Research Articles

Orlovskis Z, Canale MC, Haryono M, Lopes JRS, Kuo CH*, Hogenhout S* (2016) A few sequence polymorphisms among isolates of maize bushy stunt phytoplasma associate with organ proliferation symptoms in infected maize plants. Annals of Botany accepted. 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

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

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

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

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. [link] #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.

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

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

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.

McGaugh SE*, Bowden RM, Kuo CH, 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, Kuo CH, 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

Kuo CH, 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, Kuo CH, 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

Kuo CH, 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

Kuo CH, Ochman H* (2009) Deletional bias across the three domains of life. Genome Biology and Evolution 1: 145-152. DOI: 10.1093/gbe/evp016

Kuo CH, 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

Kuo CH*, 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

Kuo CH*, 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

Kuo CH*, 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

Kuo CH*, 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

Kuo CH*, 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

Kuo CH*, 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

Kuo CH*, 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

Genome Announcements

Lo WS, Haryono M, Gasparich GE, Kuo CH* (2016) Complete genome sequence of Spiroplasma sp. TU-14. Genome Announcements 5: e01465-16. DOI: 10.1128/genomeA.e01465-16

Shen WY, Lo WS, Lai YC, Kuo CH* (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

Lo WS, Gasparich GE, Kuo CH* (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, Cho ST, Chen CL, Yang JY*, Kuo CH* (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

Lo WS, Liu PY, Kuo CH* (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

Lo WS, Lai YC, Lien YW, Wang TH, Kuo CH* (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

Huang YY, 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

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

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, 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

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

Reviews

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

Kuo CH, Ochman H* (2009) The fate of new bacterial genes. FEMS Microbiology Reviews 33: 38-43. DOI: 10.1111/j.1574-6976.2008.00140.x

Commentaries

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

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

Kuo CH*, Janzen FJ (2007) Longevity, overlapping generations, and conservation of turtle populations. Turtle and Tortoise Newsletter 11: 18-23.

Book Chapters

Kuo CH, 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. S. Walk and P. Feng. American Society for Microbiology Press. ISBN: 978-1-55581-535-6.

Kissinger JC*, Kuo CH (2007) Evolution and comparative genomics of Toxoplasma gondii. In: Toxoplasma: Molecular and Cellular Biology. Eds. J. Ajioka and D. Soldati. Horizon Press. ISBN: 978-1-904933-34-2.

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