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

评估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 项目总结 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， 结果发现了包括自剪接RNA和端粒在内的功能。像人类一样， 纤毛虫在每个细胞(即个体)内都有不同的种系和体细胞基因组， 体细胞大核基因组由合子核发育而来，通过一系列复杂的 表观遗传调控的过程。然而，大部分关于纤毛虫的研究只集中在一种 少数可培养的(即模式)谱系，如草履虫、四膜虫和棘毛虫。这里, 新兴的单细胞转录和基因组技术与现有的 生物信息学方法，包括富含分类群的系统基因组学管道，以解决关于 三种不可培养纤毛虫基因组和微生物群的进化 斑潜蝇、大斑潜蝇和条斑夜蛾--据估计 在大约10亿年前就已经分化了。 通过对三个目标形态种的自然种群进行抽样，拟议的工作将测试两个 假设：H1：神秘的纤毛虫物种拥有相似的形态和蛋白质编码基因， 但在生殖系/胞体结构上不同；以及H2：纤毛虫含有物种特有的微生物群 它们有助于这些生物在其环境中发挥作用，其中包括人类 病原体。数据收集将结合光学显微镜和单细胞组学(转录组学 和基因组学)。数据分析将依赖于现有的生物信息学工具，其中一些已经 是在私家侦探的实验室里研发出来的。对结果数据的解释将产生对以下方面的见解：1) 纤毛虫和更广泛的真核生物的基因组进化；以及2)生物多样性和可能的 内、外共生细菌在天然纤毛虫种群中的作用 拟议的工作将在史密斯学院进行，这是一所以女性为主的 本科院校。每年，约5-10名本科生将直接参加 研究和更多的人将在PI教授的课程中了解结果。支持 无论是这个研究项目的目标还是本科生参与者的成功，PI都将 与该项目支持的博士后研究员一起工作。因为私家侦探致力于 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出版约1份手稿 合著者(S)，经常带学生参加国内和国际会议。 1！

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!