Assessing evolutionary patterns in uncultivable ciliates and their microbiomes by combining single-cell transcriptomics and single-cell genomics

通过结合单细胞转录组学和单细胞基因组学评估不可培养的纤毛虫及其微生物组的进化模式

• 批准号: 9813172
• 负责人: Laura Aline Katz
• 金额: $ 40.02万
• 依托单位: SMITH COLLEGE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-19 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9813172
• 关键词: Address; Aging; Architecture; Award; Bacteria; Bacterial Genome; Biodiversity; Bioinformatics; Biological; Biological Models; Biology; Cell Nucleus; Cells; Cellular biology; Chromosomes; Code; Color; Complex; Data; Data Analyses; Data Collection; Databases; Ecology; Environment; Epigenetic Process; Equus caballus; Eukaryota; Euplotes; Evolution; First Generation College Students; Fluorescent in Situ Hybridization; Fresh Water; Genbank; Gene Expression Profile; Genes; Genome; Genomics; Habitats; Health; Human; Individual; Institution; International; Introns; Learning; Light; Location; Malignant Neoplasms; Manuscripts; Methods; Microbe; Microscope; Modeling; Morphology; Names; New England; Organism; Oxytricha; Paramecium; Participant; Pattern; Peer Review; Population; Postdoctoral Fellow; Process; Proteins; Protocols documentation; Publishing; RNA Splicing; Research; Research Personnel; Research Project Grants; Role; Running; Sampling; Series; Site; Societies; Students; Study models; Taxon; Techniques; Telomere Capping; Testing; Tetrahymena; Time; Training; United States National Institutes of Health; Woman; Work; bioinformatics tool; college; genomic data; human pathogen; innovation; insight; interest; light microscopy; meetings; method development; microbial; microbiome; microorganism; neuronal cell body; success; symbiont; symposium; telomere; tool; transcriptome; transcriptomics; undergraduate student; whole genome

Assessing evolutionary patterns in uncultivable ciliates and their microbiomes by combining single-cell transcriptomics and single-cell genomics PROJECT SUMMARY Ciliates, the focus of the proposed work, have long been models for studies of genomes, resulting in the discovery of features including self-splicing RNA and telomeres. Like humans, ciliates have distinct germline and somatic genomes within every cell (i.e. individual) and the somatic ‘macronuclear’ genomes develop from zygotic nuclei through a complex series of epigenetically-regulated processes. Yet the bulk of studies on ciliates have focused on only a few cultivable (i.e. model) lineages such as Paramecium, Tetrahymena, and Oxytricha. Here, emerging single-cell transcriptomic and genomic techniques are combined with existing bioinformatics methods, including a taxon-rich phylogenomic pipeline, to address questions on the evolution of both the genomes and microbiomes of three uncultivable ciliate species – Chilodonella uncinata, Halteria grandinella and Loxodes striatus – that are estimated to have diverged approximately one billion years ago. By sampling natural populations of three target morphospecies, the proposed work will test two hypotheses: H1: Cryptic species of ciliates share similar morphology and protein-coding genes, but differ in germline/soma architecture; and H2: Ciliates contain species-specific microbiomes that contribute to the function of these organisms in their environments and that include human pathogens. Data collection will combine light microscopy and single-cell ‘omics (transcriptomics and genomics). Data analyses will rely on existing bioinformatics tools, some of which have been developed in the PI’s lab. Interpretation of the resulting data will yield insights into: 1) genome evolution in ciliates, and more broadly eukaryotes; and 2) the biodiversity and possible function of endo- and ectosymbiotic bacteria in natural ciliate populations. The proposed work will take place at Smith College, an all women’s predominantly undergraduate institution. Each year, ~5-10 undergraduates will participate directly in the research and many more will learn about the results in courses taught by the PI. To support both the aims of this research project and the success of undergraduate participants, the PI will work with a postdoctoral fellow supported by this project. Because of the PI’s commitment to diversity and inclusion, ~50% of participants will be students of color and/or first-generation college students. The PI also publishes about 1 manuscript each year with undergraduate coauthor(s) and regularly takes students to national and international meetings. 1!

不可培养纤毛虫及其微生物群的进化模式 结合单细胞转录组学和单细胞基因组学 项目摘要 纤毛虫是拟议工作的重点，长期以来一直是基因组研究的模型， 从而发现了包括自剪接RNA和端粒在内的特征。像人类一样， 纤毛虫在每个细胞（即个体）中具有不同的生殖系和体细胞基因组， 体细胞“大核”基因组从合子核通过一系列复杂的 表观遗传调控过程。然而，大部分关于纤毛虫的研究只集中在一个 一些可培养的（即模式）谱系，如草履虫属、四膜虫属和尖毛虫属。在这里， 新兴的单细胞转录组学和基因组学技术与现有的 生物信息学方法，包括分类丰富的基因组管道，以解决问题， 三种不可培养的纤毛虫物种的基因组和微生物组的进化- Chilodonella uncinata，Halteria grandinella和Loxodes striatus -据估计， 在大约10亿年前开始分化 通过对三个目标形态种的自然种群进行采样，拟议的工作将测试两个 假设：H1：纤毛虫的隐藏物种具有相似的形态和蛋白质编码基因， 但在种系/索马结构上不同; H2：纤毛虫含有种特异性微生物组 这有助于这些有机体在其环境中的功能，包括人类 病原体数据收集将结合联合收割机和单细胞组学（转录组学 基因组学）。数据分析将依赖于现有的生物信息学工具，其中一些工具 是在私家侦探的实验室里研发的对所得数据的解释将产生以下见解：1） 纤毛虫和更广泛的真核生物的基因组进化;和2）生物多样性和可能的 自然纤毛虫种群中内外共生细菌的功能。 拟议的工作将在史密斯学院进行，这是一所以女性为主的学校。 本科院校。每年，约5-10名本科生将直接参加 研究和更多的将了解由PI教授的课程的结果。支持 本研究项目的目标和本科生参与者的成功，PI将 与该项目支持的博士后研究员合作。因为私家侦探的承诺 多样性和包容性，约50%的参与者将是有色人种和/或第一代学生 大学生PI每年还与本科生一起发表约1篇手稿 共同作者，并定期带学生参加国家和国际会议。 一个！