纤毛虫因独特的两型核结构而成为研究DNA重组最为理想的模式之一。围绕此过程和机理的研究对于了解物种形成和分化、基因组进化及遗传调控机制等科学问题均具有重要的学术意义和价值。目前在全球范围内有关此过程与机理的研究仍在起步和探索阶段，大量未知问题等待解答。本项目拟以纤毛虫的重要代表——扇形游仆虫为材料，利用高通量测序、组学分析和分子生物学手段等开展下列研究：1）刻画纤毛虫大小核基因组的重组模式，包括染色体断裂位点及接头序列特征、内部切除序列与大核注定序列的关系、基因倍性特征等；2）揭示纤毛虫大小核基因组的重组机制，包括内部切除序列的删除、大核基因的重排等机制；3）优化接合生殖的诱导条件，揭示其生活史中大小核的变化及过程、界定相关的调控基因。该工作将为新的模式材料构建、深入研究纤毛虫遗传调控机制以及物种分化与形成奠定基础，也将加深人们对整个真核生物基因组起源和进化的认识。

Genome evolution in ciliates has to be interpreted in light of their dual genomes, the presence of both germline and somatic genomes within each cell. During sexual conjugation, the macronucleus is transformed through a series of chromosomal rearrangements, including fragmentation, elimination of internal excised sequences, and amplification. The processes and mechanisms of chromosomal rearrangements during macronuclear development are quite diverse, both within a given ciliate species as well as among different ciliates. Studies about the processes and mechanisms can enhance views on the dynamic nature of eukaryotic genomes and add to the growing information on genome evolution. The current problem is that studies on ciliate genome rearrangements are still in the early stage, and are focusing on only a handful of low differentiated species. It is urgent to carry out more in-depth researches on genome rearrangements and the related mechanisms, especially in the highly differentiated species. This project focuses on the highly differentiated euplotids, Euplotes vannus, using the combination of analyses of high throughput sequencing, bioinformatics and traditional molecular methods. We aim to: 1) reveal the genome rearrangement patterns, e.g. the chromosomal breakage sites, pointer sequences, the relationships between macronucleus destined sequences and internal eliminated sequences, gene copy numbers, etc.; 2) explore the mechanisms of genome rearrangements in Euplotes, e.g. deletion of internal eliminated sequences, reorganization of the macronucleus destined sequences, etc.; 3) develop E. vannus into a new model organism, including optimizing the methods for inducing conjugation, revealing the detailed morphology during conjugation, and defining the related regulatory genes. This project will provide insights for further studies of genetic regulatory mechanisms in ciliates and make people to better understand the genome origin and evolution of the whole eukaryotes.