Evolution of germline and somatic genomes in the ciliate Chilodonella uncinata

描述（由申请人提供）：纤毛虫Chilodonella uncinata的生殖细胞和体细胞基因组的进化拟议的工作旨在阐明分子进化的原则，驱动纤毛虫Chilodonella uncinata的生殖细胞（微核）和体细胞（大核）基因组之间的分化。纤毛虫，像大多数动物一样，有明显分化的生殖细胞和体细胞基因组;然而，在纤毛虫中，这两个基因组被安置在每个单独的细胞/生物体中，而不是像动物那样在单独的组织中。Chilodonella uncinata是纤毛纲Phyllopharyngea的成员，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。这一特性使得从这一纤毛虫物种的生殖细胞核和体细胞核中容易地分离和分析基因座成为可能。本研究将检验三个相互关联的假设，即生殖系和体细胞基因组之间基因家族进化的性质、染色体扩增与基因表达之间的关系以及C.钩状的将使用分子方法（例如，传统PCR、步移PCR、转录组高通量测序）和显微镜工具（例如，荧光原位杂交（FISH））的组合来检验假设。将使用群体遗传学（例如最大似然法）和系统发育方法分析所得分子数据，并将根据显微镜图像进行解释。建议的工作成果将包括进一步了解的生物学C。uncinata的，并使与其他研究充分的纤毛虫（即四膜虫和草履虫）进行比较。除了这一具体结果，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中基因组进化的动态提供更多的见解。第一章 公共卫生相关性：微生物提供了探索基因组过程的模型系统，并且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）。拟议的工作，重点是生殖细胞和体细胞基因组在纤毛虫之间的差异，与分析与衰老和疾病（即某些癌症）相关的体细胞基因组的变化相似。因此，这项研究中阐明的分子机制可能会产生类似于影响人类健康的基因组变化的过程的见解。)

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. )