郭志鴻

郭志鴻
Kuo, Chih-Horng
副研究員

Ph.D. (2008) Genetics, University of Georgia
M.S. (2003) Genetics, Iowa State University
B.S. (1998) Botany, National Taiwan University

TEL: 

+886-2-2787-1127 (Office)
+886-2-2787-1044 (Lab)

研究主題:具宿主依存性細菌之基因體演化

       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

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Selected publication list

 

  • 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
     
  • Bondage DD, Lin JS, Ma LS, Kuo CH, Lai EM* (2016) VgrG C terminus confers the type VI effector transport specificity and is required for binding with PAAR and adaptor–effector complex. Proceedings of the National Academy of Sciences of the United States of America 113: E3931-E3940. DOI: 10.1073/pnas.1600428113
  • Wu WL, Lai SJ, Yang JT, Chern J. Liang SY, Chou CC, Kuo CH, Lai MC*, Wu SH* (2016) Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1T identified the role of protein phosphorylation in methanogenesis and osmoregulation. Scientific Reports 6: 29013. DOI: 10.1038/srep29013
  • Chang CLT, Chung CY, Kuo CH, Kuo TF, Yang CW*, Yang WC* (2016) Beneficial effect of Bidens pilosa on body weight gain, food conversion ratio, gut bacteria and coccidiosis in chickens. PLOS ONE 11: e0146141. DOI: 10.1371/journal.pone.0146141
  • Lo WS, Huang YY, Kuo CH* (2016) Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiology Reviews 40: 855-874. DOI: 10.1093/femsre/fuw028
  • Cho ST, Chang HH, Egamberdieva D, Kamilova F, Lugtenberg B, Kuo CH* (2015) Genome analysis of Pseudomonas fluorescens PCL1751: a rhizobacterium that controls root diseases and alleviates salt stress for its plant host. PLOS ONE 10: e0140231. DOI: 10.1371/journal.pone.0140231
     
  • Lo WS, Gasparich GE, Kuo CH* (2015) Found and lost: the fates of horizontally acquired genes in arthropod-symbiotic Spiroplasma. Genome Biology and Evolution 7: 2458-2472. DOI: 10.1093/gbe/evv160
  • Kuo CH* (2015) Scrambled and not-so-tiny genomes of fungal endosymbionts. Proceedings of the National Academy of Sciences of the United States of America 112: 7622-7623. DOI: 10.1073/pnas.1508360112
  • Huang HH, Cho ST, Lo WS, Wang YC, Lai EM, Kuo CH* (2015) Complete genome sequence of Agrobacterium tumefaciens Ach5. Genome Announcements 3: e00570-15. DOI: 10.1128/genomeA.00570-15
  • McGaugh SE*, Bronikowski AM*, Kuo CH*, Reding DM, Addis EA, Flagel LE, Janzen FJ, Schwartz TS* (2015) Rapid molecular evolution across amniotes of the IIS/TOR network. Proceedings of the National Academy of Sciences of the United States of America 112: 7055-7060. DOI: 10.1073/pnas.1419659112
  • Paredes JC, Herren JK, Schüpfer F, Marin R, Clavero S, Kuo CH, Lemaitre B*, Béven L* (2015) Genome sequence of the Drosophila melanogaster male-killing Spiroplasma MSRO endosymbionts. mBio 6: e02437-14. DOI: 10.1128/mBio.02437-14
  • Chang HH, Cho ST, Canale MC, Mugford ST, Lopes JRS, Hogenhout SA, Kuo CH* (2015) Complete genome sequence of "Candidatus Sulcia muelleri" ML, an obligate nutritional symbiont of maize leafhopper (Dalbulus maidis). Genome Announcements 3: e01483-14. DOI: 10.1128/genomeA.01483-14
  • Liu AC, Chou CY, Chen LL, Kuo CH* (2015) Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis. Journal of Biotechnology 194: 124-131. DOI: 10.1016/j.jbiotec.2014.11.026
  • Su HJ, Hogenhout SA, Al-Sadi AM, Kuo CH* (2014) Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids. PLoS ONE 9: e113049. DOI: 10.1371/journal.pone.0113049
  • Lo WS, Chen HJ, Chen CY, Kuo CH* (2014) Complete genome sequence of Vibrio vulnificus 93U204, a bacterium isolated from diseased tilapia in Taiwan. Genome Announcements 2: e01005-14. DOI: 10.1128/genomeA.01005-14
  • Ku C, Lo WS, Kuo CH* (2014) Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria. Biochemical and Biophysical Research Communications 446: 927-932. DOI: 10.1016/j.bbrc.2014.03.039
     
  • Radjacommare R, Usharani R, Kuo CH, Fu H* (2014) Distinct phylogenetic relationships and biochemical properties of Arabidopsis ovarian tumor-related deubiquitinases support their functional differentiation. Frontiers in Plant Science 5: 84. DOI: 10.3389/fpls.2014.00084

  • Tung CH#, Cheng YR#, Lin CY, Ho JS, Kuo CH, Yu JK*, Su YH* (2014) A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biological Bulletin 226: 69-80. #Equal contribution.

  • Chang TH#, Lo WS#, Ku C, Chen LL, Kuo CH* (2014) Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biology and Evolution 6: 500-509. DOI: 10.1093/gbe/evu033 #Equal contribution.

  • Ku C, Lo WS, Chen LL, Kuo CH* (2014) Complete genome sequence of Spiroplasma apis B31T (ATCC 33834), a bacterium associated with May disease of honeybees (Apis mellifera). Genome Announcements 2: e01151-13. DOI: 10.1128/genomeA.01151-13

  • Lo WS, Ku C, Chen LL, Chang TH, Kuo CH* (2013) Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biology and Evolution 5: 1512-1523. DOI: 10.1093/gbe/evt108

  • Ku C, Lo WS, Chen LL, Kuo CH* (2013) Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma. Genome Biology and Evolution 5: 1151-1164. DOI: 10.1093/gbe/evt084

  • Lo WS, Chen LL, Chung WC, Gasparich GE, Kuo CH* (2013) Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics 14: 22. DOI: 10.1186/1471-2164-14-22

  • Shelomi M, Lo WS, Kimsey LS, Kuo CH* (2013) Analysis of the gut microbiota of walking sticks (Phasmatodea). BMC Research Notes 6: 368. DOI: 10.1186/1756-0500-6-368

  • Ku C, Chung WC, Chen LL, Kuo CH* (2013) The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus (L.) G. Don: plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS ONE 8: e68518. DOI: 10.1371/journal.pone.0068518

  • Ku C, Hu JM, Kuo CH* (2013) Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8: e62548. DOI: 10.1371/journal.pone.0062548

  • Chung WC, Chen LL, Lo WS, Kuo PA, Tu J, Kuo CH* (2013) Complete genome sequence of Serratia marcescens WW4. Genome Announcements 1: e00126-13. DOI: 10.1128/genomeA.00126-13

  • Kuo PA, Kuo CH, Lai YK, Graumann P, Tu J* (2013) Phosphate limitation induces the intergeneric inhibition of Pseudomonas aeruginosa by Serratia marcescens isolated from paper machines. FEMS Microbiology Ecology 84: 577-587. DOI: 10.1111/1574-6941.12086

  • Ku C, Lo WS, Kuo CH* (2013) Horizontal transfer of potential mobile units in phytoplasmas. Mobile Genetic Elements 3: e26145. DOI: 10.4161/mge.26145

  • Chung WC#, Chen LL#, Lo WS, Lin CP, Kuo CH* (2013) Comparative analysis of the peanut witches’-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PLoS ONE 8: e62770. DOI: 10.1371/journal.pone.0062770 #Equal contribution.

  • Chen LL#, Chung WC#, Lin CP, Kuo CH* (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLoS ONE 7: e34407. DOI: 10.1371/journal.pone.0034407 #Equal contribution.

 

 

 Shu-Ting Cho (卓舒婷)

Research Assistant

 

Mindia Haryono (方姣婷)

Research Assistant

 

 Yi-Ming Tsai (蔡乙鳴)

Research Assistant

 

 Hung-Jui Kung (龔泓睿)

Research Assistant