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郭志鴻 (Kuo, Chih-Horng)

研究員

  • Ph.D. (2008) Genetics, University of Georgia
  • M.S. (2003) Genetics, Iowa State University
  • B.S. (1998) Botany, National Taiwan University
  • +886-2-2787-1044(Lab)
  • +886-2-2787-1127(Office)
  • chk@gate.sinica.edu.tw
  • 共生細菌的演化與功能性基因體學
  • Lab Website
  • Google Scholar

研究主題:共生細菌的演化與功能性基因體學

在微生物的演化上,一旦一個物種發展出對真核宿主的依存性,其基因體的結構經常會有大規模的變化。為了解與這些變化相關的演化過程和其基因內容之改變,本研究室利用基因體學及轉錄體學等工具進行不同細菌物種間的比較分析。近年之研究計畫包含兩個主要的生物系統:

(1) 柔膜細菌綱 (Mollicutes)

柔膜細菌綱為一群不具有細胞壁之宿主依存性細菌,包括植物菌質體 (‘Candidatus Phytoplasma’; 為一群農業上重要之植物病原)、黴漿菌(Mycoplasma; 脊椎動物病原)、及螺旋菌質體 (Spiroplasma; 大多為昆蟲共生菌,少數物種為植物病原) 等代表性物種。其中螺旋菌質體屬內物種可能與宿主進行片利共生、互利共生、或依賴程度不等的寄生,因此跨物種的比較將有助了解細菌在生態棲位間的轉換及致病性的演化。針對此生物系統,本研究室的短期目標為調查可解釋物種間表現型差異之遺傳機制,而長期目標則是累積足夠的基因體資料以進行完整的跨屬分析。

(2) 農桿菌屬 (Agrobacterium)

農桿菌屬為一群與植物相關的細菌,由於這群細菌在植物基因轉殖上的應用和其在田間對農作物所產生的危害,在生物科技和農業的發展上都具有相當的重要性。本研究室與所內賴爾珉老師合作,共同進行農桿菌屬內物種的研究,藉以探討此屬內不同小群菌株間的遺傳歧異度、基因體演化、及功能性分析。

All publication list

Selected publication list

  • Chou L#Lin YC#Haryono M, Santos MNM, Cho ST, Weisberg AJ, Wu CF, Chang JH, Lai EM, Kuo CH* (2022) Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biology 20:16. DOI: 10.1186/s12915-021-01221-y [bioRxiv preprint DOI: 10.1101/2021.05.20.444927#Equal contribution.
  • Castillo AI#, Tsai CW#, Su CC, Weng LW, Lin YCCho ST, Almeida RPP, Kuo CH* (2021) Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan. Microbial Genomics 7:000727. DOI: 10.1099/mgen.0.000727 [bioRxiv preprint DOI: 10.1101/2021.03.24.436723#Equal contribution.
  • Tan CM#Lin YC#, Li JR, Chien YY, Wang CJ, Chou L, Wang CW, Chiu YC, Kuo CH*, JY Yang* (2021) Accelerating complete phytoplasma genome assembly by immunoprecipitation-based enrichment and MinION-based DNA sequencing for comparative analyses. Frontiers in Microbiology 12:766221. DOI: 10.3389/fmicb.2021.766221 #Equal contribution.
  • Kuo CH, Huang PY, Sheu SY, Sheu DS, Jheng LC, Chen WM* (2021) Zophobihabitans entericus gen. nov., sp. nov., a new member of the family Orbaceae isolated from the gut of a superworm Zophobas morio. International Journal of Systematic and Evolutionary Microbiology 71:005081. DOI: 10.1099/ijsem.0.005081
  • Huang W, MacLean A, Sugio A, Maqbool A, Busscher M, Cho ST, Kamoun S, Kuo CH, Immink RGH, Hogenhout SA* (2021) Parasitic modulation of host development by ubiquitin-independent protein degradation. Cell 184:5201-5214. [Issue Cover] DOI: 10.1016/j.cell.2021.08.029 [bioRxiv preprint DOI: 10.1101/2021.02.15.430920]
  • Wu CF, Weisberg AJ, Davis EW, Chou L, Khan S, Lai EM, Kuo CH, Chang JH* (2021) Diversification of the type VI secretion system in agrobacteria. mBio 12:e01927-21. DOI: 10.1128/mBio.01927-21
  • Hwang HH*, Huang FC, Chien PR, Hung SH, Kuo CH, Deng WL, Chiang EPI, Huang CC* (2021) A plant endophytic bacterium, Burkholderia seminalis strain 869T2, promotes plant growth in Arabidopsis, pai tsai, Chinese amaranth, lettuces and other vegetables. Microorganisms 9:1703. DOI: 10.3390/microorganisms9081703
  • Weng LW#Lin YC#, Su CC, Huang CTCho ST, Chen AP, Chou SJ, Tsai CW*, Kuo CH* (2021) Complete genome sequence of Xylella taiwanensis and comparative analysis of virulence gene content with Xylella fastidiosa. Frontiers in Microbiology 12:684092. DOI: 10.3389/fmicb.2021.684092 [bioRxiv preprint DOI: 10.1101/2021.03.08.434500#Equal contribution.
  • Cho STKung HJ, Huang W, Hogenhout SA, Kuo CH* (2020) Species boundaries and molecular markers for the classification of 16SrI phytoplasmas inferred by genome analysis. Frontiers in Microbiology 11:1531. DOI: 10.3389/fmicb.2020.01531 [bioRxiv preprint DOI: 10.1101/2020.01.31.928135]
  • Weisberg AJ, Davis EW, Tabima J, Belcher MS, Miller M, Kuo CH, Loper JE, Grünwald NJ, Putnam ML, Chang JH* (2020) Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. DOI: 10.1126/science.aba5256
  • Cheng YI#Chou L#, Chiu YF, Hsueh HT, Kuo CH*, Chu HA* (2020) Comparative genomic analysis of a novel strain of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. CL-1. Frontiers in Microbiology 11:82. DOI: 10.3389/fmicb.2020.00082 #Equal contribution.
  • Santos MNM, Cho ST, Wu CF, Chang CJ, Kuo CH, Lai EM* (2020) Redundancy and specificity of type VI secretion vgrG loci in antibacterial activity of Agrobacterium tumefaciens 1D1609 strain. Frontiers in Microbiology 10:3004. DOI: 10.3389/fmicb.2019.03004 [bioRxiv preprint DOI: 10.1101/740209]
  • Cho ST, Lin CP, Kuo CH* (2019) Genomic characterization of the periwinkle leaf yellowing (PLY) phytoplasmas in Taiwan. Frontiers in Microbiology 10: 2194. DOI: 10.3389/fmicb.2019.02194
  • Gasparich GE*, Kuo CH (2019) Genome analysis-based union of the genus Mesoplasma with the genus Entomoplasma. International Journal of Systematic and Evolutionary Microbiology 69: 2735-2738. DOI: 10.1099/ijsem.0.003548
  • Haryono M, Cho ST, Fang MJ, Chen AP, Chou SJ, Lai EM, Kuo CH* (2019) Differentiations in gene content and expression response to virulence induction between two Agrobacterium strains. Frontiers in Microbiology 10: 1554. DOI: 10.3389/fmicb.2019.01554
  • Wu CF, Santos MNM, Cho ST, Chang HH, Tsai YM, Smith DA, Kuo CH*, Chang JH*, Lai EM* (2019) Plant pathogenic Agrobacterium tumefaciens strains have diverse type VI effector-immunity pairs and vary in in planta competitiveness. Molecular Plant-Microbe Interactions 32: 961-971. DOI: 10.1094/MPMI-01-19-0021-R
  • Seruga Music M*, Samarzija I, Hogenhout SA*, Haryono M, Cho ST, Kuo CH* (2019) The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences. Systematic and Applied Microbiology 42: 117-127. DOI: 10.1016/j.syapm.2018.10.008
  • Haryono M, Tsai YM, Lin CT, Huang FC, Ye YC, Deng WL, Hwang HH*, Kuo CH* (2018) Presence of an Agrobacterium-type tumor-inducing plasmid in Neorhizobium sp. NCHU2750 and the link to phytopathogenicity. Genome Biology and Evolution 10: 3188-3195. DOI: 10.1093/gbe/evy249
  • Lo KJ, Lin SS, Lu CW, Kuo CH*, Liu CT* (2018) Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3). Scientific Reports 8: 12769. DOI: 10.1038/s41598-018-31128-8
  • Lo WS, Gasparich GE, Kuo CH* (2018) Convergent evolution among ruminant-pathogenic Mycoplasma involved extensive gene content changes. Genome Biology and Evolution 10: 2130-2139. DOI: 10.1093/gbe/evy172
  • Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo CH, McGaugh SE, Bronikowski AM, de Koning J, Edwards SV, Pfrender ME, Minx P, Brodie ED, Brodie ED, Warren WC, Castoe TA* (2018)Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution 10: 2110-2129. DOI: 10.1093/gbe/evy157
  • Tsai YM, Chang A, Kuo CH* (2018) Horizontal gene acquisitions contributed to genome expansion in insect-symbiotic Spiroplasma clarkii. Genome Biology and Evolution 10: 1526-1532. DOI: 10.1093/gbe/evy113
  • Lo WS, Kuo CH* (2017) Horizontal acquisition and transcriptional integration of novel genes in mosquito-associated Spiroplasma. Genome Biology and Evolution 9: 3246-3259. DOI: 10.1093/gbe/evx244
  • Huang YY, Cho ST, Haryono M, Kuo CH* (2017) Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae. PLOS ONE 12: e0179055. DOI: 10.1371/journal.pone.0179055
  • Orlovskis Z, Canale MC, Haryono M, Lopes JRS, Kuo CH*, Hogenhout S* (2017) A few sequence polymorphisms among isolates of maize bushy stunt phytoplasma associate with organ proliferation symptoms in infected maize plants. Annals of Botany 119: 869-884. DOI: 10.1093/aob/mcw213