Chih-Horng Kuo's Profiles
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Research Articles
Liu MS#, Huang TK#, Wang YC, Wang SC, Wu CH, , Lai EM* (2025) Floral stage optimization and immune evasion enhance Agrobacterium-mediated genome editing in Arabidopsis. New Phytologist accepted. [bioRxiv preprint DOI: 10.1101/2025.05.07.652770] #Equal contribution
, , Li TT, Yang YC, Hung TH*, * (2025) Comparative genomics of a poinsettia-associated phytoplasma and functional validation of its SAP11-homologous effectors that induce plant branching. [bioRxiv preprint DOI: 10.1101/2025.10.17.683024]
Nishino T#, Moriyama M#*, Mukai H#, #, Hosokawa T, , Tachikawa S, Nikoh N, Koga R, , Fukatsu T* (2025) Defensive fungal symbiosis on insect hindlegs. Science 390:279-283. DOI: 10.1126/science.adp6699 #Equal contribution [News by Erik Stokstad on Science DOI: 10.1126/science.zlhmcem] [Featured on Academia Sinica website]
Chiu YC, , Pao SH, Chen YK, Liao PQ, Mejia HM, Sheue CR, *, Yang JY* (2025) Comprehensive genomic and functional characterization of a phytoplasma associated with root retardation, early bolting, witches’-broom, and phyllody in daikon (Raphanus sativus L.). Frontiers in Microbiology 16:1654928. DOI: 10.3389/fmicb.2025.1654928
, , Wu CH, Lai EM*, * (2025) Comparative transcriptomics reveals context- and strain-specific regulatory programs of Agrobacterium during plant colonization. Microbial Genomics 11:001485. DOI: 10.1099/mgen.0.001485 [bioRxiv preprint DOI: 10.1101/2025.05.27.656240]
Chen CNN#, Lin KM#, #, , Yong TC, Chiu YF, *, Chu HA* (2025) Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon. BMC Microbiology 25:279. DOI: 10.1186/s12866-025-03993-7 [bioRxiv preprint DOI: 10.1101/2025.01.17.633688] #Equal contribution
Seruga Music M*, Polak B, Drcelic M, , * (2025) Sequencing and comparative analyses of 'Candidatus Phytoplasma solani' genomes reveal diversity of effectors and potential mobile units. Microbial Genomics 11:001401. DOI: 10.1099/mgen.0.001401
Lopez-Agudelo JC#, Goh FJ#, , Huang YS, Huang CY, Lee KT, Wang YC, , Chang HX, , Lai EM, Wu CH* (2025) Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants. Plant Biotechnology Journal published online. DOI: 10.1111/pbi.70083 [bioRxiv preprint DOI: 10.1101/2024.11.30.626145] #Equal contribution [Featured on Academia Sinica website]
Yang CH*, Huang J, Huyen TNBV, Liu X, Mitra S, Yu M, Zeng Q, Sundin G, Cox K, Förster H, Adaskaveg J, , Yuan X (2024) RejuAgro A: A novel antimicrobial for fire blight control of pome fruits and beyond. [Research Square preprint DOI: 10.21203/rs.3.rs-5050621/v1]
, Yu MY, Liu CH, Huang TC, Peng JH, Jang NY, , Ho YN, Chiang EPI, Hwang HH, Huang CC* (2024) Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms. [bioRxiv preprint DOI: 10.1101/2024.08.20.608638]
, , Chu HA, * (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]
, , , Blanchard A, Sirand-Pugnet P, Baby V, Gasparich GE, * (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]
, Yeh PH, Huang TC, Huang SY, Wu IC, Liu CH, Lin YH, Chien PR, Huang FC, Ho YN, , Hwang HH, Chiang EPI, Huang CC* (2024) A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions. ISME Communications 4:ycae041. DOI: 10.1093/ismeco/ycae041
Fernández FD*, , , Marcone C, Conci LR (2024) Improving the comprehension of pathogenicity and phylogeny in ‘Candidatus Phytoplasma meliae’ through genome characterization. Microorgamisms 12:142. DOI: 10.3390/microorganisms12010142
, Huang TC, Lai YC, Wu IC, Liu CH, Huarng YF, Hwang HH, Chiang EPI, , Huang CC* (2023) Endophytic biostimulants for smart agriculture: Burkholderia seminalis 869T2 benefits heading leafy vegetables in-field management in Taiwan. Agronomy 13:967. DOI: 10.3390/agronomy13040967
Wang SC, Chen AP, Chou SJ, *, 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]
Liu YH, Tseng TS, Wu CR, , , Huang XJ, Cheng JY, Hsu KH, Lin KF, Liu CC, Yeh CH* (2023) Rice OsHsp16.9A interacts with OsHsp101 to confer thermotolerance. Plant Science 330:111634. DOI: 10.1016/j.plantsci.2023.111634
Lee SK, Chiang MS, Hseu ZY, *, 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#, #, Leu JY, *, Chu HA* (2022) Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1. Frontiers in Microbiology 13:932840. DOI: 10.3389/fmicb.2022.932840 #Equal contribution
, , , Tan CM, Chiu YC, Yang JY*, * (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]
#, #, , Santos MNM, , Weisberg AJ, Wu CF, Chang JH, Lai EM, * (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 [Featured on Academia Sinica website]
Castillo AI#, Tsai CW#, Su CC, Weng LW, , , Almeida RPP, * (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#, #, Li JR, Chien YY, Wang CJ, , Wang CW, Chiu YC, *, 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 #Equal contribution
, 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, , Kamoun S, , 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, , Khan S, Lai EM, , 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, , 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#, #, Su CC, , , Chen AP, Chou SJ, Tsai CW*, * (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
, , Huang W, Hogenhout SA, * (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, , 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#, #, Chiu YF, Hsueh HT, *, 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, , Wu CF, Chang CJ, , 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]
Acheampong G, Owusu M, Owusu-Ofori A, Osei I, Sarpong N, Sylverken A, , , , Park SE, Marks F, Adu-Sarkodie Y, Owusu-Dabo E* (2019) Chromosomal and plasmid-mediated fluoroquinolone resistance in human Salmonella enterica infection in Ghana. BMC Infectious Diseases 19:898. DOI: 10.1186/s12879-019-4522-1
Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, , Lopes JRS, Hogenhout SA* (2019) Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLOS Pathogens 15:e1008035. DOI: 10.1371/journal.ppat.1008035 [bioRxiv preprint DOI: 10.1101/574319] [Recommendation by Ying-Bo Mao on Faculty Opinions DOI: 10.3410/f.736671560.793572240]
, Lin CP, * (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*, (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
, , Fang MJ, Chen AP, Chou SJ, Lai EM, * (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 [Recommendation by Vitaly Citovsky on Faculty Opinions DOI: 10.3410/f.736286615.793563521]
Wu CF, Santos MNM, , , , Smith DA, *, 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 [Editor's Pick]
Seruga Music M*, Samarzija I, Hogenhout SA*, , , * (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
, , , Huang FC, Ye YC, Deng WL, Hwang HH*, * (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, *, 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
, Gasparich GE, * (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, , 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
, , * (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
Chiu LW, Huang SC, Lee SK, , Lur HS*, Liu CT* (2017) Application of plant growth-promoting rhizobacteria to improve salt stress tolerance in rice (Oryza sativa L. cv. TK9) seedlings. Journal of the Agricultural Association of Taiwan 18:257-274. DOI: 10.6730/JAAT.201712_18(3-4).0004
, * (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
, , , * (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, , Lopes JRS, *, 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, , 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 [Recommendation by Alain Filloux on Faculty Opinions DOI: 10.3410/f.726430927.793522872]
Wu WL, Lai SJ, Yang JT, Chern J. Liang SY, Chou CC, , 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 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
, , Egamberdieva D, Kamilova F, Lugtenberg B, * (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
, Gasparich GE, * (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*, *, 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, , 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
Liu AC, Chou CY, , * (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
, Hogenhout SA, Al-Sadi AM, * (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
, , * (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, , 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, , 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. DOI: 10.1086/BBLv226n1p69 #Equal contribution
#, #, , , * (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
, , , , * (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
, , , * (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
, , , Gasparich GE, * (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, , Kimsey LS, * (2013) Analysis of the gut microbiota of walking sticks (Phasmatodea). BMC Research Notes 6:368. DOI: 10.1186/1756-0500-6-368
, , , * (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
, Hu JM, * (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
Kuo PA, , 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
#, #, , Lin CP, * (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
#, #, Lin CP, * (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLOS ONE 7:e34407. DOI: 10.1371/journal.pone.0034407 #Equal contribution
McGaugh SE*, Bowden RM, , Janzen FJ (2011) Field-measured heritability of the threshold for sex determination in a turtle with temperature dependent sex determination. Evolutionary Ecology Research 13:75-90.
Ochman H*, Worobey M, , Ndjango JB, Peeters M, Hahn B, Hugenholtz P (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLOS Biology 8:e1000546. DOI: 10.1371/journal.pbio.1000546 [Recommendation by Sebastian Suerbaum on Faculty Opinions DOI: 10.3410/f.8771956.9295055]
, Ochman H* (2010) The extinction dynamics of bacterial pseudogenes. PLOS Genetics 6:e1001050. DOI: 10.1371/journal.pgen.1001050
Joseph SJ, Fernandez-Robledo JA, Gardner MJ, El-Sayed NM, , Schott EJ, Wang H, Kissinger JC*, Vasta GR* (2010) The alveolate Perkinsus marinus: biological insights from EST gene discovery. BMC Genomics 11:228. DOI: 10.1186/1471-2164-11-228
, Ochman H* (2009) Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biology Direct 4:35. DOI: 10.1186/1745-6150-4-35
, Ochman H* (2009) Deletional bias across the three domains of life. Genome Biology and Evolution 1:145-152. DOI: 10.1093/gbe/evp016
, Moran NA, Ochman H* (2009) The consequences of genetic drift for bacterial genome complexity. Genome Research 19:1450-1454. DOI: 10.1101/gr.091785.109 [Recommendation by Hiroshi Akashi on Faculty Opinions DOI: 10.3410/f.1163222.623905]
*, Wares JP, Kissinger JC (2008) The apicomplexan whole genome phylogeny: an analysis of incongruence among gene trees. Molecular Biology and Evolution 25:2689-2698. DOI: 10.1093/molbev/msn213
*, Kissinger JC (2008) Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria. BMC Evolutionary Biology 8:108. DOI: 10.1186/1471-2148-8-108
*, Avise JC (2008) Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci? Genetica 132:219-225. DOI: 10.1007/s10709-007-9167-0
*, Corby-Harris V, Promislow DEL (2008) The unavoidable costs and unexpected benefits of parasitism: population and metapopulation models of parasite-mediated competition. Journal of Theoretical Biology 250:244-256. DOI: 10.1016/j.jtbi.2007.10.004
*, Avise JC (2005) Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124:179-186. DOI: 10.1007/s10709-005-2095-y
*, Janzen FJ (2004) Genetic effects of a persistent bottleneck on a natural population of ornate box turtles (Terrapene ornata). Conservation Genetics 5:425-437. DOI: 10.1023/B:COGE.0000041020.54140.45
*, Janzen FJ (2003) BottleSim: a bottleneck simulation program for long-lived species with overlapping generations. Molecular Ecology Notes 3:669-673. DOI: 10.1046/j.1471-8286.2003.00532.x [Software download at GitHub: https://github.com/chihhorngkuo/BottleSim]
Genome Announcements
, Huang FC, Chien PR, Wu CL, Chen LY, Ho CW, Song GZM, Lin WJ, Lin HJ, Huang CC, Hwang HH*, * (2025) Draft genome sequences of 12 Agrobacterium strains isolated from coastal plants in Taiwan. Microbiology Resource Announcements 14:e01046-25. DOI: 10.1128/mra.01046-25
, Huang FC, Chien PR, Wu CL, Chen LY, Ho CW, Song GZM, Lin WJ, Lin HJ, Huang CC, Hwang HH*, * (2025) Draft genome sequences of seven endophytic bacterial strains isolated from the roots of coastal plants in Taiwan. Microbiology Resource Announcements 14:e00964-25. DOI: 10.1128/mra.00964-25
#, Liu CH#, Kuo CC, Huang CC*, * (2025) Complete genome sequence of Bacillus velezensis Tcba05, a biocontrol strain for multiple plant diseases in Taiwan. Microbiology Resource Announcements 14:e00212-25. DOI: 10.1128/mra.00212-25 #Equal contribution
#, Wang SC#, Chen WM, Lai EM*, * (2024) Complete genome sequence of Sphingomonas sp. strain R1, a bacterium isolated from tomato (Solanum lycopersicum). Microbiology Resource Announcements 13:e00242-24. DOI: 10.1128/mra.00242-24 #Equal contribution
, , , Lee S, Chu CC, Hong CF*, * (2024) Complete genome sequence of Agrobacterium pusense Bbcg2-2, a strain isolated from blueberry crown gall in Taiwan. Microbiology Resource Announcements 13:e01083-23. DOI: 10.1128/mra.01083-23
, , , Hung TH, Chang TC, Bai QZ, Tai CF*, * (2024) Complete genome sequence of "Candidatus Phytoplasma australasiaticum" WF_GM2021, a plant pathogen associated with soybean witches' broom disease in Taiwan. Microbiology Resource Announcements 13:e00993-23. DOI: 10.1128/mra.00993-23
, Wu IC, Huang CC*, * (2023) Complete genome sequence of Erythrobacteraceae bacterium WH01K, a strain isolated from corals (Acropora sp.) in Taiwan. Microbiology Resource Announcements 12:e00830-23. DOI: 10.1128/mra.00830-23
Salazar JRB, Santos MNM*, Palaad J, , Castellano JL, Pena LD, Amar EC, Lai EM, * (2023) Complete genome sequence of Vibrio parahaemolyticus strain PH1273, isolated from the aquacultured shrimp in the Philippines. Microbiology Resource Announcements 12:e00532-23. DOI: 10.1128/mra.00532-23
, Chen AP, Chou SJ, , Lin CP*, * (2023) Complete genome sequence of "Candidatus Phytoplasma cynodontis" GY2015, a plant pathogen associated with Bermuda grass white leaf disease in Taiwan. Microbiology Resource Announcements 12:e00457-23. DOI: 10.1128/mra.00457-23
, Chen AP, Chou SJ, Hung TH*, * (2023) Complete genome sequence of "Candidatus Phytoplasma pruni" PR2021, an uncultivated bacterium associated with poinsettia (Euphorbia pulcherrima). Microbiology Resource Announcements 12:e00443-23. DOI: 10.1128/mra.00443-23
Li Y#, #, Liu Y, , *, Huang W* (2023) Complete genome sequence of "Candidatus Phytoplasma aurantifolia" TB2022, a plant pathogen associated with sweet potato little leaf disease in China. Microbiology Resource Announcements 12:e00308-23. DOI: 10.1128/mra.00308-23 #Equal contribution
#, Lin J#, Liu Y#, Huang P, Liu J, Hu Q, Li Y#, , Huang W*, * (2023) Complete genome sequence of "Candidatus Phytoplasma asteris" QS2022, a plant pathogen associated with lettuce chlorotic leaf rot disease in China. Microbiology Resource Announcements 12:e00306-23. DOI: 10.1128/mra.00306-23 #Equal contribution
, Chiu MC, Huang CC*, * (2022) Complete genome sequence of Curtobacterium sp. C1, a beneficial endophyte with the potential for in-plant salinity stress alleviation. Molecular Plant-Microbe Interactions 35:731-735. DOI: 10.1094/MPMI-01-22-0027-A
, Zwolińska A, Huang W, Wouters RHM, Mugford ST, Hogenhout SA, * (2020) Complete genome sequence of "Candidatus Phytoplasma asteris" RP166, a plant pathogen associated with the rapeseed phyllody disease in Poland. Microbiology Resource Announcements 9:e00760-20. DOI: 10.1128/MRA.00760-20
, , , * (2019) Complete genome sequence of Spiroplasma alleghenense PLHS-1T (ATCC 51752), a bacterium isolated from the scorpion fly (Panorpa helena). Microbiology Resource Announcements 8:e00317-19. DOI: 10.1128/MRA.00317-19
, , Chen CY*, * (2018) Draft genome sequence of Vibrio vulnificus 86573B, a bacterium isolated from diseased tilapia in Taiwan. Microbiology Resource Announcements 7:e00813-18. DOI: 10.1128/MRA.00813-18
, , , , * (2018) Complete genome sequence of Spiroplasma monobiae MQ-1T (ATCC 33825), a bacterium isolated from the vespid wasp (Monobia quadridens). Genome Announcements 6:e00347-18. DOI: 10.1128/genomeA.00347-18
, , , * (2018) Complete genome sequence of Spiroplasma floricola 23-6T (ATCC 29989), a bacterium isolated from tulip tree (Liriodendron tulipifera L.). Genome Announcements 6:e00302-18. DOI: 10.1128/genomeA.00302-18
, , , Santos MNM, Lai EM, * (2018) Complete genome sequence of Agrobacterium tumefaciens 1D1609. Genome Announcements 6:e00253-18. DOI: 10.1128/genomeA.00253-18
, Chen CL, Yang Y, Wang TF*, * (2018) Draft genome sequence of Burkholderia sp. strain WAC0059, a bacterium isolated from the medicinal fungus Antrodia cinnamomea. Genome Announcements 6:e00027-18. DOI: 10.1128/genomeA.00027-18
, , * (2017) Complete genome sequence of Spiroplasma corruscae EC-1T (DSM 19793), a bacterium isolated from a lampyrid beetle (Ellychnia corrusca). Genome Announcements 5:e00964-17. DOI: 10.1128/genomeA.00964-17
, , Gasparich GE, * (2017) Complete genome sequence of Spiroplasma sp. NBRC 100390. Genome Announcements 5:e00008-17. DOI: 10.1128/genomeA.00008-17
, , Gasparich GE, * (2017) Complete genome sequence of Spiroplasma sp. TU-14. Genome Announcements 5:e01465-16. DOI: 10.1128/genomeA.01465-16
, , , * (2016) Complete genome sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a bacterium isolated from a horse fly (Tabanus abactor). Genome Announcements 4:e01201-16. DOI: 10.1128/genomeA.01201-16
, Gasparich GE, * (2016) Complete genome sequence of Spiroplasma turonicum Tab4cT, a bacterium isolated from horse flies (Haematopota sp.). Genome Announcements 4:e01010-16. DOI: 10.1128/genomeA.01010-16
Chang SH, , Chen CL, Yang JY*, * (2015) Draft genome sequence of a 16SrII-A subgroup phytoplasma associated with the purple coneflower (Echinacea purpurea) witches’-broom disease in Taiwan. Genome Announcements 3:01398-15. DOI: 10.1128/genomeA.01398-15
, , * (2015) Complete genome sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a bacterium isolated from soldier beetle (Cantharis carolinus). Genome Announcements 3:e01253-15. DOI: 10.1128/genomeA.01253-15
, , , , * (2015) Complete genome sequence of Spiroplasma litorale TN-1T (DSM 21781), a bacterium isolated from green-eyed horsefly (Tabanus nigrovittatus). Genome Announcements 3:e01116-15. DOI: 10.1128/genomeA.01116-15
, , , Wang YC, Lai EM, * (2015) Complete genome sequence of Agrobacterium tumefaciens Ach5. Genome Announcements 3:e00570-15. DOI: 10.1128/genomeA.00570-15
, , Canale MC, Mugford ST, Lopes JRS, Hogenhout SA, * (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
, Chen HJ, Chen CY, * (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
, , , * (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
, , , Kuo PA, Tu J, * (2013) Complete genome sequence of Serratia marcescens WW4. Genome Announcements 1:e00126-13. DOI: 10.1128/genomeA.00126-13
Reviews
Mijatović Scouten J, , Sung LK, Wen YHV, , Lai EM, Chang JH* (2025) Function, evolution, and ecology of type VI secretion systems of plant-associated bacteria. Annual Review of Phytopathology 63:333-356. DOI: 10.1146/annurev-phyto-121423-084620
Weisberg AJ*, , Chang JH, Lai EM, * (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
Bertaccini A*, Arocha-Rosete Y, Contaldo N, Duduk B, Fiore N, Montano HG, Kube M, , Martini M, Oshima K, Quaglino F, Schneider B, Wei W, Zamorano A (2022) Revision of the 'Candidatus Phytoplasma' species description guidelines. International Journal of Systematic and Evolutionary Microbiology 72:005353. DOI: 10.1099/ijsem.0.005353
Citti C*, Dordet-Frisoni E, Nouvel LX, , Baranowski E (2018) Horizontal gene transfers in mycoplasmas (Mollicutes). Current Issues in Molecular Biology 29:3-22. DOI: 10.21775/cimb.029.003
, , * (2016) Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiology Reviews 40:855-874. DOI: 10.1093/femsre/fuw028
, Ochman H* (2009) The fate of new bacterial genes. FEMS Microbiology Reviews 33:38-43. DOI: 10.1111/j.1574-6976.2008.00140.x
Book Chapters
Mejia HM, Chiu YC, *, Yang JY* (2025) Exploring phytoplasma genomes through advanced sequencing and enrichment techniques. In: Phytoplasmas: Genomes, Plant Hosts and Vectors. Ed. Wei W. Commonwealth Agricultural Bureaux International (CABI). DOI: 10.1079/9781800627031.0003
Gasparich GE*, , (2025) Mycoplasmatota. In: Bergey's Manual of Systematics of Archaea and Bacteria. Ed. Whitman W. Bergey’s Manual Trust. DOI: 10.1002/9781118960608.pbm00025.pub3
, , * (2023) Genomic studies of Asian phytoplasmas. In: Phytoplasma Diseases in Asian Countries Vol III: Characterization, Epidemiology and Management. Eds. Tiwari AK, Oshima K, Yadav A, Esmaeilzadeh-Hosseini S, Hanboonsong Y, Lakhanpaul S. Elsevier. DOI: 10.1016/B978-0-323-91671-4.00002-2. ISBN: 978-0-323-91671-4.
Gasparich GE*, , Foissac X (2020) Spiroplasma. In: Bergey's Manual of Systematics of Archaea and Bacteria. Eds. Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB. Bergey’s Manual Trust. DOI: 10.1002/9781118960608.gbm01262.pub2a
, Ochman H*, Raghavan R (2011) The genomics of Escherichia coli and beyond. In: The Population Genetics of Bacteria: A Tribute to Thomas S. Whittam. Eds. Walk S, Feng P. American Society for Microbiology Press. ISBN: 978-1-55581-535-6.
Kissinger JC*, (2007) Evolution and comparative genomics of Toxoplasma gondii. In: Toxoplasma: Molecular and Cellular Biology. Eds. Ajioka JW, Soldati D. Horizon Press. ISBN: 978-1-904933-34-2.
Case Reports
Owusu M, Acheampong G, Annan A, Marfo KS, Osei I, Amuasi J, Sarpong N, Im J, Mogeni OD, , , Jeon HJ, Panzner U, Park SE, Marks F, Owusu-Dabo E*, Adu-Sarkodie Y (2019) Ralstonia mannitolilytica sepsis: a case report. Journal of Medical Case Reports 13:318. DOI: 10.1186/s13256-019-2235-0
Owusu M, Marfo KS, Acheampong G, Arthur A, Sarpong N, Im J, Mogeni OD, Annan A, , , Park SE, Marks F, Owusu‐Dabo E*, Adu‐Sarkodie Y (2018) Gonococcal sepsis in a 32-year-old female: a case report. BMC Research Notes 11:253. DOI: 10.1186/s13104-018-3346-1
Owusu M, Owusu-Dabo E*, Acheampong G, Osei I, Amuasi J, Sarpong N, Annan A, , , Park SE, Marks F, Adu-Sarkodie Y (2017) Pseudomonas oryzihabitans sepsis in a 1-year-old child with multiple skin rashes: a case report. Journal of Medical Case Reports 11:77. DOI: 10.1186/s13256-017-1230-6
Conference Proceedings
Weisberg A*, Davis II E, Tabima J, Putnam M, Miller M, Belcher M, Grünwald N, Ream W, Lai EM, , Loper J, Chang J (2022) Evolution and epidemiology of global populations of nursery-associated Agrobacterium. Ecological Genetics 20:26-27. DOI: 10.17816/ecogen112374
, , * (2019) Genomic similarities among 16SrI phytoplasmas and implications on species boundaries. Phytopathogenic Mollicutes 9:73-74. DOI: 10.5958/2249-4677.2019.00037.9
, 林長平, * (2016) 植物菌質體之比較基因體學探討. 重要植物病原細菌與菌質體研討會: pp. 63–80. 國立中興大學植物病理學系.
Commentaries
Balish M, Bertaccini A, Blanchard A, Brown DR*, Browning G, Chalker V, Frey J, Gasparich G, Hoelzle L, Knight T, Knox C, , Manso-Silván L, May M, Pollack JD, Ramirez AS, Spergser J, Taylor-Robinson D, Volokhov D, Zhao Y (2019) Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. therein. International Journal of Systematic and Evolutionary Microbiology 69:3650–3653. DOI: 10.1099/ijsem.0.003632
* (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
, , * (2013) Horizontal transfer of potential mobile units in phytoplasmas. Mobile Genetic Elements 3:e26145. DOI: 10.4161/mge.26145
*, Janzen FJ (2007) Longevity, overlapping generations, and conservation of turtle populations. Turtle and Tortoise Newsletter 11:18-23.
Editorials
Fukatsu T*, Kakizawa S, Harumoto T, Sugio A, (2024) Editorial: Spiroplasma, mycoplasma, phytoplasma, and other genome-reduced and wall-less Mollicutes: their genetics, genomics, mechanics, interactions and symbiosis with insects, other animals and plants. Frontiers in Microbiology 15:1477536. DOI: 10.3389/fmicb.2024.1477536
Czajkowski R*, Zhu L, , Li Z (2024) Editorial: Insights in microbial symbioses 2022/2023. Frontiers in Microbiology 15:1367452. DOI: 10.3389/fmicb.2024.1367452
Others
Gasparich GE*, , Manso-Silván L, Blanchard A, Balish MF (2024) International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes: minutes of the closed meeting, 7 July 2024, Gran Canaria, Spain. International Journal of Systematic and Evolutionary Microbiology 74:006576. DOI: 10.1099/ijsem.0.006576
Popular Science
林婷嫻, 張語辰, (2017/10/02) 宛若細菌偵探的演化生物學家郭志鴻. 中央研究院研之有物人物訪談. 中央研究院. [link]
, * (2015/10/29) 蚊科昆蟲共生菌的致病基因演化. 中央研究院週報第1540期知識天地. 中央研究院. [PDF]
Discussions related to microbiology, mostly written in Traditional Chinese (i.e., 中文微生物科普短文), are posted in the Facebook group MiTalk 微生物生態情報網.