Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)

International Journal of Systematic and Evolutionary Microbiology

Volumn 59, Issue 10, 2009, Pages 2582-2593

  Zhao, Yan ^a   Wei, Wei ^a   Lee, Ing Ming ^a   Shao, Jonathan ^a   Suo, Xiaobing ^a   Davis, Robert E ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BACILLUS; CLOSTRIDIUM; COMPUTER PROGRAM; ECOLOGICAL NICHE; GEL ELECTROPHORESIS; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYTOPLASMA; PLANT DISEASE; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; TAXONOMY; UNINDEXED SEQUENCE;

BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; INTERNET; MOLECULAR SEQUENCE DATA; ONLINE SYSTEMS; PHYLOGENY; PHYTOPLASMA; PLANT DISEASES; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PRUNUS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOFTWARE;

CANDIDATUS PHYTOPLASMA; CLOSTRIDIUM; HEXAPODA; PEACH YELLOW LEAFROLL PHYTOPLASMA; POSIBACTERIA;

EID: 70350719153     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.010249-0     Document Type: Article

References (57)

1. Al-Saady, N. A., Khan, A. J., Calari, A., Al-Subhi, A. M. & Bertaccini, A. (2008). 'Candidatus Phytoplasma omanense', associated with witches'-broom of Cassia italica (Mill.) Spreng. in Oman. Int J Syst Evol Microbiol 58, 461-466.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
3. Arocha, Y., Antesana, O., Montellano, E., Franco, P., Plata, G. & Jones, P. (2007). 'Candidatus Phytoplasma lycopersici', a phytoplasma associated with 'hoja de perejil' disease in Bolivia. Int J Syst Evol Microbiol 57, 1704-1710.
4. Bai, X. D., Zhang, J. H., Ewing, A., Miller, S. A., Radek, A. J., Shevchenko, D. V., Tsukerman, K., Walunas, T., Lapidus, A. & other authors (2006). Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol 188, 3682-3696.
5. Cai, H., Wei, W., Davis, R. E., Chen, H. & Zhao, Y. (2008). Genetic diversity among phytoplasmas infecting Opuntia species: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group. Int J Syst Evol Microbiol 58, 1448-1457.
6. Chiykowski, L. N. & Sinha, R. C. (1990). Differentiation of MLO diseases by means of symptomatology and vector transmission. Zentralbl Bakteriol Hyg Suppl 20, 280-287.
7. Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. & Lim, Y. W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259-2261.
8. Davis, R. E. & Sinclair, W. A. (1998). Phytoplasma identity and disease etiology. Phytopathology 88, 1372-1376.
9. Davis, R. E., Jomantiene, R., Kalvelyte, A. & Dally, E. L. (2003). Differential amplification of sequence heterogeneous ribosomal RNA genes and classification of the 'Fragaria multicipita' phytoplasma. Microbiol Res 158, 229-236.
10. Davis, R. E., Jomantiene, R. & Zhao, Y. (2005). Lineage-specific decay of folate biosynthesis genes suggests ongoing host adaptation in phytoplasmas. DNA Cell Biol 24, 832-840.
11. Euzéby, J. P. (1997). List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47, 590-592.
12. Firrao, G., Carraro, L., Gobbi, E. & Locci, R. (1996). Molecular characterization of a phytoplasma causing phyllody in clover and other herbaceous hosts in northern Italy. Eur J Plant Pathol 102, 817-822.
13. Firrao, G., Cibb, K. & Streten, C. (2005). Short taxonomic guide to the genus 'Candidatus Phytoplasma'. J Plant Pathol 87, 249-263.
14. Granett, A. L. & Gilmer, R. M. (1971). Mycoplasma associated with X-disease in various Prunus species. Phytopathology 61, 1036-1037.
15. Gundersen, D. E. & Lee, I.-M. (1996). Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathol Mediterr 35, 144-151.
16. Gundersen, D. E., Lee, I.-M., Rehner, S. A., Davis, R. E. & Kingsbury, D. T. (1994). Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification. J Bacteriol 176, 5244-5254.
17. Hogenhout, S. A., Oshima, K., Ammar, el-D., Kakizawa, S., Kingdom, H. N. & Namba, S. (2008). Phytoplasmas: bacteria that manipulate plants and insects. Mol Plant Pathol 9, 403-423.
18. 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.
19. Jomantiene, R., Davis, R. E., Valiunas, D. & Alminaite, A. (2002). New group 16SrIII phytoplasma lineages in Lithuania exhibit interoperon sequence heterogeneity. Eur J Plant Pathol 108, 507-517.
20. Jung, H. Y., Sawayanagi, T., Kakizawa, S., Nishigawa, H., Miyata, S., Oshima, K., Ugaki, M., Lee, J. T., Hibi, T. & Namba, S. (2002). ' Candidatus Phytoplasma castaneae', a novel phytoplasma taxon associated with chestnut witches'-broom disease. Int J Syst Evol Microbiol 52, 1543-1549.
21. Kirkpatrick, B. C., Fisher, G. A., Fraser, J. D. & Purcell, A. H. (1990). Epidemiological and phylogenetic studies on western X-disease mycoplasma-like organisms. Zentralbl Bakteriol Hyg Suppl 20, 287-297.
22. Kube, M., Schneider, B., Kuhl, H., Dandekar, T., Heitmann, K., Migdoll, A. M., Reinhardt, R. & Seemüller, E. (2008). The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC Genomics 9, 306.
23. Lee, I.-M., Davis, R. E., Chen, T.-A., Chiykowske, L. N., Fletcher, J., Hiruki, C. & Schaff, D. A. (1992a). A genotype-based system for identification and classification of mycoplasmalike organisms (MLOs) in the aster yellows MLO strain cluster. Phytopathology 82, 977-986.
24. Lee, I.-M., Gundersen, D. E., Davis, R. E. & Chiykowske, L. N. (1992b). Identification and analysis of a genomic strain cluster of mycoplasmalike organisms associated with Canadian peach (eastern) X-disease, Western X-disease, and clover yellow edge. J Bacteriol 174, 6694-6698.
25. Lee, I.-M., Davis, R. E. & Hsu, H.-T. (1993a). Differentiation of strains in the aster yellows mycoplasmalike organism strain cluster by serological assays with monoclonal antibodies. Plant Dis 77, 815-817.
26. Lee, I.-M., Hammond, R. W., Davis, R. E. & Gundersen, D. E. (1993b). Universal amplification and analysis of pathogen 16S rDNA for classification and identification of mycoplasmalike organisms. Phytopathology 83, 834-842.
27. Lee, I.-M., Gundersen-Rindal, D. E., Davis, R. E. & Bartoszyk, I.-M. (1998). Revised classification scheme of phytoplasmas based on RFLP analysis of 16S rRNA and ribosomal protein gene sequences. Int J Syst Bacteriol 48, 1153-1169.
28. Lee, I.-M., Davis, R. E. & Gundersen-Rindal, D. E. (2000). Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 54, 221-255.
29. Lee, I.-M., Martini, M., Macone, C. & Zhu, S. F. (2004a). Classification of phytoplasma strains in the elm yellows group (16SrV) and proposal of 'Candidatus Phytoplasma ulmi' for the phytoplasma associated with elm yellows. Int J Syst Evol Microbiol 54, 337-347.
30. Lee, I.-M., Gundersen-Rindal, D. E., Davis, R. E., Bottner, K. D., Marcone, C. & Seemüller, E. (2004b). 'Candidatus Phytoplasma asteris', a novel phytoplasma taxon associated with aster yellows and related diseases. Int J Syst Evol Microbiol 54, 1037-1048.
31. Lee, I.-M., Bottner, K. D., Secor, G. & Rivera-Varas, V. (2006). 'Candidatus Phytoplasma americanum', a phytoplasma associated with a potato purple top wilt disease complex. Int J Syst Evol Microbiol 56, 1593-1597.
32. Liefting, L. W. & Kirkpatrick, B. C. (2003). Cosmid cloning and sample sequencing of the genome of the uncultivable mollicute, Western X-disease phytoplasma, using DNA purified by pulsed-field gel electrophoresis. FEMS Microbiol Lett 221, 203-211.
33. Liefting, L. W., Andersen, M. T., Beever, R. E., Gardner, R. C. & Foster, L. S. (1996). Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma. Appl Environ Microbiol 62, 3133-3139.
34. Macbeath, J. H., Nyland, G. & Spurr, A. R. (1972). Morphology of mycoplasma-like bodies associated with peach X-disease in Prunus persica. Phytopathology 62, 935-937.
35. Marcone, C., Neimark, H., Ragozzino, A., Lauer, U. & Seemüller, E. (1999). Chromosome sizes of phytoplasmas composing major phylogenetic groups and subgroups. Phytopathology 89, 805-810.
36. Martini, M., Lee, I.-M., Bottner, K. D., Zhao, Y., Botti, S., Bertaccini, A., Harrison, N. A., Carraro, L., Marcone, C. & Osler, R. (2007). Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. Int J Syst Evol Microbiol 57, 2037-2051.
37. McCoy, R. E., Caudwell, A., Chang, C. J., Chen, T. A., Chiykowski, L. N., Cousin, M. T., Dale, J. L., de Leeuw, G. T. N., Golino, D. A. & other authors (1989). Plant diseases associated with mycoplasmalike organisms. In The Mycoplasmas, vol. 5, pp. 545-560. Edited by R. F. Whitcomb & J. G. Tully. New York: Academic Press.
38. Murray, R. G. E. & Schleifer, K. H. (1994). Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int J Syst Bacteriol 44, 174-176.
39. Myers, E. W. & Miller, W. (1988). Optimal alignments in linear space. Comput Appl Biosci 4, 11-17.
40. Oshima, K., Kakizawa, S., Nishigawa, H., Jung, H.-Y., Wei, W., Suzuki, S., Arashida, R., Nakata, D., Miyata, S. & other authors (2004). Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 36, 27-29.
41. Quaglino, F., Zhao, Y., Bianco, P. A., Wei, W., Casati, P., Durante, G. & Davis, R. E. (2009). New 16Sr subgroups and distinct SNP lineages among grapevine Bois noir phytoplasma populations. Ann Appl Biol 154, 279-289.
42. Rosselló-Mora, R. & Amann, R. (2001). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39-67.
43. Sears, B. B. & Kirkpatrick, B. C. (1994). Unveiling the evolutionary relationships of plant pathogenic mycoplasmalike organisms. ASM News 60, 307-312.
44. Seemüller, E., Garnier, M. & Schneider, B. (2002). Mycoplasmas of plants and insects. In Molecular Biology and Pathogenicity of Mycoplasmas, pp. 91-115. Edited by S. Razin & R. Herrmann. New York: Kluwer Academic/Plenum.
45. Sinha, R. C. & Chiykowski, L. N. (1980). Transmission and morphological features of mycoplasma-like bodies associated with peach X-disease. Can J Plant Pathol 2, 119-124.
46. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
47. Stoddard, E. M. (1934). Progress report of investigations on a new peach trouble. Conn Pomol Soc Proc 43, 115-117.
48. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
49. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
50. Tran-Nguyen, L. T., Kube, M., Schneider, B., Reinhardt, R. & 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.
51. Valiunas, D., Staniulis, J. & Davis, R. E. (2006). 'Candidatus Phytoplasma fragariae', a novel phytoplasma taxon discovered in yellows diseased strawberry, Fragaria × ananassa. Int J Syst Evol Microbiol 56, 277-281.
52. Wei, W., Davis, R. E., Lee, I.-M. & Zhao, Y. (2007). Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 57, 1855-1867.
53. Wei, W., Davis, R. E., Jomantiene, R. & Zhao, Y. (2008a). Ancient, recurrent phage attacks and recombination events shaped dynamic sequence-variable mosaic structures at the root of phytoplasma genome evolution. Proc Natl Acad Sci U S A 105, 11827-11832.
54. Wei, W., Lee, I.-M., Davis, R. E., Suo, X. & Zhao, Y. (2008b). 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.
55. Weisburg, W. G., Tully, J. G., Rose, D. L., Petzel, J. P., Oyaizu, H., Yang, D., Mandelco, L., Sechrest, J., Lawrence, T. G. & other authors (1989). A phylogenetic analysis of the mycoplasmas: basis for their classification. J Bacteriol 171, 6455-6467.
56. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S. & other authors (2005). Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res 33, D39-D45.
57. Zhao, Y., Davis, R. E. & Lee, I. M. (2005). Phylogenetic positions of 'Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins. Int J Syst Evol Microbiol 55, 2131-2141.