海洋纤毛虫具沟急游虫的基因组重组过程与进化探讨

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 ciliates 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, especially in the highly differentiated species. This project focuses on the marine species, Strombidium sulcatum, using the combination of analyses of high throughput transcriptome data and traditional molecular methods. We aim to: 1) characterize gene scrambling, gene copy numbers and gene family evolution in the highly differentiated oligotrichs; 2) reveal the chromosomal breakage sites and the relationships between macronucleus destined sequences and internal eliminated sequences to elaborate the genome rearrangements patterns; 3) explore evolutionary relationships of the genome rearrangement patterns within different taxa. This project will yield important insights into the impact of genome structure on gene family evolution in eukaryotes and provide insights for further studies of genetic regulatory mechanisms in ciliates.

纤毛虫的基因组进化由其独特的两型核来演绎和完成。由于其类群间大核倍性的高度差异，大小核间的重组模式呈现高度的分化。围绕此过程和机理的研究对于了解物种形成和分化具有重要的理论意义并因此成为国际间相关领域的研究热点。当前的问题是：有关纤毛虫基因重组模式与机制的研究仍在探索阶段且仅来自极少数低等分化的淡水种类，因此在分化程度更高的尤其海洋类群中和更深入的工作亟待开展。本项目拟以海洋纤毛虫--具沟急游虫为材料，在转录组测序、分析的基础上，开展下列探讨：1）刻画基因乱序在海洋纤毛虫等高等寡毛类中的特征、基因家族的命运、多倍性形成等具普遍性和不明的问题；2）揭示染色体断裂位点特征、内部切除序列与大核注定序列的关系，阐述大小核基因组的重组模式； 3）结合转录组信息，探讨纤毛虫不同类群中基因组的进化关系。该工作将为探讨纤毛虫物种分化-形成机理提供重要的资讯，同时也为纤毛虫遗传调控机制的深入研究奠定基础。

本项目3年来以旋唇纲纤毛虫等主要代表类群为实验材料，对其基因组重组、rDNA多态性及拷贝数、形态分类、系统关系重建等开展了系统的研究。主要成果包括：1）急游虫、柠檬类瘦尾虫、黄色伪角毛虫、大弹跳虫的a-tubulin、Actin、TBP、ABC转运蛋白等基因的大小核重组研究，为纤毛虫乃至其他真核生物基因组进化研究提供了有价值的参考；2）完成了50余种纤毛虫单细胞rDNA拷贝数的测定和20余种rDNA多态性的测定，对基于rDNA的分子系统学、分子生态学、物种鉴定、条形码研究等提供了重要的参考资料；3）基于SSU-rDNA、ITS-5.8S和LSU-rDNA等多基因信息及二级结构分析，结合形态学、发生学对旋唇纲尾柱类的系统关系进行了梳理和重建；4）完成了对7属16种纤毛虫的鉴定和描述工作， DNA建库以及不详属种的重厘定、重定义、纤毛图式资料的补足等；5）海洋尾丝虫的无菌培养及液氮冻存技术的摸索，为其他纤毛虫培养提供了参考。以上成果在国际主流刊物发表文章9篇，9人次参加国际国内学术会议并做口头或者墙报报告。

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