Phytoplasma phylogeny and detection based on genes other than 16s rRNA

Phytoplasmas: Genomes, Plant Hosts and Vectors

Volumn , Issue , 2009, Pages 93-113

  Hodgetts, Jennifer ^a   Dickinson, Matthew ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78049407965     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (53)

1. Angelini, E., Negrisolo, E., Clair, D., Borgo, M. and Boudon-Padieu, E. (2003) Phylogenetic relationships among Flavescence dorée strains and related phytoplasmas determined by heteroduplex mobility assay and sequence of ribosomal and nonribosomal DNA. Plant Pathology 52, 663-672.
2. Anthony, R.M., Brown, T.J. and French, G.L. (2000) Rapid diagnosis of bacteremia by universal amplifi cation of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. Journal of Clinical Microbiology 38, 781-788.
3. Arnaud, G., Malembic-Maher, S., Salar, P., Bonnet, P., Maixner, M., Marcone, C., Boudon- Padieu, E. and Foissac, X. (2007) Multilocus sequence typing confi rms the close genetic interrelatedness of three distinct fl avescence dorée phytoplasma strain clusters and group 16SrV phytoplasmas infecting grapevine and alder in Europe. Applied and Environmental Microbiology 73, 4001-4010.
4. Bai, X., Zhang, J., Ewing, A., Miller, S.A., Radek, A.J., 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. Journal of Bacteriology 188, 3682-3696.
5. Barbara, D.J., Morton, A., Clark, M.F. and Davies, D.L. (2002) Immunodominant membrane proteins from two phytoplasmas in the aster yellows clade (chlorante aster yellows and clover phyllody) are highly divergent in the major hydrophilic region. Microbiology 148, 157-167.
6. Berg, M. and Seemüller, E. (1999) Chromosomal organization and nucleotide sequence of the genes coding for the elongation factors G and Tu of the apple proliferation phytoplasma. Gene 226, 103-109.
7. Berg, M., Davies, D.L., Clark, M.F., Vetten, H.J., Maier, G., Marcone, C. and Seemüller, E. (1999) Isolation of the gene encoding an immunodominant membrane protein of the apple proliferation phytoplasma, and expression and characterization of the gene product. Microbiology 145, 1937-1943.
8. Blomquist, C.L., Barbara, D.J., Davies, D.L., Clark, M.F. and Kirkpatrick, B.C. (2001) An immunodominant membrane protein gene from the Western X-disease phytoplasma is distinct from those of other phytoplasmas. Microbiology 147, 571-580.
9. Daire, X., Clair, D., Reinert, W. and Boudon-Padieu, E. (1997) Detection and differentiation of grapevine yellows phytoplasmas belonging to the elm yellows group and to the stolbur subgroup by PCR amplifi cation of non-ribosomal DNA. European Journal of Plant Pathology 103, 507-514.
10. De La Rue, S., Padovan, A. and Gibb, K. (2001) Stylosanthes is a host for several phytoplasmas, one of which shows unique 16S-23S intergenic spacer region heterogeneity. Journal of Phytopathology 149, 613-619.
11. Firrao, G., Gibb, K. and Streten, C. (2005) Short taxonomic guide to the genus 'Candidatus phytoplasma'. Journal of Plant Pathology 87, 249-263.
12. Goodwin, P.H., Xue, B.G., Kuske, C.R. and Sears, M.K. (1994) Amplifi cation of plasmid DNA to detect plant pathogenic mycoplasmalike organisms. Annals of Applied Biology 124, 27-36.
13. Gundersen, D.E., Lee, I.-M., Rehner, S.A., Davis, R.E. and Kingsbury, D.T. (1994) Phylogeny of mycoplasmalike organisms (Phytoplasmas): a basis for their classifi cation. Journal of Bacteriology 176, 5244-5254.
14. Harrison, N.A., Womack, M. and Carpio, M.L. (2002) Detection and characterization of a lethal yellowing (16SrIV) group phytoplasma in Canary Island date palms affected by lethal decline in Texas. Plant Disease 86, 676-681.
15. Hodgetts, J., Ball, T., Boonham, N., Mumford, R. and Dickinson, M. (2007) Use of terminal restriction fragment length polymorphism (T-RFLP) for Identification of phytoplasmas in plants. Plant Pathology 56, 357-365.
16. Hodgetts, J., Boonham, N., Mumford, R., Harrison, N. and Dickinson, M. (2008) Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'. International Journal of Systematic and Evolutionary Microbiology 58, 1826-1837.
17. Hodgetts, J., Boonham, N., Mumford, R. and Dickinson, M. (2009) Panel of 23S rRNA gene-based real-time PCR assays for improved universal and group specific detection of phytoplasmas. Applied and Environmental Microbiology 75, 2945-2950.
18. Hren, M., Boben, J., Rotter, A., Kralj, P., Gruden, K. and Ravnikar, M. (2007) Real-time PCR detection systems for Flavescence doreé and Bois noir phytoplasmas in grapevine: comparison with conventional PCR detection and application in diagnostics. Plant Pathology 56, 785-796.
19. 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. International Journal of Systematic and Evolutionary Microbiology 54, 1243-1255.
20. James, T.Y., Kauff, F., Schoch, C.L. et al. (2006) Restructuring the early evolution of Fungi using a six-gene phylogeny. Nature 443, 818-822.
21. Jarausch, W., Saillard, C., Dosba, F. and Bové, J.-M. (1994) Differentiation of mycoplasmalike organisms (MLOs) in European fruit trees by PCR using specific primers derived from the sequence of a chromosomal fragment of the apple proliferation MLO. Applied and Environmental Microbiology 60, 2916-2923.
22. Jomantiene, R., Zhao, Y. and Davis, R.E. (2007) Sequence-variable mosaics: composites of recurrent transposition characterizing the genomes of phylogenetically diverse phytoplasmas. DNA and Cell Biology 26, 557-564.
23. Kakizawa, S., Oshima, K., Kuboyama, T., Nishigawa, H., Jung, H.-Y., Sawayanagi, T., Tsuchizaki, T., Miyata, S.-I., Ugaki, M. and Namba, S. (2001) Cloning and expression analysis of phytoplasma protein translocation genes. Molecular Plant-Microbe Interactions 14, 1043-1050.
24. Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. (2005) The tree of eukaryotes. Trends in Ecology and Evolution 20, 670-676.
25. Kube M., Schneider, B., Kuhl, H., Dandekar, T., Heitmann, K., Migdoll, A.M., Reinhardt, R. and Seemüller, E. (2008) The linear chromosome of the plantpathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC Genomics 9, 306.
26. Lee, I.-M., Gundersen-Rindal, D.E., Davis, R.E. and Bartoszyk, I.M. (1998) Revised classifi cation scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. International Journal of Systematic Bacteriology 48, 1153-1169.
27. Lee, I.-M., Zhao, Y. and Bottner, K.D. (2006) SecY gene sequence analysis for fi ner differentiation of diverse strains in the aster yellows phytoplasma group. Molecular and Cellular Probes 20, 87-91.
28. Liefting, L.W., Andersen, M.T., Beever, R.E., Gardner, R.C. and Forster, R.L. (1996) Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma. Applied and Environmental Microbiology 62, 3133-3139.
29. Lim, P.-O. and Sears, B.B. (1991) DNA sequence of the ribosomal protein genes rpl2 and rps19 from a plant pathogenic mycoplasma-like organism. FEMS Microbiology Letters 84, 71-74.
30. Lim, P.-O. and Sears, B.B. (1992) Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from two ribosomal protein gene sequences. Journal of Bacteriology 174, 2606-2611.
31. Marcone, C., Lee, I.-M., Davis, R.E., Ragozzino, A. and Seemüller, E. (2000) Classifi cation of aster yellows-group phytoplasmas based on combined analyses of rRNA and tuf gene sequences. International Journal of Systematic and Evolutionary Microbiology 50, 1703-1713.
32. Martini, M., Lee, I.-M., Bottner, K.D., Zhao, Y., Botti, S., Bertaccini, A., Harrison, N.A., Carraro, L., Marcone, C., Khan, A.J. and Osler, R. (2007) Ribosomal protein genebased phylogeny for fi ner differentiation and classifi cation of phytoplasmas. International Journal of Systematic and Evolutionary Microbiology 57, 2037-2051.
33. Mpunami, A.A., Tymon, A., Jones, P. and Dickinson, M.J. (1999) Genetic diversity in the coconut lethal yellowing disease phytoplasmas of East Africa. Plant Pathology 48, 109-114.
34. Musić, M.Š., Krajačić, M. and Škorić, D. (2008) The use of SSCP analysis in the assessment of phytoplasma gene variability. Journal of Microbiological Methods 73, 69-72.
35. Nei, M. and Li, W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the USA 76, 5269-5273.
36. Nicolaisen, M. and Bertaccini, A. (2007) An oligonucleotide microarray-based assay for Identification of phytoplasma 16S ribosomal groups. Plant Pathology 56, 332-336.
37. Oshima, K., Kakizawa, S., Nishigawa, H., Jung, H.-Y., Wei, W., Suzuki, S., Arashida, R., Nakata, D., Miyata, S.-I., Ugaki, M. and Namba, S. (2004) Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nature Genetics 36, 27-29.
38. Schneider, B., Gibb, K.S. and Seemüller, E. (1997) Sequence and RFLP analysis of the elongation factor Tu gene used in differentiation and classifi cation of phytoplasmas. Microbiology 143, 3381-3389.
39. Shen, W.C. and Lin, C.P. (1993) Production of monoclonal antibodies against a mycoplasmalike organism associated with sweet potato witches' broom. Phytopathology 83, 671-675.
40. 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 sequence of the 16S-23S rRNA spacer region. Applied and Environmental Microbiology 62, 2988-2993.
41. Streten, C. and Gibb, K.S. (2003) Identification of genes in the tomato big bud phytoplasma and comparison to those in sweet potato little leaf-V4 phytoplasma. Microbiology 149, 1797-1805.
42. Streten, C. and Gibb, K.S. (2005) Genetic variation in 'Candidatus Phytoplasma australiense'. Plant Pathology 54, 8-14.
43. Tomlinson, J.A., Boonham, N., Hughes, K.J.D., Griffin, R.L. and Barker, I. (2005) Onsite DNA extraction and real-time PCR for detection of Phytophthora ramorum in the fi eld. Applied and Environmental Microbiology 71, 6702-6710.
44. Tomlinson, J.A., Barker, I. and Boonham, N. (2007) Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the fi eld. Applied and Environmental Microbiology 73, 4040-4047.
45. Toth, K.F., Harrison, N. and Sears, B.B. (1994) Phylogenetic relationships among members of the class Mollicutes deduced from rps3 gene sequences. International Journal of Systematic and Evolutionary Microbiology 44, 119-124.
46. 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 1: rp-A) and 'Ca. P. asteris' strains OY-M and AY-WB. Journal of Bacteriology 190, 3979-3991.
47. Wagner, M., Fingerhut, C., Gross, H.J. and Schön, A. (2001) The fi rst phytoplasma RNaseP RNA provides new insights into the sequence requirements of this ribozyme. Nucleic Acids Research 29, 2661-2665.
48. Wang, K. and Hiruki, C. (2005) Distinctions between phytoplasmas at the subgroup level detected by heteroduplex mobility assay. Plant Pathology 54, 625-633.
49. Wang, K., Hiruki, C. and Yeh, F. (2003) Molecular evolution of phytoplasmas based on polymorphisms in the 16S rRNA genes and the 16/23S spacer regions. Proceedings of the Japanese Academy Series B 79, 155-162.
50. Wei, W., Kakizawa, S., Suzuki, S., Jung, H.Y., Nishigawa, H., Miyata, S., Oshima, K., Ugaki, M., Hibi, T. and Namba, S. (2004) In planta dynamic analysis of onion yellows phytoplasma using localized inoculation by insect transmission. Phytopathology 94, 244-250.
51. Wei, W., Davis, R.E., Lee, I.-M. and Zhao, Y. (2007) Computer-simulated RFLP analysis of 16S rRNA genes: Identification of ten new phytoplasma groups. International Journal of Systematics and Evolutionary Microbiology 57, 1855-1867.
52. Wei, W., Lee, I.-M., Davis, R.E., Suo, X. and Zhao, Y. (2008) Automated RFLP pattern comparison and similarity coeffi cient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. International Journal of Systematic and Evolutionary Microbiology 58, 2368-2377.
53. Yu, Y.-L., Yeh, K.-W. and Lin, C.-P. (1998) An antigenic protein gene of a phytoplasma associated with sweet potato witches' broom. Microbiology 144, 1257-1262.