Reviews

• Weisberg AJ*, Wu Y, Chang JH, Lai EM, Kuo CH* (2023) Virulence and ecology of agrobacteria in the context of evolutionary genomics. Annual Review of Phytopathology 61:1-23. DOI: 10.1146/annurev-phyto-021622-125009
• 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

Research articles

• Chang HY, Yen HC, Chu HA, Kuo CH* (2024) Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes. Botanical Studies 65:35. DOI: 10.1186/s40529-024-00442-y [bioRxiv preprint DOI: 10.1101/2024.08.22.609105]
• Yan XH, Pei SC, Yen HC, Blanchard A, Sirand-Pugnet P, Baby V, Gasparich GE, Kuo CH* (2024) Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales–Entomoplasmatales clade within the class Mollicutes. Microbial Genomics 10:001321. DOI: 10.1099/mgen.0.001321 [bioRxiv preprint DOI: 10.1101/2024.08.17.608393]
• Wang SC, Chen AP, Chou SJ, Kuo CH*, Lai EM* (2023) Soil inoculation and blocker-mediated sequencing show effects of the antibacterial T6SS on agrobacterial tumorigenesis and gallobiome. mBio 14:e00177-23. DOI:10.1128/mbio.00177-23 [bioRxiv preprint DOI: 10.1101/2022.10.28.514271] [Featured on Academia Sinica website]
• Lee SK, Chiang MS, Hseu ZY, Kuo CH*, Liu CT* (2022) A photosynthetic bacterial inoculant exerts beneficial effects on the yield and quality of tomato and affects bacterial community structure in an organic field. Frontiers in Microbiology 13:959080. DOI: 10.3389/fmicb.2022.959080
• Cheng YI, Lin YC, Leu JY, Kuo CH*, Chu HA* (2022) Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus TA-1. Frontiers in Microbiology 13:932840. DOI: 10.3389/fmicb.2022.932840
• Huang CT, Cho ST, Tan CM, Chiu YC, Yang JY*, Kuo CH* (2022) Comparative genome analysis of ‘Candidatus Phytoplasma luffae’ reveals the influential roles of potential mobile units in phytoplasma evolution. Frontiers in Microbiology 13:773608. DOI: 10.3389/fmicb.2022.773608 [bioRxiv preprint DOI: 10.1101/2021.09.09.459700]
• 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] [Featured on Academia Sinica website]
• Castillo AI, Tsai CW, Su CC, Weng LW, Lin YC, Cho 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]
• Tan CM, Lin YC, Li JR, Chien YY, Wang CJ, Chou L, Wang CW, Chiu YC, Kuo CH*, Yang JY* (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
• 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]
• Weng LW, Lin YC, Su CC, Huang CT, Cho 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]
• Cho ST, Kung HJ, Huang W, Hogenhout SA, Kuo CH* (2020) Species boundaries and molecular markers for 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 CL-1. Frontiers in Microbiology 11:82. DOI: 10.3389/fmicb.2020.00082
• 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
• 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 Frontiers in Microbiology 10:1554. DOI: 10.3389/fmicb.2019.01554 [Recommendation by Vitaly Citovsky on Faculty Opinions; DOI: 10.3410/f.736286615.793563521]
• 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 Molecular Plant-Microbe Interactions 32:961-971. DOI: 10.1094/MPMI-01-19-0021-R [Editor's Pick]
• 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 NCHU2750 and the link to phytopathogenicity. Genome Biology and Evolution 10:3188-3195. DOI: 10.1093/gbe/evy249
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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