Evolution of germline and somatic genomes in the ciliate Chilodonella uncinata

描述(申请人提供)：纤毛虫胚系和体细胞基因组的进化拟议的工作旨在阐明驱动纤毛虫胚系(微核)和体细胞(大核)基因组分化的分子进化原理。纤毛虫和大多数动物一样，有明显分化的生殖系和体细胞基因组；然而，在纤毛虫中，这两个基因组存在于每个单独的细胞/有机体中，而不是像动物那样存在于单独的组织中。Uncinata是纤毛纲的一员，因此具有广泛加工的大核基因组，具有数百万个基因大小的染色体。这一特性使得从这种纤毛虫的种系和体细胞核中分离和分析基因座成为可能。这项拟议的工作将检验三个相互关联的假设，即种系和体细胞基因组之间的基因家族进化的性质，染色体扩增与基因表达的关系，以及钩藤异构体大核的结构。假说将结合使用分子方法(例如传统的聚合酶链式反应、步行聚合酶链式反应、高通量转录组测序)和显微镜工具(例如荧光原位杂交)进行验证。由此产生的分子数据将使用群体遗传学(例如最大似然法)和系统发育方法进行分析，并将根据显微镜图像进行解释。拟议工作的成果将包括加深对钩吻线虫生物学的了解，并能够与其他研究得很好的纤毛虫(即四膜虫和草履虫)进行比较。除了这一具体结果之外，将拟议工作的结果与其他真核生物的知识相结合，将为真核生物生命树上基因组进化的动态提供更多的洞察力。1) 与公共健康相关：微生物提供了探索基因组过程的模型系统，并在历史上提供了与人类健康相关的见解(例如，在纤毛虫中发现端粒)。这项拟议的工作侧重于纤毛虫生殖系和体细胞基因组之间的差异，与对人体细胞中与衰老和疾病(即一些癌症)相关的体细胞基因组变化的分析相似。因此，这项研究中阐明的分子机制可能会对影响人类健康的类似基因组变化的过程产生洞察力。)

DESCRIPTION (provided by applicant): Evolution of germline and somatic genomes in the ciliate Chilodonella uncinata The proposed work aims to elucidate principles of molecular evolution that drive the differentiation between the germline (micronuclear) and somatic (macronuclear) genomes of the ciliate Chilodonella uncinata. Ciliates, like most animals, have clearly differentiated germline and somatic genomes; however, in ciliates, these two genomes are housed within each individual cell/organism in contrast to being in separate tissues as in animals. Chilodonella uncinata is a member of the ciliate class Phyllopharyngea and hence has an extensively processed macronuclear genome with millions of gene-sized chromosomes. This property makes it possible to readily separate and analyze loci from both the germline and somatic nuclei of this ciliate species. The proposed work will test three interrelated hypotheses on the nature of gene family evolution between the germline and somatic genomes, the relationship between chromosome amplification and gene expression, and the architecture of heteromeric macronuclei of C. uncinata. Hypotheses will be tested using a combination of molecular approaches (e.g. traditional PCR, walking PCR, high-throughput sequencing of transcriptome) and microscopy tools (e.g. fluorescence in situ hybridization (FISH)). The resulting molecular data will be analyzed using population genetics (e.g. maximum likelihood approaches) and phylogenetic methods, and will be interpreted in light of microscopy images. The outcomes of the proposed work will include furthering knowledge of the biology of C. uncinata and enabling comparisons with other well-studied ciliates (i.e. Tetrahymena and Paramecium). Beyond this specific outcome, combining the results of the proposed work with knowledge of other eukaryotes will provide additional insights into the dynamics of genome evolution across the eukaryotic tree of life. 1) PUBLIC HEALTH RELEVANCE: Microbial organisms provide model systems to explore genome processes and historically have provided insights that are relevant to human health (e.g. discovery of telomeres in ciliates). The proposed work, which focuses on the differences between germline and somatic genomes in a ciliate, has parallels with analyses of changes in somatic genomes associated with aging and disease (i.e. some cancers) in human cells. Hence, the molecular mechanisms elucidated in this study are likely to yield insights into processes analogous to genome changes that impact human health. )