进展中的纤毛虫学研究:新格局、新窗口与新拓展

Ciliatology Studies by OUC Group: Current Achievements and Future Perspectives

本文综述了作者及所在团队近30年来在海洋纤毛虫领域所取得的系列创新型研究成果。主要概括如下:(1)开拓了中国沿海自由生活类群的区系分类、生态学以及养殖动物病原学等研究,覆盖了温带、热带海区各生境中纤毛门内40余目级阶元,构建了我国长期缺失的海洋类群的物种与基因多样性资料,阐述了特定时空格局下的区系构成与群落演替规律以及主要海水养殖动物的危害性病原等,建立了包括新纲、新目、新科、新属和新种等在内的大量新阶元,系统地描述了近千种的形态分类学信息;(2)完成了1 700余种/种群DNA库、1 400余条标记基因库等纤毛虫遗传资料库的构建;在标记基因序列分析基础上,对纤毛门13个纲、55个目级阶元的系统发育进行了深层次的梳理和探讨,解答了纤毛虫系统演化、阶元定位等方面的诸多科学问题;(3)在细胞发生学研究方面,以腹毛类纤毛虫为材料,围绕无性生殖期间的个体发育,研究刻画了100余种-属的细胞分化与模式构建过程,揭示了大量发生学新现象并形成了领域内首部全视角专著《腹毛类纤毛虫的细胞发生模式》;(4)在基因组学与基因进化研究方面,针对进化地位特殊、环境依赖以及类群代表性种类,阶段性地完成了近百种单细胞基因组的常规测序和6个种的深度分析,研究揭示了钩刺斜管虫大小核基因重组模式等进化生物学新现象;(5)在基因条形码研究方面,以重要模式生物游仆虫属、草履虫属等类群为材料,开展了DNA条形码的筛选和技术优化探索,提出了COI基因和28S rRNA基因D1~D2区可有效刻画近缘种或隐存种这一新观点;(6)在表观遗传学研究方面,探讨了四膜虫组蛋白单甲基化酶TXR1对复制延伸的影响、N6-腺嘌呤甲基化的全基因组分布模式及决定因素、反式和顺式作用元件对核小体分布的协同作用以及RNAi和Polycomb通路关键蛋白对转座子沉默与激活的调控作用与机制。上述研究成果历史性地改变了纤毛虫学研究格局,极大地提升了我国原生动物学研究的国际地位。

In this paper,we reviewed a series of innovative research achievements made by the authors and their teams in the field of marine ciliates in the past 30 years.(1)Pioneering studies on the taxonomy and ecology of ciliate fauna in the northern and southern China seas and the pathogenic protozoan in aquaculture have been systematically carried out.More than 40 orders of ciliates from various biotopes in temperate and subtropical sea areas including species of long-term-unknown free-living groups in China and protozoan pathogens of commercial aquaculture species and their background information,faunistic composition and community succession at spatial and temporal levels have been systematically depicted.Nearly 1 000 species have been founded and assigned to new taxa(e.g.classes,orders,families).Corresponding to that,three monographs entitled“Free-living Ciliates in the Bohai and Yellow Seas,China”,“Pathogenic Protozoa in Mariculture”,and“Ciliate Atlas:Species Found in the South China Sea”,have been published.(2)Benefited from the world’s largest genomic DNA library of marine ciliates constructed by the author’s team,the phylogenetic relationships of 55 orders in 13 classes have been thoroughly reconstructed and investigated,and the systematic position of some higher taxa has been clarified.(3)In the field of cell development,ontogenetic patterns of more than 100 genera/species of hypotrich ciliates during asexual reproduction and physiological reorganization have been investigated,and a large number of new morphogenetic phenomena have been revealed.As a consequence,the first full-perspective monograph in the field entitled“Ontogenetic Patterns of Hypotrich Ciliates”,has been published.(4)In the field of genomics and gene evolution,a genome/transcriptome databank has been constructed for more than 90 species,including pathogenic species in aquaculture and species with unique phylogenetic position,cosmopolitan distributions and adapted to the extreme environment.New biological phenomena,such as highly fragmented and concise somatic genome,gene scrambling and genome rearrangement between somatic and germline genomes,special gene expression and regulation mechanism,have thus been discovered.(5)In the field of gene barcoding,the optimization of DNA barcode screening technology for ciliates has been completed,and the efficiency of characterizing related species or cryptic species by COI gene and D1~D2 region of 28S rRNA gene has been clarified based on the framework of comprehensive taxonomy.(6)In the field of epigenetics,the effect of histone monomethyltransferase TXR1 on DNA replication elongation,the genome distribution pattern and determinants of DNA N6-adenine methylation(6mA),the coordinated regulation of nucleosome distribution by cis-and trans-elements,and the fine-tuning of transposon expression by key components of RNAi and polycomb pathways have been investigated in the model organism,Tetrahymena thermophila.These impressive contributions have revolutionized the global pattern of ciliatology study and greatly enhanced the international status and discourse power of protozoological researches in China.