真核生物的信息不仅对我们对地球上所​​有生物多样性的理解产生了后果，而且在最广泛的意义上我们如何解释细胞和进化生物学。这项研究将促进我们对构成斯特拉米诺氏菌，肺泡和根瘤菌（SAR）的微生物真核生物的主要进化组（进化枝）的了解。 SAR是多种微观真核生物的主要进化枝，最近通过进化分析确定，其他数据已强有力地支持SAR作为独立的进化谱系。这一发现迫使对几种真核特征的演变进行重新评估，最著名的是光合作用。在SAR中有许多多样化的谱系，但遗传数据很少见，只集中在几个谱系中：apicomplexa（例如疟疾寄生虫），兆木（例如寄生虫水霉）和硅藻（例如，生态上重要的浮游植物）。该项目提议使用遗传数据增加SAR物种的数量，并大量增加每个物种收集的遗传数据的量。用于基因组数据的生物将进行成像，并将整合到生命百科全书（EOL），以提供有关微生物真核多样性的全面资源。尽管它们具有全球生态学重要性，但在所有SAR进化核心中，不到50％的SAR进化片中甚至在公共数据库中以单个基因组为代表。这里提出的工作将至少增加250个新型基因组规模数据集（转录组，基因组草案，单细胞放大基因组），主要集中于捕获SAR内的多样性。这些数据集将公开可用，从而大大增加了我们对这些生物发展的发展的理解。已建立的系统基因组和新兴相似性网络方法的应用将实现多层分析，该分析将为这些生物的进化分析提供新的信息。这将包括：1）使用有针对性的环境18S调查以及高通量流摄像头成像的多样性发现； 2）高通量转录组测序； 3）无法培养类群的单细胞基因组学。系统发育分析将捕获SAR内早期进化的基础的遗传镶嵌物。除了SAR进化枝的不同成员的基因组规模资源的增加之外，提出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在一起。本科生，研究生和博士后研究员将接受尖端技术的培训，并将为显微镜的教师培训提供讲习班。该项目将通过招募来自代表性不足的群体的学生并在微生物生命树上开发高中课程来增加参与者的多样性。

项目成果

Illuminating the first bacteria

• DOI: 10.1126/science.abh2814
• 发表时间: 2021-05-07
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Katz, Laura A.

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.