Laboratory of Evolutionary Genomics
P.I.: Prof. Hongan LONG


  • 研究方向



    A. 生活史在高变环境下的演化规律与机制

    B. 基因组演化以及稳定性机制

    C. 环境胁迫下的突变形成

    D. 医疗及环境水体中病原微生物演化

    E. 水产养殖病害纤毛虫的生物防治

    We are interested in the generation and change of biodversity, with a focus on mutation rate and life history evolution. The research models are quite broad, including ciliates, bacteria, yeast, etc. Our research strategy combines population genetics theory, experimental evolution, -omics sequencing, genetic techniques, and bioinformatic tools. The lab deems the training of independent researchers as our first task and research as the second. Graduate students would receive complete training of scientific research and multiple undergrad assistants are also provided for their research. We are now exploring the following topics:

    A. Phenotypic plasticity of ciliates, and its role in evolution

    B. Genome instability and evolution of marine microbial organisms

    C. Ecological dependence of mutation rate

    D. Evolution of pathogens in medical and natural environments

    E. Biocontrol of pathogenic ciliates in aquaculture

  • 招聘/招生




  • 承担课题

    • 国家自然科学基金国际(地区)合作项目(2019.10-2024.9)

    • 国家自然科学基金面上项目(2023.01-2026.12)

    • 国家海外高层次人才引进项目(青*年*千*人;2019-2021)

  • 讲授课程

    • 本科生课程:

    • 《微生物学》理论(40课时,2.5学分;春季学期,水产学院;龙红岸独立讲授);

    • 《统计建模与推断》(48课时,3学分;春季学期,海德学院;张俣独立讲授

    • 《模式生物发育与进化》(32课时,2学分;春季学期,全校通识课,水产学院;龙红岸与其他5位老师合开)

    • 研究生课程:

    • 《生物大数据分析》(进化所免费培训班,48课时;负责人:龙红岸,授课团队:进化基因组学实验室全体师生、朱明壮、杨伟等老师)

  • 近期论文及成果

    Recent publications

    Full texts of publications can also be downloaded from Researchgate

    Zhang, Y.; Li, H.; Wang, Y.; Nie, M.; Zhang, K.; Pan, J.; Zhang, Y.; Ye, Z.; Zufall, R.; Lynch, M.; Long, H. 2024. Mitogenomic architecture and evolution of the soil ciliates Colpoda. mSystems 9: e01161-23 [Zhang et al. mSystems 2024.pdf]

    Long, H.; Johri, P.; Gout, J.F.; Ni, J.; Hao, Y.; Licknack, T.; Wang, Y.; Pan, J.; Berenice Jiménez-Marín; Lynch, M. 2023Paramecium genetics, genomics and evolution.  Annual Review of Genetics 57: 391-410 [Long et al. ARG 2023.pdf]

    Lynch, M.; Ali, F.; Lin, T.; Wang, Y.; Ni, J.; Long, H. 2023 The divergence of mutation rates and spectra across the Tree of Life. EMBO Reports e57561 [Lynch et al. EMBO Reports 2023.pdf]

    Ni, J.; Pan, J.; Wang, Y.; Chen, T.; Feng, X.; Li, Y.; Lin, T.; Lynch, M.; Long, H.; Li, W. 2023. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. Marine Life Science and Technology 5:564-572. [Ni et al. MLST 2023.pdf]

    Zhou, X.; Pan, J.; Wang, Y.; Lynch, M.; Long, H.; Zhang, Y. 2023. de novo structural variations of Escherichia coli detected by Nanopore long-read sequencing. Genome Biology and Evolution 15(6): evad106  [Zhou et al. GBE 2023.pdf]

    Wu, K.; Li, H.; Cui, X.; Feng, R.; Chen, W.; Jiang, Y.; Tang, C.; Wang, Y.; Shen, X.; Liu, Y.; Lynch, M.; Long, H. 2022Mutagenesis and resistance development of bacteria challenged by silver nanoparticles. Antimicrobial Agents and Chemotherapy [Wu et al. AAC 2022.pdf]

    Pan, J.; Li, W.; Ni, J.; Wu, K.; Konigsberg, I.; Rivera, C.; Tincher, C.; Gregory, C.; Zhou, X.; Doak, T.; Lee, H.; Wang, Y.; Gao, X.; Lynch, M.; Long, H. 2022Rates of mutations and transcript errors in the foodborne pathogen Salmonella enterica subsp. enterica. Molecular Biology and Evolution 39(4): msac081[Pan et al. MBE 2022.pdf]

    Cao, Y.; Zhang, Y.; Wang, X.; Chen, M. 2021 [book chapter]. Graphical modeling of multiple biological pathways in genomic studies. In: Zhao Y, Chen DG (eds) Modern Statistical Methods for Health Research. Springer International Publishing. [Cao et al 2021 Springer.pdf]

    Pan, J.; Williams, E.; Sung, W.; Lynch, M.; Long, H. 2021. The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria. Marine Life Science and Technology 3(1):20-27.[Pan et al. MLST 2021.pdf]

    Nguyen, D.; Wu, B.; Long*, H.; Zhang, N.; Patterson, C.; Simpson, S.; Morris, K.; Thomas, W.; Lynch, M.; Hao, W. 2020. Variable spontaneous muation and loss of heterozygosity among heterozygous genomes in yeast. Molecular Biology and Evolution 37(11): 3118-3130. [Nguyen et al. MBE 2020.pdf]

    Li, H.; Wu, K.; Ruan, C.; Pan, J.; Wang, Y.; Long, H. 2019. Cost-reduction strategies in massive genomics experiments. Marine Life Science and Technology1: 15-21. [Li et al. MLST 2019.pdf]

    Long, H.; Miller, S.F.; Williams, E.; Lynch, M. 2018. Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria. Molecular Biology and Evolution 35(10):2414-2421. [Long et al Mol Biol Evol 2018.pdf   

    Long, H.; Sung, W.; Kucukyildirim,S.; Williams,E.; Miller, S.;Guo, W.; Patterson, C.; Gregory, C.; Strauss, C.; Stone, C.; Berne, C.; Kysela, D.; Shoemaker, W.; Muscarella, M.; Luo, H.; Lennon, J.; Brun, Y.; Lynch, M. 2018. Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology and Evolution 2: 237-240. [Long et al Nat Ecol Evol 2018.pdf]

    Strauss, C.; Long, H.; Patterson, C.; Te, R.; Lynch, M. 2017. Genome-wide mutation rate response to pH change in the coral reef pathogen Vibrio shilonii AK1. mBio 8 (4): e01021-17. [Strauss et al. mBio 2017.pdf]

    Long, H.; Miller, S.F.; Strauss, C.; Zhao, C.; Cheng, L.; Ye, Z.; Griffin, K.; Te, R.; Lee, H.; Chen, C.; Lynch, M. 2016. Antibiotic treatment enhances the genome-wide mutation rate of target cells. PNAS 113(18): E2498-E2505. [Long et al. PNAS 2016.pdf]

    Long, H.; Kucukyildirim#, S.; Sung, W.; Williams, E.; Lee, H.; Ackerman, M.; Doak, T.; Tang, H.; Lynch, M. 2015. Background mutational features of the radiation-resistant bacterium Deinococcus radioduransMolecular Biology and Evolution 32(9): 2383-2392. [Long et al. MBE 2015.pdf]

    Long, H.; Paixão, T.; Azevedo, R.; Zufall, R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophilaGenetics 195(2): 527-540. [Long et al. Genetics 2013.pdf]

  • 奖项

    2021 中国海洋大学优秀教师

    2019 中国海洋大学第21届天泰奖一等奖;中国海洋大学优秀班主任;中国海洋大学第20届五四青年奖

    2018 李氏基金会杰出创新奖

    2016 美国遗传学会DeLill Nasser遗传学职业发展奖

    2018 Li Foundation Heritage Prize-Excellence in Creativity

    2016 DeLill Nasser Award for Professional Development in Genetics, Genetics Society of America

  • 学生












    潘娇 2023年6月 博士

    吴琨 2023年6月 博士

    周霞 2023年6月 硕士