Multigene characterization of a new ‘Candidatus Phytoplasma rubi’-related strain associated with blackberry witches’ broom

References

1. Angelini E., Clair D., Borgo M., Bertaccini A., Boudon-Padieu E. 2001; Flavescence dorée in France and Italy – Occurrence of closely related phytoplasma strains and their near relationships to Palatinate grapevine yellows and an alder yellows phytoplasma. Vitis 40:79–86
   [Google Scholar]
2. Arnaud G., Malembic-Maher S., Salar P., Bonnet P., Maixner M., Marcone C., Boudon-Padieu E., Foissac X. 2007; Multilocus sequence typing confirms the close genetic interrelatedness of three distinct flavescence dorée phytoplasma strain clusters and group 16SrV phytoplasmas infecting grapevine and alder in Europe. Appl Environ Microbiol 73:4001–4010 [View Article][PubMed]
   [Google Scholar]
3. Bertaccini A. 2014; Phytoplasma collection. http://www.ipwgnet.org/. Accessed 10 August 2015.
4. Bertaccini A., Duduk B., Paltrinieri S., Contaldo N. 2014; Phytoplasmas and phytoplasma diseases: a severe threat to agriculture. Am J Plant Sci 5:1763–1788 [View Article]
   [Google Scholar]
5. Borroto Fernández E. G., Calari A., Hanzer V., Katinger H., Bertaccini A., Laimer M. 2007; Phytoplasma infected plants in Austrian forests: role as a reservoir?. Bull Insectol 60:391–392
   [Google Scholar]
6. Cieslinska M. 2011; Detection and characterization of phytoplasmas associated with diseases of Rubus spp. in Poland. J Plant Pathol 93:51–56
   [Google Scholar]
7. Davis R. E., Dally E. L. 2001; Revised subgroup classification of group 16SrV phytoplasmas and placement of flavescence dorée-associated phytoplasmas in two distinct subgroups. Plant Dis 85:790–797 [View Article]
   [Google Scholar]
8. Davis R. E., Dally E. L., Converse R. H. 2001; Molecular identification of a phytoplasma associated with witches’ broom disease of black raspberry in Oregon and its classification in group 16SrIII, new subgroup Q. Plant Dis 85:1121 [View Article]
   [Google Scholar]
9. Deng S., Hiruki C. 1991; Amplification of 16S rRNA genes from culturable and non-culturable mollicutes. J Microbiol Methods 14:53–61 [View Article]
   [Google Scholar]
10. Ermacora P., Carraro L., Martini M., Ferrini F., Loi N. 2003; Presence of Rubus stunt in blackberry in northeastern Italy. J Plant Pathol 85:306
    [Google Scholar]
11. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
12. Fránová J., Prˇibylová J., Koloniuk I., Podrábská K., Špak J. 2015; Multigene sequence analysis of aster yellows phytoplasma associated with primrose yellows. J Phytopathol (in press) [View Article]
    [Google Scholar]
13. 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
    [Google Scholar]
14. Gundersen D. E., Lee I.-M., Schaff D. A., Harrison N. A., Chang C. J., Davis R. E., Kinsbury D. T. 1996; Genomic diversity and differentiation among phytoplasma strains in 16S rRNA group I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int J Syst Bacteriol 46:64–75 [View Article][PubMed]
    [Google Scholar]
15. 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 [View Article][PubMed]
    [Google Scholar]
16. Jung H. Y., Sawayanagi T., Kakizawa S., Nishigawa H., Wei W., Oshima K., Miyata S., Ugaki M., Hibi T., Namba S. 2003; ‘Candidatus phytoplasma ziziphi’, a novel phytoplasma taxon associated with jujube witches’-broom disease. Int J Syst Evol Microbiol 53:1037–1041 [View Article][PubMed]
    [Google Scholar]
17. Lai F., Song C. S., Ren Z. G., Lin C. L., Xu Q. C., Li Y., Piao C. G., Yu S. S., Guo M. W., Tian G. Z. 2014; Molecular characterization of a new member of the 16SrV group of phytoplasma associated with Bischofia polycarpa (Levl.) Airy Shaw witches’ broom disease in China by a multiple gene-based analysis. Australas Plant Path 43:557–569 [View Article]
    [Google Scholar]
18. Lee I.-M., Gundersen D. E., Hammond R. W., Davis R. E. 1994; Use of mycoplasmalike organism (MLO) group-specific oligonucleotide primers for nested-PCR assays to detect mixed-MLO infections in a single host plant. Phytopathology 84:559–566 [View Article]
    [Google Scholar]
19. Lee I.-M., Bertaccini A., Vibio M., Gundersen D. E. 1995; Detection of multiple phytoplasmas in perennial fruit trees with decline symptoms in Italy. Phytopathology 85:728–735 [View Article]
    [Google Scholar]
20. Lee I.-M., Gundersen-Rindal D. E., Davis R. E., 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 [View Article]
    [Google Scholar]
21. Lee I.-M., Davis R. E., Gundersen-Rindal D. E. 2000; Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 54:221–255 [View Article][PubMed]
    [Google Scholar]
22. Lee I.-M., Gundersen-Rindal D. E., Davis R. E., Bottner K. D., Marcone C., Seemüller E. 2004; ‘Candidatus Phytoplasma asteris’, a novel phytoplasma taxon associated with aster yellows and related diseases. Int J Syst Evol Microbiol 54:1037–1048 [View Article][PubMed]
    [Google Scholar]
23. Lee I.-M., Martini M., Marcone 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 [View Article][PubMed]
    [Google Scholar]
24. Lee I.-M., Bottner-Parker K. D., Zhao Y., Davis R. E., Harrison N. A. 2010; Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences. Int J Syst Evol Microbiol 60:2887–2897 [View Article][PubMed]
    [Google Scholar]
25. Li Z. N., Song J. G., Zhang C. P., Yu X. Q., Wu K. K., Wu W. J., Wu Y. F., Xiang Y. 2010; Berberis phyllody is a phytoplasma-associated disease. Phytoparasitica 38:99–102 [View Article]
    [Google Scholar]
26. Li Z. N., Zhang L., Man J.-Y., Wu Y.-F. 2012; Detection and identification of elm yellows group phytoplasma (16SrV) associated with alfalfa witches’ broom disease. J Phytopathol 160:311–313 [View Article]
    [Google Scholar]
27. Lorenz K.-H., Schneider B., Ahrens U., Seemüller E. 1995; Detection of the apple proliferation and pear decline phytoplasmas by PCR amplification of ribosomal and nonribosomal DNA. Phytopathology 85:771–776 [View Article]
    [Google Scholar]
28. Malembic-Maher S., Salar P., Filippin L., Carle P., Angelini E., Foissac X. 2011; Genetic diversity of European phytoplasmas of the 16SrV taxonomic group and proposal of ‘Candidatus Phytoplasma rubi’. Int J Syst Evol Microbiol 61:2129–2134 [View Article][PubMed]
    [Google Scholar]
29. Martini M., Murari E., Mori N., Bertaccini A. 1999; Identification and epidemic distribution of two Flavescence dorée-related phytoplasmas in Veneto (Italy). Plant Dis 83:925–930 [View Article]
    [Google Scholar]
30. Martini M., Lee I.-M., Bottner K. D., Zhao Y., Botti S., Bertaccini A., Harrison N. A., Carraro L., Marcone C., other authors. 2007; Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. Int J Syst Evol Microbiol 57:2037–2051 [View Article][PubMed]
    [Google Scholar]
31. Min H., Li Z. N., Wu Y. F., Hu S. B., Zhang C. P., Wu K. K. 2009; Phytoplasma associated with a witches’ broom disease of Gleditsia sinensis (Fabaceae) newly reported in China. Plant Pathol 58:790 [View Article]
    [Google Scholar]
32. Padovan A. C., Gibb K. S., Bertaccini A., Vibio M., Bonfiglioli R. E., Magarey P. A., Sears B. B. 1995; Molecular detection of the Australian grapevine yellows phytoplasmas and comparison with grapevine yellows phytoplasmas from Italy. Aust J Grape Wine Res 1:25–31 [View Article]
    [Google Scholar]
33. Parente A. M., Abreu I., Salema R. 1999; Immunodetection of phytoplasmas in wild blackberry in northern Portugal. Z Pflkrankh Pflschutz 106:618–623
    [Google Scholar]
34. Prince J. P., Davis R. E., Wolf T. K., Lee I.-M., Mogen B. D., Dally E. L., Bertaccini A., Credi R., Barba M. 1993; Molecular detection of diverse mycoplasmalike organisms (MLOs) associated with grapevine yellows and their classi-fication with aster yellows, X-disease, and elm yellows MLOs. Phytopathology 83:1130–1137 [View Article]
    [Google Scholar]
35. Ramkat R., Ruinelli M., Maghuly F., Schoder L., Laimer M. 2014; Identification of phytoplasmas associated with Rubus spp. as prerequisite for their successful elimination. In Phytoplasmas and Phytoplasma Disease Management: How to Reduce Their Economic Impact pp 159–166Edited by Bertaccini A. Bologna, Italy: COSToffice;
    [Google Scholar]
36. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
37. Schaff D., Lee I.-M., Davis R. E. 1992; Sensitive detection and identification of mycoplasma-like organisms in plants by polymerase chain reactions. Biochem Biophys Res Commun 186:1503–1509 [View Article][PubMed]
    [Google Scholar]
38. Schneider B., Seemüller E., Smart C. D., Kirkpatrick B. C. 1995; Phylogenetic classification of plant pathogenic mycoplasmalike organisms or phytoplasmas. In Molecular and Diagnostic Procedures in Mycoplasmology pp 369–380Edited by Razin S., Tully J. G. New York: Academic Press; [CrossRef]
    [Google Scholar]
39. Sertkaya G., Osler R., Musetti R., Ermacora P., Martini M. 2004; Detection of phytoplasmas in Rubus spp. by microscopy and molecular techniques in Turkey. Acta Hortic 656:181–186 [View Article]
    [Google Scholar]
40. Tamura K., Nei M., Kumar S. 2004; Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035 [View Article][PubMed]
    [Google Scholar]
41. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013 mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
42. Valiunas D., Jomantiene R., Davis R. E. 2007; Phytoplasmas detected in cultivated fruit plants in Lithuania. Bull Insectol 60:139–140
    [Google Scholar]
43. Win N. K., Lee S. Y., Bertaccini A., Namba S., Jung H. Y. 2013; ‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora . Int J Syst Evol Microbiol 63:636–640 [View Article][PubMed]
    [Google Scholar]
44. Yue H. N., Sun R. H., Wei T., Wu Y. F. 2009; First report of a 16SrV-B group phytoplasma associated with a leafroll-type disease of apricots in northern China. J Plant Pathol 91:500
    [Google Scholar]
45. Zhao Y., Wei W., Lee I.-M., Shao J., Suo X., Davis R. E. 2009; Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). Int J Syst Evol Microbiol 59:2582–2593 [View Article][PubMed]
    [Google Scholar]