Systematics and evolutionary genomics of protozoa

Evolution and functional genomics of ciliated protozoa

Genetic engineering technology of ciliated protozoa

1999.09 - 2002.06, Institute of Hydrobiology, Chinese Academy of Sciences, PhD;

1996.09 - 1999.06, Wuhan University, Master;

1992.09 - 1996.06, Wuhan University, Bachelor.

2018/09 - present,   Institute of Hydrobiology, Chinese Academy of Sciences, Deputy director, Professor;

2002.07 – 2018.09, Institute of Hydrobiology, Chinese Academy of Sciences, Assistant Professor, Associate Professor, and Professor;

2007.01 – 2008.12, University of Rochester, USA，Senior visiting scholar and post-doc;

2004.07 – 2005.01, University of California, Santa Barbara, USA, Senior visiting scholar;

2002.10 – 2003.03, Hong Kong Baptist University, Visiting Scholar.

(1)  Advanced aquatic biology

(2)  Higher aquatic biology zooplankton periclastic organisms

(3)  Advances in life science of aquatic organisms

(1)  Wang GY, Chai XC, Zhang J, Yang WT, Jiang CQ, Chen K, Miao W*, Xiong J*. A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data. bioRxiv, 2020.

(2)  Xiong J, Yang WT, Chen K, Jiang CQ, Ma Y, Chai XC, Yan GX, Wang GY, Yuan DX, Liu YF, Bidwell SL, Zafar N, Hadjithomas M, Krishnakumar V, Coyne RS, Orias E, Miao W*. Hidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena. PLoS Biology. 2019, 17(6): e3000294.

(3)  Yang WT, Jiang CQ, Zhu Y, Chen K, Wang GY, Yuan DX, Miao W*, Xiong J*. Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena. Database, 2019.

(4)  Jiang CQ, Wang GY, Xiong J, Yang WT, Sun ZY, Feng JM, Warren A*, Miao W*. Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics. Molecular Phylogenetics and Evolution, 2019,132: 25-35.

(5)  Chen K, Wang GY, Xiong J, Jiang CQ, Miao W*. Exploration of Genetic Variations through Single cell Whole genome Sequencing in the Model Ciliate Tetrahymena thermophila[J]. Journal of Eukaryotic Microbiology, 2019, 66(6): 954-965.

(6)  Jiang CQ, Wei W, Yan G, Shi TY, Miao W*. Transcriptome Analysis Reveals the Molecular Mechanism of Resting Cyst Formation in Colpoda aspera[J]. Journal of Eukaryotic Microbiology, 2019 Mar, 66(2):212-220.

(7)  Zhang J, Yan G, Tian M, Ma Y, Xiong J, Miao W*. A DP-like transcription factor protein interacts with E2fl1 to regulate meiosis in Tetrahymena thermophila. Cell Cycle, 2018, 17(5):634-642.

(8)  Tian M, Yang WT, Zhang J, Dang H, Lu XY, Fu CJ, Miao W*. Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease. Nucleic Acids Research, 2017, 45:6848-6863.

(9)  Feng LF, Wang GY, Hamilton EP, Xiong J, Yan GX, Chen K, Chen X, Dui W, Plemens A, Khadr L, Dhanekula A, Juma M, Dang HQ, Kapler GM, Orias E, Miao W*, Liu YF*. A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement. Nucleic Acids Research, 2017, 45:9481-9502.

(10)  Zhang J, Tian M, Yan GX, Shodhan A, Miao W*. E2fl1 is a meiosis-specific transcription factor in the protist Tetrahymena thermophila. Cell Cycle, 2017,16(1):123-135.

(11)  Xiong J#, Gao S#, Dui W, Yang WT, Chen X, Taverna SD, Pearlman RE, Ashlock W, Miao W*, Liu YF*. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Research, 2016, 44:10091-10105.

(12)  Yan GX, Zhang J, Shodhan A, Tian M, Miao W*. Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila. Cell Cycle, 2016, 15(18):2506-2514. (

(13) Yan GX, Dang H, Tian M, Zhang J, Shodhan A, Ning YZ, Xiong J, Miao W*. Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila. Cell Cycle, 2016, 15(14):1855-1864. 2016.7.17

(14)  Feng JM, Jiang CQ, Warren A, Tian M, Cheng J, Liu GL, Xiong J, Miao W*. Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea. Molecular Phylogenetics and Evolution, 2015, 90:104-111.

(15) Xiong J, Wang G, Cheng J, Tian M, Pan X, Warren A, Jiang C, Yuan D, Miao W*. Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer. Scientific Reports, 2015, 5:15470.

(16) Xiong J, Feng JM, Yuan DX, Zhou J, Miao W*. Tracing the structural evolution of eukaryotic ATP binding cassette transporter superfamily. Scientific Reports, 2015, 5:16724.

(17) Tian M, Chen XL, Xiong Q, Xiong J, Xiao CL, Ge F*, Yang FQ*, Miao W*. Phosphoproteomic Analysis of Protein Phosphorylation Networks in Tetrahymena thermophila, a Model Single-celled Organism. Molecular & Cellular Proteomics, 2014, 13:503-519.

(18) Feng L, Fu C, Yuan D, Miao W*. A P450 gene associated with robust resistance to DDT in ciliated protozoan, Tetrahymena thermophila by efficient degradation. Aquatic Toxicology, 2014, 149:126-132.

(19)   Ye J, Chang Y, Yan Y, Xiong J, Xue XM, Yuan D, Sun GX, Zhu YG*, Miao W*. Identification and characterization of the arsenite methyltransferase from a protozoan, Tetrahymena pyriformis. Aquatic Toxicology, 2014, 149:50-57.

(20)   Chang Y, Liu G, Guo L, Liu H, Yuan D, Xiong J, Ning Y, Fu C, Miao W*. Cd‐Metallothioneins in Three Additional Tetrahymena Species: Intragenic Repeat Patterns and Induction by Metal Ions. Journal of Eukaryotic Microbiology, 2014, 61(4):333-342.

(21)  Xiong J, Lu YM, Feng JM, Yuan DX, Tian M, Chang Y, Fu CJ, Wang GY, Zeng HH*, Miao W*. Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics. Database-OXFORD, 2013, bat008.

(22)  Gao S, Xiong J, Zhang CC, Berquist BR, Yang RD, Zhao M, Molascon AJ, Kwiatkowski SY, Yuan DX, Qin ZH, Wen JF, Kapler GM, Andrews PC, Miao W*, Liu YF*. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. Genes & Development, 2013, 27:1662-1679.

(23) Cervantes MD, Hamilton EP, Xiong J, Lawson MJ, Yuan DX, Hadjithomas M, Miao W*, Orias E*.  Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila. Plos Biology, 2013, 11(3): e1001518.

(1) A high-density fermentation method for Tetrahymena themophila, invention in 2016, author no. 1, patent number ZL201410024085.7;

(2) CYP5013C2 protein, its encoding gene and the protein expression in Tetrahymena, invention, 2015, author no. 1, patent number ZL201310124935.6;

(3) TpyArsM protein and its coding gene and application from Tetrahymena, invention, 2015, author no. 1, patent number ZL201410001904.6;

(4) The expression vector of chitinase in Tetrahymena and its application, invention, 2012, author no. 3, patent number ZL20110430564.5;

(5) Transgenic vector of Tetrahymena containing HSP70 promoter and GFP, preparation method and application, invention, 2011, author no. 2, patent number ZL200910062093.X.

(1) Systematics and evolutionary genomics of protozoa

Based on the identification and taxonomy of representative species of ciliates, flagellates and amoebas with free-living, parasitic and mutualism life styles, establishing the experimental and bioinformatics tools for these species, and sequencing and collecting the omics data, aims to understand the phylogeny, systematics and adaptive evolution of protozoa.

(2)  Evolution and functional genomics of ciliated protozoa

Establishing various ciliate research models, and sequencing and collecting the omics data, performing comparative genomics, epigenomics, experimental evolutionary genomics analysis, aim to understand the basic evolution, biodiversity, ecological adaptation and reproductive evolution of single-celled eukaryotes.

(3) Genetic engineering technology of ciliated protozoa

Identification of important gene resources in ciliated protozoa, and development of genetic engineering technology, especially using the Tetrahymena expression system, which could be potentially used in environmental science and agriculture.

（1） “Comparison of adaptive mechanism between sexual and asexual reproduction in Tetrahymena thermophila based on the experimental evolutionary genomics”. The Allied Genetics Conference 2016. Orlando, Florida, USA, July, 2016. 

   (2)  “Comparative genomics reveals insights into genome divergence and speciation of Tetrahymena”. FASEB Ciliate Molecular Biology. Camerino, Italy, July, 2015.

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已指导学生

郭利娜  硕士研究生  071002-动物学  

冯立芳  博士研究生  071004-水生生物学  

陆星亦  硕士研究生  071002-动物学  

畅悦  硕士研究生  071002-动物学  

钟秋萍  硕士研究生  071007-遗传学  

畅悦  博士研究生  071004-水生生物学  

田苗  博士研究生  071004-水生生物学  

姜传奇  博士研究生  071007-遗传学  

王光营  博士研究生  071007-遗传学  

杨文涛  硕士研究生  085238-生物工程  

马雪凤  硕士研究生  071007-遗传学  

张晶  博士研究生  071007-遗传学  

陈凯  博士研究生  071007-遗传学  

韦薇  博士研究生  071007-遗传学  

现指导学生

杨文涛  博士研究生  071007-遗传学  

闫冠雄  博士研究生  071007-遗传学  

柴小翠  硕士研究生  085238-生物工程  

刘真诚  硕士研究生  071007-遗传学  

马扬  博士研究生  071007-遗传学  

周园园  博士研究生  071007-遗传学  

熊文君  硕士研究生  071007-遗传学  

王雪艳  博士研究生  071007-遗传学  

(1)  The National Science Fund for Distinguished Young Scholars (2016);

(2)  Ten Thousand Talent Program (2019).