請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/2483完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 林長平(Chan-Pin Lin) | |
| dc.contributor.author | Shg-Ting Cho | en |
| dc.contributor.author | 卓舒婷 | zh_TW |
| dc.date.accessioned | 2021-05-13T06:40:48Z | - |
| dc.date.available | 2020-08-25 | |
| dc.date.available | 2021-05-13T06:40:48Z | - |
| dc.date.copyright | 2017-08-25 | |
| dc.date.issued | 2017 | |
| dc.date.submitted | 2017-07-12 | |
| dc.identifier.citation | Agrios, G. N. 1997. Plant diseases caused by Mollicutes: phytoplasmas and spiroplasmas. Pages 457-470 in: Plant Pathology. 4th ed. G. N. Agrios, ed. Academic Press, New York, USA.
Arocha, Y., Horta, D., Piñol, B., Palenzuela, I., Picornell, S., Almeida, R., and Jones, P. 2005. First report of a phytoplasma associated with Bermuda‐grass white leaf disease in Cuba. Plant Pathol. 54:233. Bai, X., Zhang, J., Ewing, A., Miller, S. A., Jancso Radek, A., Shevchenko, D. V., Tsukerman, K., Walunas, T., Lapidus, A., Campbell, J. W., and Hogenhout, S. A. 2006. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J. Bacteriol. 188:3682-3696. Bai, X., Correa, V. R., Toruño, T. Y., Ammar, E. D., Kamoun, S., and Hogenhout, S. A. 2009. AY-WB phytoplasma secretes a protein that targets plant cell nuclei. Mol. Plant Microbe Interact. 22:18-30. Bar-Joseph, M., Zelcer, A., and Loebenstein, G. 1975. Association of mycoplasmalike organisms with bermudagrass yellow leaf. Phytopathology 65:640-641. Beanland, L., Hoy, C. W., Miller, S. A., and Nault, L. R. 2000. Influence of aster yellows phytoplasma on the fitness of aster leafhopper (Homoptera: Cicadellidae). Ann. Entomol. Soc. Am. 93:271-276. Benson, D. A., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. 2014. GenBank. Nucleic Acids Res. 42: D32-D37. Bertaccini, A., and Duduk, B. 2010. Phytoplasma and phytoplasma diseases: a review of recent research. Phytopathol. Mediterr. 48:355-378. Bosco, D., Minucci, C., Boccardo, G., and Conti, M. 1997. Differential acquisition of chrysanthemum yellows phytoplasma by three leafhopper species. Entomol. Exp. Appl. 83:219-224. Bové, J. M. 1997. Spiroplasmas: infectious agents of plants, arthropods and vertebrates. Wien. Klin. Wochenschr. 109:604-612. Çağlar, B. K., Satar, S., and Elbeaino, T. 2013. Detection and molecular characterization of bermuda grass (Cynodon dactylon) white leaf phytoplasma from Turkey. Int. J. Agric. Biol. 15:90-94. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T. L. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:1. Chang, S. H., Cho, S. T., Chen, C. L., Yang, J. Y., and Kuo, C. H. 2015. Draft genome sequence of a 16SrII-A subgroup phytoplasma associated with purple coneflower (Echinacea purpurea) witches’ broom disease in Taiwan. Genome Announc. 3: e01398-15. Chaube, S., Kumar, S., Dubey, D., Tiwari, A. K., Upadhyaya, P. P., and Rao, G. P. 2015. Identification of a novel phytoplasma (16Sr XIV-A subgroup) associated with little leaf and witches’ broom of Cannabis sativa L. ssp. sativa and C. sativa L. ssp. indica in India. Phytoparasitica 43:275-279. Chen, C. T., Lee, C. S., and Chen, M. J. 1972. Mycoplasma-like organisms in Cynodon dactylon and Brachiaria distachya affected by white leaf diseases. Rep. Taiwan Sugar Exp. Stn. 56:49-55. Cho, S. T., Chang, H. H., Egamberdieva, D., Kamilova, F., Lugtenberg, B., and Kuo, C. H. 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. Cho, S. T., Lin, C.P., and Kuo, C. H. 2016. Comparative genomics of phytoplasmas. Pages 63-80 in: Proceedings of the Symposium on the Important Plant Pathogenic Bacteria and Phytoplasmas. Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan. Chou, H. H., and Holmes, M. H. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17:1093-1104. Chung, W. C., Chen, L. L., Lo, W. S., Lin, C. P., and Kuo, C. H. 2013. Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PLoS ONE 8: e62770. Cokol, M., Nair, R., and Rost, B. 2000. Finding nuclear localization signals. EMBO Rep. 1:411-415. Contaldo, N., Bertaccini, A., Paltonieri, S., M. Windsor, H., and Windsor, G. D. 2012. Axenic culture of plant pathogenic phytoplasmas. Phytopathol. Mediterr. 51:607-617. Cronjé, P., Dabek, A. J., Jones, P. and Tymon, A. M. 2000. First report of a phytoplasma associated with a disease of date palms in North Africa. Plant Pathol. 49:801. Dafalla, G. A., and Cousin, M. T. 1988. Fluorescence and electron microscopy of Cynodon dactylon affected with a white leaf disease in the Sudan. J. Phytopathol. 122:25-34. Darling, A. C., Mau, B., Blattner, F. R., and Perna, N. T. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403. Doi, Y.M., Teranaka, M., Yora, K., and Asuyama, H. 1967. Mycoplasma or PLT-group-like microorganisms found in the phloem elements of plants infected with mulberry dwarf, potato witches' broom, aster yellows, or paulownia witches' broom. Ann. Phytopathol. Soc. Jpn. 33:259-266. Draper, J., Mur, L. A., Jenkins, G., Ghosh-Biswas, G. C., Bablak, P., Hasterok, R., and Routledge, A. P. 2001. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 127:1539-1555. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. EFSA Panel on Plant Health. 2014. Scientific opinion on pest categorization of Grapevine Flavescence dorée. EFSA J. 12:3851. Felsenstein, J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166. Fischer, A., Santana-Cruz, I., Wambua, L., Olds, C., Midega, C., Dickinson, M., Kawicha, P., Khan, Z., Masiga, D., Jores, J., and Schneider, B. 2016. Draft genome sequence of “Candidatus Phytoplasma oryzae” strain Mbita1, the causative agent of Napier grass stunt disease in Kenya. Genome Announc. 4: e00297-16. Foissac, X., and Wilson, M. R. 2010. Current and possible future distributions of phytoplasma diseases and their vectors. Pages 309-324 in: Phytoplasmas: Genomes, Plant Hosts and Vectors. Weintraub, P. G., and Jones P, eds. CABI, Wallingford, UK. Guindon, S., and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704. Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., Han, C. C., Ohtsubo, E., Nakayama, K., Murata, T., Tanaka, M., Tobe, T., Iida, T., Takami, H., Honda, T., Sasakawa, C., Ogasawara, N., Yasunaga, T., Kuhara, S., Shiba, T., Hattori, M., and Shinagawa, H. 2001. Complete genome sequence of enterohemorrhagic Eschelichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:11-22. Hogenhout, S. A., and Loria, R. 2008. Virulence mechanisms of Gram-positive plant pathogenic bacteria. Curr. Opin. Plant Biol. 11:449-456. Hoshi, A., Oshima, K., Kakizawa, S., Ishii, Y., Ozeki, J., Hashimoto, M., Komatsu, K., Kagiwada, S., Yamaji, Y., and Namba, S. 2009. A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium. Proc. Natl. Acad. Sci. U.S.A. 106:6416-6421. Hulsen, T., Huynen, M. A., de Vlieg, J., and Groenen, P. M. 2006. Benchmarking ortholog identification methods using functional genomics data. Genome Biol. 7: R31. Hyatt, D., Chen, G. L., LoCascio, P. F., Land, M. L., Larimer, F. W., and Hauser, L. J. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. Imlau, A., Truernit, E., and Sauer, N. 1999. Cell-to-cell and long-distance trafficking of the green fluorescent protein in the phloem and symplastic unloading of the protein into sink tissues. Plant Cell 11:309-322. IRPCM Phytoplasma/Spiroplasma Working Team - Phytoplasma taxonomy group. 2004. ‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int. J. Syst. Evol. Microbiol. 54:1243-1255. Kakizawa, S., and Yoneda, Y. 2015. The role of genome sequencing in phytoplasma research. Phytopathogenic Mollicutes 5:19-24. Kanehisa, M., Sato, Y., and Morishima, K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428:726-731. Karimi, M., Inzé, D., and Depicker, A. 2002. GATEWAY™ vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci. 7:193-195. Kirkpatrick, B. C. 1992. Mycoplasma-like organisms—plant and invertebrate pathogens. Pages 4050-4067 in: The Prokaryotes. 2nd ed. A. Balows, H. G. Truper, M. Dworkin, W. Harder, and K. H. Schleifer, eds. Springer-Verlag, New York, USA. Krogh, A., Larsson, B., Von Heijne, G., and Sonnhammer, E. L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580. Ku, C., Lo, W. S., and Kuo, C. H. 2013. Horizontal transfer of potential mobile units in phytoplasmas. Mob. Genet. Elements 3: e62770. Kube, M., Schneider, B., Kuhl, H., Dandekar, T., Heitmann, K., Migdoll, A. M., Reinhardt, R., and Seemüller, E. 2008. The linear chromosome of the plant-pathogenic mycoplasma ‘Candidatus Phytoplasma mali’. BMC Genomics 9:306. Lagesen, K., Hallin, P., Rødland, E. A., Stærfeldt, H. H., Rognes, T., and Ussery, D. W. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108. Lee, I. M., Hammond, R. W., Davis, R. E., and Gundersen, D. E. 1993. Universal amplification and analysis of pathogen 16S rDNA for classification and identification of mycoplasmalike organisms. Phytopathology 83:834-42. Lee, I. M., Pastore, M., Vibio, M., Danielli, A., Attathom, S., Davis, R. E., and Bertaccini, A. 1997. Detection and characterization of a phytoplasma associated with annual blue grass (Poa annua) white leaf disease in southern Italy. Eur. J. Plant Pathol. 103:251-254. Lee, I. M., Gundersen-Rindal, D. E., Davis, R. E., and Bartoszyk, I. M. 1998. Revised classification scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int. J. Syst. Bacteriol. 48:1153-1169. Lee, I. M., Davis, R. E., and Gundersen-Rindal, D. E. 2000. Phytoplasma: phytopathogenic Mollicutes. Annu. Rev. Microbiol. 54:221-255. Li, H., and Durbin, R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. Li, L., Stoeckert, C. J., and Roos, D. S. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189. Lo, W. S., Huang, Y. Y., and Kuo, C. H. 2016. Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiol. Rev. 40:855-874. Lowe, T. M., and Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964. Lu, Y. T., Li, M. Y., Cheng, K. T., Tan, C. M., Su, L. W., Lin, W. Y., Shih, H. T., Chiou, T. J., and Yang, J. Y. 2014. Transgenic plants that express the phytoplasma effector SAP11 show altered phosphate starvation and defense responses. Plant Physiol. 164:1456-1469. Lupas, A., Van Dyke, M., and Stock, J. 1991. Predicting coiled coils from protein sequences. Science. 252:1162-1164. MacLean, A. M., Sugio, A., Makarova, O. V., Findlay, K. C., Grieve, V. M., Tóth, R., Nicolaisen, M., and Hogenhout, S. A. 2011. Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants. Plant Physiol. 157:831-841. MacLean, A. M., Orlovskis, Z., Kowitwanich, K., Zdziarska, A. M., Angenent, G. C., Immink, R. G., and Hogenhout, S. A. 2014. Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner. PLoS Biol. 12: e1001835. Magoč, T., and Salzberg, S. L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957-2963. Marchler-Bauer, A., Bo, Y., Han, L., He, J., Lanczycki, C. J., Lu, S., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z. X., Yamashita, R. A., Zhang, D. C., Zheng, C. J., Geer, L. Y., and Bryant, S. H. 2017. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 45: D200-D203. Marcone, C., Ragozzino, A., and Seemüller, E. 1997a. Detection of Bermuda grass white leaf disease in Italy and characterization of the associated phytoplasma by RFLP analysis. Plant Dis. 81:862-866. Marcone, C., Ragozzino, A., and Seemüller, E. 1997b. Dodder transmission of alder yellows phytoplasma to the experimental host Catharanthus roseus (periwinkle). For. Pathol. 27:347-350. Marcone, C., Neimark, H., Ragozzino, A., Lauer, U., and Seemüller, E. 1999. Chromosome sizes of phytoplasmas composing major phylogenetic groups and subgroups. Phytopathology 89:805-810. Marcone, C., Schneider, B., and Seemüller, E. 2004. ‘Candidatus Phytoplasma cynodontis’, the phytoplasma associated with Bermuda grass white leaf disease. Int. J. Syst. Evol. Microbiol. 54:1077-1082. Marzachì, C., Veratti, F., and Bosco, D. 1998. Direct PCR detection of phytoplasmas in experimentally infected insects. Ann. Appl. Biol. 133:45-54. Mayer, C. J., Vilcinskas, A., and Gross, J. 2008. Phytopathogen lures its insect vector by altering host plant odor. J. Chem. Ecol. 34:1045-1049. McCoy, R. E., Caudwell, A., Chang, C. J., Chen, T. A., Chiykowski, L. N., Cousin, M. T., Dale, J. C., de Leeuw, G. T. N., Golino, D. A., Hackett, K. J., Kirkpatrick, B. C., Marwitz, R., Petzold, H., Sinha, R. H., Sugiura, M., Whitcomb, R. F., Yang, I. L., Zhu, B. M., and Seemüller, E. 1989. Plant diseases associated with mycoplasma like organisms. Pages 546-640 in: The Mycoplasmas. Vol. 5. R. F. Whitcomb and J. G. Tully, eds. Academic Press, New York, USA. Minato, N., Himeno, M., Hoshi, A., Maejima, K., Komatsu, K., Takebayashi, Y., Kasahara, H., Yusa, A., Yamaji, Y., Oshima, K., Kamiya, Y., and Namba, S. 2014. The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways. Sci. Rep. 4:7399. Moran, N. A., McCutcheon, J. P., and Nakabachi, A. 2008. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42:165-190. Nakai, K., and Horton, P. 1999. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24:34-35. Nemhauser, J. L., Mockler, T. C., and Chory, J. 2004. Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol. 2: e258. Obura, E., Masiga, D., Midega, C. A. O., Wachira, F., Pickett, J. A., Deng, A. L., and Khan, Z. R. 2010. First report of a phytoplasma associated with Bermuda grass white leaf disease in Kenya. New Dis. Rep. 21:23. Orlovskis, Z., Canale, M. C., Thole, V., Pecher, P., Lopes, J. R., and Hogenhout, S. A. 2015. Insect-borne plant pathogenic bacteria: getting a ride goes beyond physical contact. Curr. Opin. Insect Sci. 9:16-23. Orlovskis, Z. 2017. Role of phytoplasma effector proteins in plant development and plant-insect interactions. Ph.D. thesis, University of East Anglia, Norwich, Norfolk, UK. Oshima, K., Shiomi, T., Kuboyama, T., Sawayanagi, T., Nishigawa, H., Kakizawa, S., Miyata, S., Ugaki, M., and Namba, S. 2001. Isolation and characterization of derivative lines of the onion yellows phytoplasma that do not cause stunting or phloem hyperplasia. Phytopathology 91:1024-1029. Oshima, K., Kakizawa, S., Nishigawa, H., Jung, H. Y., Wei, W., Suzuki, S., Arashida, R., Nakata, D., Miyata, S., Ugaki, M., and Namba, S. 2004. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat. Genet. 36:27-29. Pérez-López, E., Luna-Rodríguez, M., Olivier, C. Y., and Dumonceaux, T. J. 2016. The underestimated diversity of phytoplasmas in Latin America. Int. J. Syst. Evol. Microbiol. 66:492-513. Petersen, T. N., Brunak, S., von Heijne, G., and Nielsen, H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods. 8:785-786. Porra, R. J., Thompson, W. A., and Kriedemann, P. E. 1989. Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochim. Biophys. Acta. 975:384-394. Rambaut, A. 2007. FigTree, a graphical viewer of phylogenetic trees. See http://tree. bio. ed. ac. uk/software/figtree. Rao, G. P., Raj, S. K., Snehi, S. K., Mall, S., Singh, M., and Marcone, C. 2007. Molecular evidence for the presence of ‘Candidatus Phytoplasma cynodontis’, the Bermuda grass white leaf agent, in India. Bull. Insectol. 60:145-146. Rao, G. P., Mall, S., Singh, M., and Marcone, C. 2009. First report of a ‘Candidatus Phytoplasma cynodontis’-related strain (group 16SrXIV) associated with white leaf disease of Dichanthium annulatum in India. Australas. Plant Dis. Notes 4:56-58. Rao, G. P., Mall, S., and Marcone, C. 2010. ‘Candidatus Phytoplasma cynodontis’ (16SrXIV group) affecting Oplismenus burmannii (Retz.) P. Beauv. and Digitaria sanguinalis (L.) Scop. in India. Australas. Plant Dis. Notes 5:93-95. Rao, G. P., Tiwari, A. K., and Dubey, D. 2017a. Identification and characterization of two phytoplasma subgroups (16SrXI-D and 16SrXIV-A) associated with lychee (Litchi chinensis Sonn) in India. J. Plant Dis. Prot. 124:235-239. Rao, G. P., Prakasha, T. L., Priya, M., Thorat, V., Kumar, M., Baranwal, V. K., Mishra, and Yadav, A. 2017b. First report of association of Candidatus Phytoplasma cynodontis (16SrXI-B Group) with streak, yellowing, and stunting disease in durum and bread wheat genotypes from central India. Plant Dis. 101:1314. Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., and Mesirov, J. P. 2011. Integrative genomics viewer. Nat. Biotech. 29:24-26. Salehi, M., Izadpanah, K., Siampour, M., and Taghizadeh, M. 2009. Molecular characterization and transmission of Bermuda grass white leaf phytoplasma in Iran. J. Plant Pathol. 91:655-661. Sarindu, N., and Clark, M. F. 1993. Antibody production and identity of MLOs associated with sugar‐cane whiteleaf disease and bermuda‐grass whiteleaf disease from Thailand. Plant Pathol. 42:396-402. Seemüller, E., Carraro, L., Jarausch, W., and Schneider, B. 2011. Apple proliferation phytoplasma. Pages 67-74 in: Virus and Virus-Like Diseases of Pome and Stone Fruits. Hadidi, A., Barba, M., Candresse, T., and Jelkmann, W., eds. St. Paul, Minnesota, USA. Smart, C. D., Schneider, B., Blomquist, C. L., Guerra, L. J., Harrison, N. A., Ahrens, U., Lorenz, K.-H., Seemüller, E., and Kirkpatrick, B. C. 1996. Phytoplasma-specific PCR primers based on sequences of the 16-23S rRNA spacer region. Appl. Environ. Microbiol. 62:2988-2993. Streten, C., and Gibb, K. S. 2006. Phytoplasma diseases in sub-tropical and tropical Australia. Australas. Plant Pathol. 35:129-146. Sugawara, K., Honma, Y., Komatsu, K., Himeno, M., Oshima, K., and Namba, S. 2013. The alteration of plant morphology by small peptides released from the proteolytic processing of the bacterial peptide TENGU. Plant Physiol. 162:2005-2014. Sugio, A., MacLean, A. M., Grieve, V. M., and Hogenhout, S. A. 2011a. Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 108: E1254-E1263. Sugio, A., MacLean, A. M., Kingdom, H. N., Grieve, V. M., Manimekalai, R., and Hogenhout, S. A. 2011b. Diverse targets of phytoplasma effectors: from plant development to defense against insects. Annu. Rev. Phytopathol. 49:175-195. Sugio, A., MacLean, A. M., and Hogenhout, S. A. 2014. The small phytoplasma virulence effector SAP11 contains distinct domains required for nuclear targeting and CIN‐TCP binding and destabilization. New Phytol. 202:838-848. Sung, Y. C., Lin, C. P. and Chen, J. C. 2014. Optimization of virus-induced gene silencing in Catharanthus roseus. Plant Pathol. 63:1159-1167. Sunpapao, A. 2016. Preliminary molecular identification of Phytoplasma associated with Axonopus compressus white leaf disease. Songklanakarin J. Plant Sci. 3:40-43. Talavera, G., and Castresana, J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56:564-577. Tan, C. M., Li, C. H., Tsao, N. W., Su, L. W., Lu, Y. T., Chang, S. H., Lin, Y. Y., Liou, J. C., Hsieh, L. C., Yu, J. Z., Sheue, C. R., Wang, S. Y., Lee, C. F., and Yang, J. Y. 2016. Phytoplasma SAP11 alters 3-isobutyl-2-methoxypyrazine biosynthesis in Nicotiana benthamiana by suppressing NbOMT1. J. Exp. Bot. 67:4415-4425. Tran‐Nguyen, L. T. T., Blanche, K. R., Egan, B., and Gibb, K. S. 2000. Diversity of phytoplasmas in northern Australian sugarcane and other grasses. Plant Pathol. 49:666-679. Tran-Nguyen, L. T. T., Kube, M., Schneider, B., Reinhardt, R., and Gibb, K. S. 2008. Comparative genome analysis of “Candidatus Phytoplasma australiense” (subgroup tuf-Australia I; rp-A) and “Ca. Phytoplasma asteris” strains OY-M and AY-WB. J. Bacteriol. 190:3979-3991. Wei, W., Lee, M., Davis, R. E., Suo, X., and Zhao, Y. 2008. Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int. J. Syst. Evol. Microbiol. 58:2368-2377. Weintraub, P. G., and Beanland, L. 2006. Insect vectors of phytoplasmas. Annu. Rev. Entomol. 51:91-111. Win, N. K. K. and Jung, H. Y. 2012 ‘Candidatus Phytoplasma cynodontis’ associates with white leaf disease of golden beard grass (Chrysopogon acicalatus). Trop. Plant Pathol. 37:76-79. Yang, C. Y., Huang, Y. H., Lin, C. P., Lin, Y. Y., Hsu, H. C., Wang, C. N., Yu, L., Liu, D., Shen, B. N., and Lin, S. S. 2015. MiR396-targeted SHORT VEGETATIVE PHASE is required to repress flowering and is related to the development of abnormal flower symptoms by the PHYL1 effector. Plant Physiol. 168:1702-1716. Yang, Z. 2007. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 24:1586-1591. Zerbino, D. R., and Birney, E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829. Zhao, Y., and Davis, R. E. 2016. Criteria for phytoplasma 16Sr group/subgroup delineation and the need of a platform for proper registration of new groups and subgroups. Int. J. Syst. Evol. Microbiol. 66:2121-2123. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/2483 | - |
| dc.description.abstract | 植物菌質體‘Candidatus Phytoplasma cynodontis’ 為百慕達草白葉病(bermudagrass white leaf; BGWL)的病原菌，此草皮病害於1972年在台灣初次被發現。該細菌性病原菌可於寄主植物的篩管中及媒介昆蟲體內增殖，致使植物產生葉片白化與植株矮化等病徵，進而影響受感染之運動場草皮與牧草的品質，並使草皮水土保持的功能降低。即便已經過多年的努力，目前仍然無法在實驗室中離體培養植物菌質體，因此相關的研究一直面臨很大的困難。為了突破此限制，本論文針對於桃園觀音採集到的病株GY2015進行全基因體定序，藉以瞭解其基因組成。經過基因體組裝目前得到5條連續序列，總長為502,218 bp，共含有425個蛋白編碼基因(protein-coding gene)。為了能對不同植物菌質體間基因組成演化有更多的了解，我們挑選了另外六株已發表且寄主不同的植物菌質體基因體序列進行分子演化及比較基因體學分析，結果顯示不同菌株間的遺傳歧異度有著相當大的差異。此外，BGWL植物菌質體GY2015擁有一組尚未在其他植物菌質體中發現過的新型potential mobile unit (PMU)。由於已知PMU可能與基因體的穩定性及效應因子基因水平轉移有關，此發現拓展了我們於植物菌質體遺傳多樣性的了解。另外我們也發現，前人從其他植物菌質體物種中找到的效應因子基因SAP11、SAP54/PHYL1和TENGU在BGWL植物菌質體的基因體中皆不存在，意味著BGWL植物菌質體可能擁有不同的效應因子。我們透過生物資訊分析預測出45個候選效應因子基因，且從基因轉殖植物的表現型初步篩選出一個可能為效應因子基因的候選基因，表現該基因的轉殖植物出現葉片白化、植株矮化、叢生及不孕花等多項類似植物菌質體感染的性狀。未來針對這些候選效應因子進行功能研究，將有助於我們對此病原菌之深入認識。本篇針對一株與現有較完整基因體學研究的植物菌質體在演化上距離較遠的物種進行研究，透過比較基因體學分析，可增進我們對植物菌質體於演化、遺傳學及病理學上的認識。 | zh_TW |
| dc.description.abstract | ‘Candidatus Phytoplasma cynodontis’ is a causative agent of a turf disease—bermudagrass white leaf (BGWL), which was first reported in Taiwan in 1972. This phytopathogenic bacterium is transmitted by insects and is restricted to sieve tubes of infected plants. The symptoms include chlorosis and dwarfism, thus decreasing the quality of sports fields and pasture, as well as lowering the protection against soil erosion. Despite extensive effort, phytoplasmas have remained uncultivable outside of their hosts, making the investigation of their biology extremely difficult. To circumvent this difficulty, we conducted whole genome sequencing for a diseased plant collected in Guanyin (Taoyuan, Taiwan) to investigate the gene content of this bacterium (GY2015). The draft genome assembly contains five contigs with a combined size of 502,218 bp and 425 protein-coding genes. To better understand the evolution of gene content within this genus, we selected six other phytoplasma genomes for molecular phylogenetics and comparative genomics analysis. The results indicated that the gene content is highly diversified across different phytoplasma species. Moreover, the BGWL phytoplasma harbors a new type of potential mobile unit (PMU) that has not been described in other phytoplasmas. Because PMUs could promote genome instability and horizontal transfer of effector genes, this finding expands our understanding of phytoplasma genetic diversity. Finally, none of the three characterized phytoplasma effectors (i.e., SAP11, SAP54/PHYL1, and TENGU) was found in this BGWL phytoplasma genome, suggesting that this bacterium harbors novel effectors. Our bioinformatics prediction identified 45 putative effector genes and our preliminary screening through expression in transgenic Arabidopsis identified one candidate that induced morphological phenotypes similar to phytoplasma infection (e.g., chlorosis, dwarfism, witches’-broom, and sterile flower). Future functional characterization of these putative effectors could further improve our knowledge of this plant pathogen. In this study, we focus on a phytoplasma species that represents a highly diverged lineage from all of the other phytoplasmas with genomic studies. Through comparative genomic analysis, this study promoted our understanding on the evolution, genetics, and pathology of phytoplasmas. | en |
| dc.description.provenance | Made available in DSpace on 2021-05-13T06:40:48Z (GMT). No. of bitstreams: 1 ntu-106-R04633020-1.pdf: 11013670 bytes, checksum: 43f7d995c92eb2abce204b5066cf1b8d (MD5) Previous issue date: 2017 | en |
| dc.description.tableofcontents | CONTENTS
CONTENTS 1 摘要 3 ABSTRACT 4 LIST OF FIGURES 6 LIST OF TABLES 6 INTRODUCTION 7 MATERIALS AND METHODS 14 1. Collection of biological materials 14 2. Confirmation of phytoplasma infection by 16S rDNA 15 3. Confirmation of phytoplasma infection by transmission electron microscopy (TEM) 16 4. Chloroplast observation by microscopy 16 5. Chlorophyll fluorescence and content measurement 16 6. Whole genome shotgun sequencing 17 7. de novo genome assembly 18 8. Molecular phylogenetic inference 19 9. Gene annotation and homologous gene identification 20 10. Genome alignment 21 11. Ka/Ks ratio 21 12. Effector gene and subcellular localization signal prediction 21 13. Generation of transgenic Arabidopsis lines 23 14. Growth conditions and confirmation of transgenic Arabidopsis plants 25 15. Quantitative RT-PCR experiments 25 RESULTS AND DISCUSSIONS 27 1. BGWL phytoplasma diseased plant observation, collection, and confirmation 27 1.1. Field disease detection 27 1.2. Microscopy observation on chloroplast morphology 28 1.3. Chlorophyll fluorescence and content measurement 30 1.4. Confirmation of phytoplasma by 16S rDNA PCR 31 1.5. Confirmation of phytoplasma by TEM observation 31 2. Comparative genomics analysis of phytoplasmas 32 2.1. BGWL phytoplasma genome assembly 32 2.2. Phylogenetic analysis of 16S rDNA sequence and the 16Sr group 34 2.3. Genome alignment with ‘Ca. P. oryzae’ Mbita1 36 2.4. Genome statistic comparison 37 2.5. Gene content, metabolic pathway comparison statistic comparison 38 2.6. Effector prediction and comparison 41 2.7. Molecular evolution of potential mobile units (PMUs) 42 3. Effector identification 44 3.1. Modified putative effector prediction and criteria 44 3.2. Generation and analyses of candidate effector genes Arabidopsis lines 45 CONCLUSIONS 48 REFERENCES 93 SUPPLEMENTARY DATA 104 | |
| dc.language.iso | en | |
| dc.title | 百慕達草白葉病植物菌質體的基因體比較分析以及其效應因子之研究 | zh_TW |
| dc.title | Comparative Genomics Analysis and Effector Characterization of the Bermudagrass White Leaf (BGWL) Phytoplasma | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 105-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.coadvisor | 郭志鴻(Chih-Horng Kuo) | |
| dc.contributor.oralexamcommittee | 黃皓瑄(Hau-Hsuan Hwang),鄭秋萍(Chiu-Ping Cheng),陳仁治(Jen-Chih Chen) | |
| dc.subject.keyword | 植物菌質體,百慕達草白葉病,比較基因體學,效應因子,植物與微生物交互作用分子機制, | zh_TW |
| dc.subject.keyword | phytoplasma,bermudagrass white leaf (BGWL),comparative genomics,effector,molecular plant-microbe interactions, | en |
| dc.relation.page | 112 | |
| dc.identifier.doi | 10.6342/NTU201701523 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2017-07-13 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 植物病理與微生物學研究所 | zh_TW |
| 顯示於系所單位： | 植物病理與微生物學系 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-106-1.pdf | 10.76 MB | Adobe PDF | 檢視/開啟 |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。