研究团队
Research Groups

  • 研究方向

     


    空格围绕纤毛虫原生动物的多样性与系统演化、细胞结构的发生与分化、表观遗传调控、性别决定、基因组重排与基因进化等基础科学问题，主要研究包括：

    （1）聚焦我国温带、亚热带-热带沿海与内陆湿地环境中的自由生活类群，研究其区系、形态分类、物种多样性、群落结构、生态学功能与地位、时空与地理分布；

    （2）以四膜虫等模式物种为材料，探讨以甲基化修饰为主的表观遗传信息对基因表达和复制的调控机制；

    （3）以游仆虫、草履虫等为材料，阐明其有性生殖过程中大、小核发育、分化及基因重组的模式和机制，解析其性别分化和决定的相关基因及分子机制；

    （4）探讨旋唇纲等高等分化类群无性生殖期间细胞器结构及模式的形成与个体发育；

    （5）围绕纤毛虫演化、分化过程中的重要事件和机制，探讨胞器分化、结构与功能等重要生理过程中相关功能基因的调控机制；

    （6）探讨纤毛门内各高阶阶元间的亲缘关系、系统发育与演化；构建纤毛虫各代表类群的DNA库、条形码数据库、标记基因库、组学信息库等遗传信息库，开展纤毛虫重要类群的组学信息分析;

    （7）以具有双元核型的纤毛虫为特色研究材料，聚焦减数分裂这一重要生命过程，揭示减数分裂期间染色体的转录及重组机制等。




  • 承担课题

    · 国家自然科学基金“杰青”项目：纤毛虫原生动物基础生物学（2022-2026）

    · 国家自然科学基金重点项目：淡水湿地中纤毛虫原生动物多样性格局与档案资料的建立：以东湖（武汉）与微山湖水系为例（2021-2025）

    · 国家自然科学基金“优青”项目（海外）：纤毛虫染色体生物学（2022-2024）

    · 国家自然科学基金面上项目：多小核草履虫交配型昼夜节律逆转的分子机制探究（2023-2026）

    · 国家自然科学基金面上项目：以海洋纤毛虫为材料：大小核基因重组模式及机制探讨（2023-2026）

    · 国家自然科学基金面上项目：中国南黄海近岸海区浮游前口类纤毛虫的生物多样性与地理分布（2023-2026）

    · 国家自然科学基金面上项目：以纤毛虫原生动物-嗜热四膜虫为模式：组蛋白甲基化酶TXR1的细胞周期性波动对复制-转录冲突的调控（2021-2024）

    · 国家自然科学基金面上项目：我国南黄海沿岸湿地底栖纤毛虫原生动物：物种、基因、生态系多样性（2020-2023）

    · 国家自然科学基金青年项目：以嗜热四膜虫为模式：真核生物DNA N6-腺嘌呤甲基化的关键调控因子的作用机制研究（2023-2025）

    · 山东省自然科学基金“杰青”项目：以四膜虫为模式的减数分裂研究（2023-2025）

    · 山东省自然科学基金“杰青”项目：纤毛虫模式动物的基因重组及性别决定机制研究（2021-2023）

    · 山东省“泰山学者”青年专家计划：纤毛虫功能基因及组学研究（2021-2025）

    · 中国博士后创新人才支持计划：DNA N6-腺嘌呤甲基化酶复合体依赖的甲基化维持及动态变化的调控机制研究（2021-2023）


  • 近期论文及成果


    2024 Liu Y.Q., Niu J.H., Ye F., Solberg T., Lu B.R., Wang C.D., Nowacki M., Gao S., Dynamic DNA N6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus.Genome Research, 34(2):256-271.

    2024 Sheng Y.L., Wang Y.Y., Yang W.T., Wang X.Q., Lu J.W., Pan B., Nan B., Liu Y.Q., Ye F., Li C., Song J.K., Dou Y.L., Gao S., Liu Y.F. Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote. Genome Research, 34(5):740-756

    2023 Pan B., Ye F., Li T., Wei F., Warren A., Wang Y.Y., Gao S. Potential role of N6-adenine DNA methylation in alternative splicing and endosymbiosis in Paramecium bursaria. iScience, 26(5):106676

    2023 Gao Y.Y., Solberg T., Wang, C.D., Gao F. Small RNA-mediated genome rearrangement pathways in ciliates. Trends in Genetics, 39(2): 94−97.

    2022 Wang C.D., Solberg T., Maurer-Alcalá X.X., Swart C.E., Gao F., Nowacki M. A small RNA guided PRC2 complex eliminates DNA as an extreme form of transposon silencing. Cell Reports, 40: 111263.

    2022 Qiao Y., Cheng T., Zhang J., Alfarraj S.A., Tian M., Liu Y. & Gao S. Identification and utilization of a mutated 60S ribosomal subunit coding gene as an effective and cost-efficient selection marker for Tetrahymena genetic manipulation. International Journal of Biological Macromolecules, 204: 1−8.

    2022 Li R., Zhuang W.B., Feng X.C., Al-Farraj S.A., Warren A. & Hu X.Z. Phylogeny of the anaerobic ciliate genus Sonderia (Protista: Ciliophora: Plagiopylea), including the description of three novel species and a brief revision of the genus. Marine Life Science and Technology, 4: 493−512.

    2022 Ma M.Z., Xu Y., Lu B.R., Li Y.Q., Song W.B., Petroni G., Al-Farrah SA., & Yan Y. Molecular Phylogeny and taxonomy of four Remanella species (Protozoa, Ciliophora): a flagship genus of karyorelictean ciliates, with descriptions of three new species. Zoological Research, 43: 827−842.

    2022 Ma M.Z., Li Y.Q., Maurer-Alcala X., Wang Y.R. & Yan Y. Deciphering phylogenetic relationships in class Karyorelictea (Protista, Ciliophora) based on updated multi-gene information with establishment of a new order Wilbertomorphida n. ord. Molecular Phylogenetics and Evolution, 169: 107406.

    2022 Zhang G.A.T., Zhao Y., Chi Y., Warren A., Pan H.B. & Song, W.B. Updating the phylogeny and taxonomy of pleurostomatid ciliates (Protista: Ciliophora) with establishment of a new family, a new genus and two new species. Zoological Journal of the Linnean Society, 196: 105–123.

    2021 Xu J., Zhao X.L., Mao F.B., Basrur V., Ueberheide B., Chait B.T., Allis C.D., Taverna S.D., Gao S., Wang W. & Liu Y. A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies. Nucleic Acids Research, 49, 5407–5425

    2021 Zheng W.B., Wang C.D., Lynch M. & Gao S. The compact macronuclear genome of the ciliate Halteria grandinella: a transcriptome-like genome with 23,000 nanochromosomes. mBio, 12: e01964-20.

    2021 Chi Y., Chen X., Li Y., Wang C., Zhang T., Ayoub A., Warren A., Song W. & Wang Y.Y. New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses. Science China Life Science, 64: 606–620.

    2021 Liu Y., Nan B., Niu J., Kapler G. & Gao S. An optimized and versatile counter-flow centrifugal elutriation workflow to obtain synchronized eukaryotic cells. Frontiers in Cell and Developmental Biology, 9:664418.

    2021 Wang, C.D., Gao, Y.Y., Lu, B.R., Chi, Y., Zhang, T.T., El-Serehy, H. A., Al-Farraj, S. A., Li, L.F., Song, W.B. & Gao, F. Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl. Molecular Phylogenetics and Evolution, 159: 107112.

    2021 Zhang T.T., Li C., Zhang X., Wang C.D., Roger A.J. & Gao F. Characterization and comparative analysis of mitochondrial genomes in single-celled eukaryotes shed light on the diversity and evolution of the linear molecular architecture.International Journal of Molecular Science, 22: 2546.

    2021 Ma M.Z., Xu Y., Yan Y., Li Y.Q., Warren A. & Song W.B. Taxonomy and molecular information of four karyorelictids in genera Apotrachelocerca and Tracheloraphis (Protozoa, Ciliophora), with notes on their systematic positions and description of two new species. Zoological Journal of the Linnean Society, 192: 690–709. 

    2021 Sheng Y., Pan B., Wei F., Wang Y.Y. & Gao S. Case study of the response of N6-methyladenine DNA modification to environmental stressors in the unicellular eukaryote Tetrahymena thermophila. mSphere, 6: e01208-20.

    2020 Sheng Y., Duan L., Cheng T., Qiao Y., Stover N.A., Gao S. The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses. Science China Life Science, 63: 1534–1542. 

    2020 Zheng W., Chen J., Doak T.C., Song W.B., Yan Y. ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data. Bioinformatics, 36: 3632–3636.

    2020 Chi Y., Duan L.L., Luo X.T., Cheng T., Warren A., Huang J. & Chen X.R. A new contribution to the taxonomy and molecular phylogeny of three freshwater, well-known species of the ciliate genus Spirostomum (Protozoa: Ciliophora: Heterotrichea). Zoological Journal of the Linnean Society, 189:158–177.

    2020 Tian, M., Agreiter C., Loidl J. Spatial constraints on chromosomes are instrumental to meiotic pairing. Journal of Cell Science, 133(22): jcs.253724

    2019 Wang Y.Y., Sheng Y.L., Liu Y.Q., Zhang W.X., Cheng T., Duan L.L., Pan B., Qiao Y., Liu Y.F. & Gao S. A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription. Nucleic Acids Research, 47: 11771–11789.

    2019 Zhao X.L., Xiong J., Mao F.B., Sheng Y.L., Chen X., Feng L.F., Dui W., Yang W.T., Kapusta A., Feschotte C., Coyne R.S., Miao W., Gao S. & Liu Y.F. RNAi-dependent polycomb repression controls transposable elements in Tetrahymena.Genes & Development. 33: 348–364.

    2019 Chen X., Jiang Y.H., Gao F., Zheng W.B., Krock T.J., Stover N.A., Lu C., Katz L.A. & Song W.B. Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. Molecular Ecology Resources, 19:1292–1308.

    2019 Zhang T.T., Fan X.P., Gao F., Al-Farraj S.A., El-Serehy H.A., Song W.B. Further analyses on the phylogeny of the subclass Scuticociliatia (Protozoa, Ciliophora) based on both nuclear and mitochondrial data. Molecular Phylogenetics and Evolution,139: 106565. 

    2019 Wang Y.R., Wang C.D., Jiang Y.H., Katz L.A., Gao F. & Yan Y. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. Science China Life Science, 62: 203–214.

    2019 Lu B., Li L., Hu X.Z., Ji D., Al-Rasheid K.A.S. & Song W.B. Novel contributions to the peritrich family Vaginicolidae (Protista, Ciliophora), with morphological and phylogenetic analyses of three poorly-known species within genera Pyxicola, Cothurnia and Vaginicola. Zoological Journal of the Linnean Society, 187: 1–30

    2018 Zhao Y., Yi Z.Z., Warren A. & Song W.B. Species delimitation for the molecular taxonomy and ecology of a widely distributed microbial eukaryotes genus Euplotes (Alveolata, Ciliophora). Proceedings of the Royal Society B-Biological Science. 285: 20172159.

    2018 Sheng Y.L., He M., Zhao F.Q., Shao C. & Miao M. Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti.Molecular Phylogenetics and Evolution, 129: 338–345.

    2018 Luo X.T., Yan Y., Shao C., Al-Farraj S.A., Bourland W. & Song W.B. Morphological, ontogenetic and molecular data support strongylidiids as being closely related to Dorsomarginalia (Protozoa, Ciliophora) and reactivation of the family Strongylidiidae Fauré-Fremiet, 1961. Zoological Journal of the Linnean Society, 184, 237–254.


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