纤毛虫作为一大类高度进化的原生动物，在细胞结构、发育模式、两型核及接合生殖等方面表现出极高的多样性，使其在遗传学、细胞学和进化生物学等领域得到广泛关注。在纤毛虫的系统发育领域，所面临的瓶颈问题在于研究手段单一和覆盖类群不足，导致纤毛虫部分分支的分子系统学研究严重滞后和高度混乱。本项目拟聚焦旋唇纲这一高等类群，利用申报团队所拥有的全球最大的纤毛虫样本库这一资源优势，选取盘头类、原腹毛类、游仆类、尾柱类、散毛类、排毛类、寡毛类等目级类群中具重要意义的代表种，采用转录组测序技术，获取高质量的标记基因，开展全面的系统发育基因组学研究，同时结合缺失种类的形态学、细胞发生学、标记性基因测序等信息，澄清和构建迄今存疑的旋唇纲纲内阶元的系统发育关系，也为解析门内相关类群的起源和演化及构建纤毛虫转录组学档案奠定重要基础。

As a group of highly evolved protozoa, ciliates show great diversity in morphological and biological characters; meanwhile, specialized organelles, dimorphic nuclei and unique ontogenetic models, make ciliates a hot spot in genetics, cytobiology and evolutionary biology. However, there are several bottlenecks in the phylogenetic studies of ciliates, including lack of more efficient marker genes and key species. In this study, we will focus on the “higher” class of ciliates----spirotrichea, with the strong support of the largest ciliate library of the world and the leading center of protozoology. The representative species including discocephalids, protohypotrichs, euplotids, urostylids, sporadotrichs, stichotrichs, oligotrichs will be chosen to obtain the transcriptomic data using high throughput sequencing. By using bioinformatic approaches, we will generate high quality marker genes and perform phylogenomic analyses based on appropriate models and algorithms. Eventually, we will combine the phylogenomic data with morphological, ontogenetic and ecological information to reconstruct the phylogenetic relationships among spirotrichous ciliates. From this work, we will provide new evidence for the evolution of ciliates as well as protozoa, and help to investigate the possible function for the genes and build the ciliate transcriptomic archives for the future study.