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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 7

The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation Open Access

Abstract

Within the 16SrII phytoplasma group, subgroups A–X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely ‘ Phytoplasma aurantifolia’ and ‘. Phytoplasma australasia’. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AAI , ANI , genus , Mollicutes , peanut witches’-broom group , phylogenomics , phytopathogen , species , species delimitation and subspecies
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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References

  1. Lee IM, Davis RE, Gundersen-Rindal DE. Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 2000; 54:221–255 [View Article] [PubMed]
     [Google Scholar]
  2. Hogenhout SA, Oshima K, Ammar E-D, Kakizawa S, Kingdom HN et al. Phytoplasmas: bacteria that manipulate plants and insects. Mol Plant Pathol 2008; 9:403–423 [View Article] [PubMed]
     [Google Scholar]
  3. Seemüller E, Marcone C, Lauer U, Ragozzino A, Göschl M. Current status of molecular classification of the Phytoplasmas. J Plant Pathol 1998; 80:3–26
     [Google Scholar]
  4. Bradbury JM. Minutes of the interim meeting, 12 and 18 July 1996, Orlando, Florida, U.S.A. Int J Syst Bacteriol 1997; 47:174–176 [View Article]
     [Google Scholar]
  5. Firrao G, Andersen M, Bertaccini A, Boudon E, Bové JM et al. “Candidatus Phytoplasma”, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int J Syst Evol Microbiol 2004; 54:1243–1255 [View Article] [PubMed]
     [Google Scholar]
  6. Bertaccini A, Arocha-Rosete Y, Contaldo N, Duduk B, Fiore N et al. Revision of the ‘Candidatus Phytoplasma’ species description guidelines. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  7. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article] [PubMed]
     [Google Scholar]
  8. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  9. Zhao Y, Wei W, Lee I-M, Shao J, Suo X et al. 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 2009; 59:2582–2593 [View Article] [PubMed]
     [Google Scholar]
  10. Kämpfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era–the polyphasic approach revisited. Environ Microbiol 2012; 14:291–317 [View Article] [PubMed]
     [Google Scholar]
  11. Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. ISME J 2021; 15:1879–1892 [View Article] [PubMed]
     [Google Scholar]
  12. Zhao Y, Wei W, Davis RE, Lee IM, Bottner-Parker KD. The agent associated with blue dwarf disease in wheat represents a new phytoplasma taxon, “Candidatus Phytoplasma tritici.”. Int J Syst Evol Microbiol 2021; 71:1–11 [View Article] [PubMed]
     [Google Scholar]
  13. Omar AF, Aljmhan KA, Alsohim AS, Pérez-López E. Potato purple top disease associated with the novel subgroup 16SrII-X phytoplasma. Int J Syst Evol Microbiol 2018; 68:3678–3682 [View Article] [PubMed]
     [Google Scholar]
  14. Zreik L, Carle P, Bové JM, Garnier M. Characterization of the mycoplasmalike organism associated with witches’-broom disease of lime and proposition of a Candidatus taxon for the organism, “‘Candidatus Phytoplasma aurantifolia.”. Int J Syst Bacteriol 1995; 45:449–453 [View Article] [PubMed]
     [Google Scholar]
  15. White DT, Billington SJ, Walsh KB, Scott PT. DNA sequence analysis supports the association of phytoplasmas with papaya (Carica papaya) dieback, yellow crinkle and mosaic. Austral Plant Pathol 1997; 26:28 [View Article]
     [Google Scholar]
  16. Gibb K, Padovan AC, Mogen BD. Studies on sweet potato little-leaf phytoplasma detected in sweet potato and other plant species growing in Northern Australia. Mol Plant Pathol 1996; 85:169 [View Article]
     [Google Scholar]
  17. Davis RI, Schneider B, Gibb KS. Detection and differentiation of phytoplasmas in Australia. Aust J Agric Res 1997; 48:535–544 [View Article]
     [Google Scholar]
  18. Schneider B, Padovan A, De La Rue S, Eichner R, Davis R et al. Detection and differentiation of phytoplasmas in Australia: an update. Aust J Agric Res 1999; 50:333–342 [View Article]
     [Google Scholar]
  19. Davis RI, Jacobson SC, Waldeck GJ, De La Rue SJ, Gibb KS. A witches’ broom of cocky apple (Planchonia careya) in north Queensland. Austral Plant Pathol 2001; 30:179 [View Article]
     [Google Scholar]
  20. Padovan AC, Gibb KS. Epidemiology of phytoplasma diseases in papaya in Northern Australia. J Phytopathol 2001; 149:649–658 [View Article]
     [Google Scholar]
  21. Streten C, Gibb KS. Phytoplasma diseases in sub-tropical and tropical Australia. Austral Plant Pathol 2006; 35:129–146 [View Article]
     [Google Scholar]
  22. Kumari S, Nagendran K, Rai AB, Singh B, Rao GP et al. Global status of phytoplasma diseases in vegetable crops. Front Microbiol 2019; 10: [View Article] [PubMed]
     [Google Scholar]
  23. Chaturvedi Y, Rao G, Tiwari A, Duduk B, Bertaccini A. Phytoplasma on ornamentals: detection, diversity and management. Acta Phytopathol Entomol Hungarica 2010; 45:31–69 [View Article]
     [Google Scholar]
  24. Hemmati C, Nikooei M, Al-Subhi AM, Al-Sadi AM. History and current status of phytoplasma diseases in the Middle East. Biology 2021; 10:226 [View Article] [PubMed]
     [Google Scholar]
  25. Trivellone V. An online global database of Hemiptera-Phytoplasma-Plant biological interactions. Biodivers Data J 2019; 7:e32910 [View Article] [PubMed]
     [Google Scholar]
  26. Yadav A, Thorat V, Bhale U, Shouche Y. Association of 16SrII-C and 16SrII-D subgroup phytoplasma strains with witches’ broom disease of Parthenium hysterophorus and insect vector Orosius albicinctus in India. Australasian Plant Dis Notes 2015; 10: [View Article]
     [Google Scholar]
  27. Alhudaib K, Arocha Y, Wilson M, Jones P. Molecular identification, potential vectors and alternative hosts of the phytoplasma associated with a lime decline disease in Saudi Arabia. Crop Protection 2009; 28:13–18 [View Article]
     [Google Scholar]
  28. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
     [Google Scholar]
  29. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and Archaea based on a standard genome relatedness index. MBio 2020; 11:1–20
     [Google Scholar]
  30. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  31. Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat Biotechnol 2020; 38:1079–1086 [View Article] [PubMed]
     [Google Scholar]
  32. Denancé N, Briand M, Gaborieau R, Gaillard S, Jacques M-A. Identification of genetic relationships and subspecies signatures in Xylella fastidiosa. BMC Genomics 2019; 20:239 [View Article] [PubMed]
     [Google Scholar]
  33. Al-Subhi AM, Hogenhout SA, Al-Yahyai RA, Al-Sadi AM. Detection, identification, and molecular characterization of the 16SrII-D phytoplasmas infecting vegetable and field crops in Oman. Plant Dis 2018; 102:576–588 [View Article] [PubMed]
     [Google Scholar]
  34. El-Sisi Y, Omar AF, Sidaros SA, Elsharkawy MM, Foissac X. Multilocus sequence analysis supports a low genetic diversity among ‘Candidatus Phytoplasma australasia’ related strains infecting vegetable crops and periwinkle in Egypt. Eur J Plant Pathol 2018; 150:779–784 [View Article]
     [Google Scholar]
  35. Chen Y-M, Chien Y-Y, Chen Y-K, Liao P-Q, Tan C-M et al. Identification of 16SrII-V phytoplasma associated with mungbean phyllody disease in Taiwan. Plant Dis 2021; 105:2290–2294 [View Article] [PubMed]
     [Google Scholar]
  36. Green MJ, Thompson DA, MacKenzie DJ. Easy and efficient DNA extraction from woody plants for the detection of phytoplasmas by polymerase chain reaction. Plant Dis 2007; 83:482–485 [View Article] [PubMed]
     [Google Scholar]
  37. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  38. Rodrigues Jardim B, Kinoti WM, Tran-Nguyen LTT, Gambley C, Rodoni B et al. 'Candidatus Phytoplasma stylosanthis’, a novel taxon with a diverse host range in Australia, characterised using multilocus sequence analysis of 16S rRNA, secA, tuf, and rp genes. Int J Syst Evol Microbiol 2021; 71:1–11 [View Article]
     [Google Scholar]
  39. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  40. Bertaccini A, Lee I-M. Phytoplasmas: an update. In Rao GP, Bertaccini A, Fiore N, Liefting LW. eds Phytoplasmas: Plant Pathogenic Bacteria - I Springer; 2018 pp 1–29
     [Google Scholar]
  41. Yang Y, Jiang L, Tian Q, Lu Y, Zhang X et al. Detection and identification of a novel subgroup 16SrII-V phytoplasma associated with Praxelis clematidea phyllody disease. Int J Syst Evol Microbiol 2017; 67:5290–5295 [View Article] [PubMed]
     [Google Scholar]
  42. Al-Subhi A, Hogenhout SA, Al-Yahyai RA, Al-Sadi AM. Classification of a new phytoplasmas subgroup 16SrII-W associated with Crotalaria witches’ broom diseases in Oman based on multigene sequence analysis. BMC Microbiol 2017; 17:221 [View Article] [PubMed]
     [Google Scholar]
  43. Cai H, Chen HR, Li F, Kong BH. First report of a phytoplasma associated with cactus witches-broom in Yunnan (China). Plant Pathol 2002; 51:394 [View Article]
     [Google Scholar]
  44. Rodrigues Jardim B, Tran-Nguyen LTT, Gambley C, Rodoni B, Constable FE. Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing. Front Microbiol 2022; 13:937648 [View Article] [PubMed]
     [Google Scholar]
  45. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
     [Google Scholar]
  46. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo assembler. Curr Protoc Bioinformatics 2020; 70:e102 [View Article] [PubMed]
     [Google Scholar]
  47. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res 2017; 27:824–834 [View Article] [PubMed]
     [Google Scholar]
  48. Mikheenko A, Saveliev V, Gurevich A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 2016; 32:1088–1090 [View Article] [PubMed]
     [Google Scholar]
  49. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  50. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  51. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  52. Bushnell B, Rood J, Singer E. BBMerge - Accurate paired shotgun read merging via overlap. PLoS One 2017; 12:e0185056 [View Article] [PubMed]
     [Google Scholar]
  53. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  54. Lefort V, Longueville J-E, Gascuel O. SMS: Smart Model Selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [View Article] [PubMed]
     [Google Scholar]
  55. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  56. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article] [PubMed]
     [Google Scholar]
  57. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  58. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. Corrigendum to: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
     [Google Scholar]
  59. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
     [Google Scholar]
  60. Chernomor O, von Haeseler A, Minh BQ. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol 2016; 65:997–1008 [View Article] [PubMed]
     [Google Scholar]
  61. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article] [PubMed]
     [Google Scholar]
  62. Lemoine F, Domelevo Entfellner J-B, Wilkinson E, Correia D, Dávila Felipe M et al. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature 2018; 556:452–456 [View Article] [PubMed]
     [Google Scholar]
  63. Cho S-T, Kung HJ, Huang W, Hogenhout SA, Kuo CH. Species boundaries and molecular markers for the classification of 16SrI phytoplasmas inferred by genome analysis. Front Microbiol 2020; 11:1531 [View Article] [PubMed]
     [Google Scholar]
  64. Cai H, Wei W, Davis RE, Chen H, Zhao Y. 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 2008; 58:1448–1457 [View Article] [PubMed]
     [Google Scholar]
  65. Cao Y, Trivellone V, Dietrich CH. A timetree for phytoplasmas (Mollicutes) with new insights on patterns of evolution and diversification. Mol Phylogenet Evol 2020; 149:106826 [View Article] [PubMed]
     [Google Scholar]
  66. Davis RI, Jacobson SC, Rue S, Tran-Nguyen L, Gunua TG et al. Phytoplasma disease surveys in the extreme north of Queensland, Australia, and the island of New Guinea. Austral Plant Pathol 2003; 32:269–277 [View Article]
     [Google Scholar]
  67. Music MS, Samarzija I, Hogenhout SA, Haryono M, Cho S-T et al. The genome of “Candidatus Phytoplasma solani” strain SA-1 is highly dynamic and prone to adopting foreign sequences. Syst Appl Microbiol 2019; 42:117–127 [View Article] [PubMed]
     [Google Scholar]
  68. Huang C-T, Cho S-T, Lin Y-C, Tan C-M, Chiu Y-C et al. Comparative genome analysis of “Candidatus phytoplasma luffae” reveals the influential roles of potential mobile units in phytoplasma evolution. Front Microbiol 2022; 13:773608 [View Article] [PubMed]
     [Google Scholar]
  69. Oshima K, Kakizawa S, Nishigawa H, Jung H-Y, Wei W et al. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 2004; 36:27–29 [View Article] [PubMed]
     [Google Scholar]
  70. Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J et al. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform 2018; 20:1140–1150 [View Article] [PubMed]
     [Google Scholar]
  71. Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 2015; 23:110–120 [View Article] [PubMed]
     [Google Scholar]
  72. Tan CM, Lin Y-C, Li J-R, Chien Y-Y, Wang C-J et al. Accelerating complete phytoplasma genome assembly by immunoprecipitation-based enrichment and MinION-based DNA sequencing for comparative analyses. Front Microbiol 2021; 12:766221 [View Article] [PubMed]
     [Google Scholar]
  73. Cho S-T, Zwolińska A, Huang W, Wouters RHM, Mugford ST et al. Complete genome sequence of “Candidatus phytoplasma asteris” RP166, a plant pathogen associated with rapeseed phyllody disease in Poland. Microbiol Resour Announc 2020; 9:e00760-20 [View Article] [PubMed]
     [Google Scholar]
  74. Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol 2022; 7:1702–1708 [View Article] [PubMed]
     [Google Scholar]
  75. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  76. Gosselin S, Fullmer MS, Feng Y, Gogarten JP. Improving phylogenies based on average nucleotide identity incorporating saturation correction and nonparametric bootstrap support. Syst Biol 2022; 71:396–409 [View Article]
     [Google Scholar]
  77. Al-Abadi SY, Al-Sadi AM, Dickinson M, Al-Hammadi MS, Al-Shariqi R et al. Population genetic analysis reveals a low level of genetic diversity of “Candidatus phytoplasma aurantifolia” causing witches’ broom disease in lime. Springerplus 2016; 5:1701 [View Article] [PubMed]
     [Google Scholar]
  78. Siampour M, Izadpanah K, Martini M, Salehi M. Multilocus sequence analysis of phytoplasma strains of 16SrII group in Iran and their comparison with related strains. Ann Appl Biol 2019; 175:83–97 [View Article]
     [Google Scholar]
  79. Schneider B, Gibb KS, Padovan A, Davis RI, De La Rue S. Comparison and characterization of tomato big bud- and sweet potato little leaf-group phytoplasmas. J Phytopathol 1999; 147:31–40 [View Article]
     [Google Scholar]
  80. Jeger M, Bragard C, Candresse T, Chatzivassiliou E et al. Pest categorisation of witches’ broom disease of lime (Citrus aurantifolia) phytoplasma. EFSA J 2017; 15:e05027 [View Article] [PubMed]
     [Google Scholar]
  81. Salehi M, Izadpanah K, Siampour M, Bagheri A, Faghihi SM. Transmission of “Candidatus phytoplasma aurantifolia” to bakraee (Citrus reticulata hybrid) by feral Hishimonus phycitis leafhoppers in Iran. Plant Dis 2007; 91:466 [View Article] [PubMed]
     [Google Scholar]
  82. Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007; 45:2761–2764 [View Article] [PubMed]
     [Google Scholar]
  83. Palmer M, Steenkamp ET, Coetzee MPA, Chan W-Y, van Zyl E et al. Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie van Leeuwenhoek 2017; 110:1287–1309 [View Article] [PubMed]
     [Google Scholar]
  84. Maayer PD, Aliyu H, Cowan DA. Reorganising the order Bacillales through phylogenomics. Syst Appl Microbiol 2019; 42:178–189 [View Article] [PubMed]
     [Google Scholar]
  85. Chang S-H, Cho S-T, Chen C-L, Yang J-Y, Kuo C-H. Draft genome sequence of A 16SrII-a subgroup phytoplasma associated with purple coneflower (Echinacea purpurea) witches’ broom disease in Taiwan. Genome Announc 2015; 3:e01398-15 [View Article] [PubMed]
     [Google Scholar]
  86. Gundersen DE, Lee IM, Rehner SA, Davis RE, Kingsbury DT. Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification. J Bacteriol 1994; 176:5244–5254 [View Article] [PubMed]
     [Google Scholar]
  87. Wei W, Zhao Y. Phytoplasma taxonomy: nomenclature, classification, and identification. Biology 2022; 11:1119 [View Article] [PubMed]
     [Google Scholar]
  88. Parker CT, Tindall BJ, Garrity GM. International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article] [PubMed]
     [Google Scholar]
  89. Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956–4042 [View Article] [PubMed]
     [Google Scholar]
  90. Malembic-Maher S, Desqué D, Khalil D, Salar P, Bergey B et al. When a palearctic bacterium meets a nearctic insect vector: genetic and ecological insights into the emergence of the grapevine Flavescence dorée epidemics in Europe. PLoS Pathog 2020; 16:e1007967 [View Article] [PubMed]
     [Google Scholar]
  91. Hemmati C, Nikooei M, Bertaccini A. Identification and transmission of phytoplasmas and their impact on essential oil composition in Aerva javanica. 3 Biotech 2019; 9:310 [View Article] [PubMed]
     [Google Scholar]
  92. Bagheri A, Faghihi MM, Khankahdani HH, Seyahooei MA, Ghanbari N et al. First report of a phytoplasma associated with sapodilla flattened stem disease in Iran. Australasian Plant Dis Notes 2017; 12:16–18 [View Article]
     [Google Scholar]
  93. Noorizadeh S, Golmohammadi M, Bagheri A, Bertaccini A. Citrus industry: phytoplasma-associated diseases and related challenges for Asia, America and Africa. Crop Protection 2022; 151:105822 [View Article]
     [Google Scholar]
  94. Oren A. A plea for linguistic accuracy - also for Candidatus taxa. Int J Syst Evol Microbiol 2017; 67:1085–1094 [View Article] [PubMed]
     [Google Scholar]
  95. Pilkington LJ, Gurr GM, Fletcher MJ, Nikandrow A, Elliott E. Vector status of three leafhopper species for Australian lucerne yellows phytoplasma. Aust J Entomol 2004; 43:366–373 [View Article]
     [Google Scholar]
  96. Salehi M, Rasoulpour R, Izadpanah K. Molecular characterization, vector identification and partial host range determination of phytoplasmas associated with faba bean phyllody in Iran. Crop Protection 2016; 89:12–20 [View Article]
     [Google Scholar]
  97. Özdemir Z. Phytoplasmas of sesame and Orosius orientalis are genetically diverse based on 16S rDNA sequencing and PCR-RFLP in Turkey. Arch Phytopathol Plant Prot 2017; 50:674–686 [View Article]
     [Google Scholar]
  98. Özdemir Z. Identification of phytoplasmas from Neoaliturus haematoceps associated with sesame phyllody disease in southwestern Turkey. J Phytopathol 2018; 166:242–248 [View Article]
     [Google Scholar]
  99. Aslam M, Tanwir S, Akhtar ZR, Ahmad JN. First report of 16Srii-D phyllody phytoplasma and associated insect vectors infecting multi-flower inbred lines of sunflower (Helianthus Annuus L.) in Faisalabad, Pakistan. Pakistan J Agric Sci 2021; 58:985–992
     [Google Scholar]
  100. Cai H, Chen HR, Kong BH, Yang GH, Liu T. First report of a phytoplasma associated with Christmas cactus witches' broom. Plant Pathology 2007; 56:346 [View Article]
     [Google Scholar]
  101. Salehi M, Esmailzadeh Hosseini SA, Salehi E, Bertaccini A. Molecular and biological characterization of a 16Srii phytoplasma associated with carrot witches’ broom in Iran. J Plant Pathol 2016; 98:83–90 [View Article]
     [Google Scholar]
  102. Marzachì C, Coulibaly A, Coulibaly N, Sangaré A, Diarra M et al. Cotton virescence phytoplasma and its weed reservoir in Mali. J Plant Pathol 2009; 91:717–721
     [Google Scholar]
  103. Martini M, Lee I-M, Bottner KD, Zhao Y, Botti S et al. Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. Int J Syst Evol Microbiol 2007; 57:2037–2051 [View Article] [PubMed]
     [Google Scholar]
  104. Khan AJ, Botti S, Al-Subhi AM, Gundersen-Rindal DE, Bertaccini AF. Molecular identification of a new phytoplasma associated with alfalfa witches’-broom in oman. Phytopathology 2002; 92:1038–1047 [View Article] [PubMed]
     [Google Scholar]
  105. Bertaccini A. Plants and phytoplasmas: when bacteria modify plants. Plants 2022; 11:1425 [View Article] [PubMed]
     [Google Scholar]
  106. Ghazanfar SA. Flora of the Sultanate of Oman. In Scripta Botanica Belgica 2007
     [Google Scholar]
  107. Schneider B, Padovan A, De La Rue S, Eichner R, Davis R et al. Detection and differentiation of phytoplasmas in Australia. Aust J Agric Res 1999; 50:333 [View Article]
     [Google Scholar]
  108. Myint T, Ward DB. A taxonomic revision of the genus Bonamia (Convulvulaceae). Phytologia 1968; 17:121–239
     [Google Scholar]
  109. Barrett RL. A review of Planchonia (Lecythidaceae) in Australia. Aust Syst Bot 2006; 19:147–153 [View Article]
     [Google Scholar]
  110. Wilson D, Blanche KR, Gibb KS. Phytoplasmas and disease symptoms of crops and weeds in the semi-arid tropics of the Northern Territory, Australia. Austral Plant Pathol 2001; 30:159 [View Article]
     [Google Scholar]
  111. De La Rue S, Padovan A, Gibb K. Stylosanthes is a host for several phytoplasmas, one of which shows unique 16S-23S intergenic spacer region heterogeneity. J Phytopathol 2001; 149:613–619 [View Article]
     [Google Scholar]
  112. De La Rue SJ, Hopkinson R, Foster S, Gibb KS. Phytoplasma host range and symptom expression in the pasture legume Stylosanthes. F Crop Res 2003; 84:327–334 [View Article]
     [Google Scholar]
  113. Wei W, Davis RE, Lee I-M, Zhao Y. Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 2007; 57:1855–1867 [View Article] [PubMed]
     [Google Scholar]
  114. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  115. Zhao Y, Davis RE, Wei W, Lee I-M. Should “Candidatus phytoplasma” be retained within the order Acholeplasmatales?. Int J Syst Evol Microbiol 2015; 65:1075–1082 [View Article] [PubMed]
     [Google Scholar]
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The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation
Int J Syst Evol Microbiol 73, 005977 (2023); https://doi.org/10.1099/ijsem.0.005977
/content/journal/ijsem/10.1099/ijsem.0.005977
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