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Phytoplasma Taxonomy
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Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. 

phytoplasma bacterial taxonomy whole genome-based average nucleotide identity (ANI) iPhyClassifier
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Subjects: Microbiology; Pathology
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Revisions: 6 times (View History)
Update Date: 01 Sep 2022
Table of Contents

    1. Phytoplasma Nomenclature: Delineation of Candidatus Phytoplasma Species

    Traditional polyphasic approach, which integrates phenotypic and genotypic data and reflects the ecological nature of the bacteria, is considered as the gold standard for bacterial taxonomy [1]. The phenotypic markers mainly include morphological, physiological, and biochemical characteristics of cultivatable bacteria [2]; however, inability to culture phytoplasma in vitro impeded the accessibility of the above-mentioned phenotypic characteristics to differentiate phytoplasmas. Several decades ago, scientists attempted to distinguish phytoplasmas by using symptoms induced by phytoplasmas, plant host range, insect vector specificity and serological correlations as markers, but were ultimately unsuccessful due to lack of consistency [3][4][5][6][7]. The subsequent development of culture-independent modern genotypic approach based on heredity information has rapidly and considerably enhanced the entire bacterial systematics, providing high levels of resolution and differentiation. In particular, the advent of DNA sequencing technology and exploitation of 16S rRNA gene sequences have tremendously facilitated taxonomy, tree of life, evolution, and diversity studies of unculturable bacteria [8][9][10]. Based on 16S rRNA gene sequences, many bacteria have been reclassified and renamed [11][12].
    As with many other unculturable bacteria, the higher rank taxa of phytoplasmas (Mycoplasmatota [originally named Tenericutes]/Mollicutes/Acholeplasmatales/incertae sedis—Family II) were named in the absence of type genus and species [13][14][15]. While the Candidatus status was used to reserve the putative lower rank taxa (Genus and Species [16]). The term Candidatus was first introduced in 1994 to nonculturable bacteria, granting appropriate status of potential taxa based on 16S rRNA gene sequences ([16]; Figure 1). Candidatus is not a rank, nor is it governed by Prokaryotic Code [17]. Currently, all phytoplasma strains are accommodated within the provisional Candidatus Phytoplasma genus. The main function of the phytoplasma taxonomic nomenclature system is naming ‘Candidatus Phytoplasma’ species as species is the most basic taxon of bacteria [18].

    2. Phytoplasma Classification: 16Sr Group/Subgroup Classification System Based on Collective RFLP Profiles

    Classification is the systematic and orderly arrangement of organisms into groups or categories according to established criteria. Different from taxonomic nomenclature system, a classification scheme is often designed to meet practical needs, emphasizing less academic significance. Therefore, different scientists may classify the same organism differently [37]. Phytoplasma classification also has followed this principle. Phenotypic approaches such as symptomology, vectorship, and serology were employed to classify phytoplasmas in early days, but this has proved not suitable or practical [38][39] as in many cases the same phytoplasma strain may induce different symptoms in different hosts, and different phytoplasma strains may share a common vector or cause diseases exhibiting similar symptoms [40]. Until the 1990s, the 16Sr group/subgroup classification scheme was established based on RFLP profiles of PCR amplified F2nR2 fragment of the 16S rRNA gene [11][26][41][42]. This classification system is most widely adopted by phytoplasma researchers so far [43][44][45][46].
    The RFLP-based phytoplasma classification scheme exploits a high-resolution subset of the 16S rRNA gene characteristics, namely, the recognition sites of 17 restriction enzymes, to differentiate diverse phytoplasmas [26][40]. The 16Sr groups delineated with this RFLP classification scheme are consistent with the 16S rRNA gene phylogenetic clades. More advantageously, by distinguishing subtle pattern differences, this RFLP analysis-based scheme is able to identify and distinguish different subgroup lineages within any given group [27][41][47][48]. Operationally, traditional RFLP analysis requires actual enzymatic gel electrophoresis and visual comparisons of various banded patterns. It is inconvenient, and few people are willing to do that anymore. The current virtual RFLP analysis approach is operated based on DNA sequences but retains the principles and criteria of the original phytoplasma classification scheme. Using accurate sequence data, the virtual gel patterns generated by computer simulated RFLP analysis can faithfully duplicate the classical and authoritative patterns established by conventional RFLP analysis. The new pattern types derived from virtual RFLP analysis have also been confirmed by actual enzymatic gel electrophoresis [47]. Furthermore, based on the virtual RFLP analysis approach, the interactive online tool iPhyClassifier was constructed, enabling and facilitating database-guided phytoplasma classification and identification [27].
    Some scientists might think that the RFLP approach is obsolete. The truth is RFLP analysis still plays an important role in the classification and differentiation of many unculturable and fastidious bacteria, and fungi [49][50][51]. Examples include classifications of genus Basidiobolus [50] and genus Vibrio [51]. In the past five years (2017 to present), around 15,000 papers have been published on the classification and differentiation of bacteria and fungi based on RFLP analysis, including nearly 1600 articles on phytoplasma classification and identification. Computer-simulated virtual RFLP analysis undoubtedly enhanced the applicability of the RFLP analysis-based classification.
    Importantly, the 16Sr group/subgroup classification system complements ‘Candidatus Phytoplasma’ species affiliation assignment. A striking example is the aster yellows (AY) phytoplasma group, which contains hundreds of known strains around the globe. The current taxonomic system assigns all the AY strains as ‘Ca. Phytoplasma asteris’-related strains, which grossly masks the differences among the strains. On the other hand, the existing 16Sr group classification scheme can differentiate the AY strains into more than two dozen subgroups, each of which has its own unique RFLP profile. In addition, some subgroups are only (or predominantly) present in certain geological regions and associated with different ecological niches [46][51].
    In addition, in certain cases, the current phytoplasma taxonomic system may even have difficulty to assign certain strains to the existing ‘Ca. Phytoplasma’ species. For example, a strain (KJ452548) in the elm yellows phytoplasma group shares 99.1–99.3% identities with ‘Ca. Phytoplasma ulmi’- and ‘Ca. Phytoplasma ziziphi’-related strains in their 16S rRNA gene sequences. So, what species should this strain be affiliated with, ‘Ca. Phytoplasma ulmi’ or ‘Ca. Phytoplasma ziziphi’? Well, the RFLP-based group/subgroup classification system can at least provide distinguishing RFLP markers to separate them and classify the strain into a new subgroup other than 16SrV-A and 16SrV-B. This example strongly demonstrates that the group/subgroup classification system effectively avoids the ambiguity caused by the term, ‘Candidatus Phytoplasma sp.’-related strain, and helps diagnosticians and regulatory agencies distinguish closely-related phytoplasma strains.
    In 2007, based on the virtual RFLP analysis of all 16S rRNA gene sequences available at the time (F2nR2 fragment of about 1250 bp), the number of phytoplasma classification groups was expanded from 19 to 28 (16SrXIX-16SrXXVIII), and some potentially new species were proposed with suggested reference strains (Table 1). In the present research, groups/subgroups corresponding to Candidatus Phytoplasma species, especially the newly named species are updated (Table 1 [52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78][79][80][81][82][83][84][85][86][87][88][89][90]). Two new groups (16SrXXXVIII and 16SrXXXIX) are established based on the criterium which requires the collective F2nR2 RFLP pattern of any new group representative has a similarity coefficient of <0.85 with that of all previously recognized 16Sr groups [47]. The reference strains of ‘Ca. Phytoplasma noviguineense’ and ‘Ca. Phytoplasma dypsidis’ were designated as representative strain of 16SrXXXVIII-A (LC228755) and 16SrXXXIX-A (MT536195), respectively.
    Currently, there are a total of 37 groups and 48 named Candidates phytoplasma species (Table 1). Each group should contain at least one Candidatus species [93]. As shown in Table 1, nearly ten novel groups have been identified since 2007 (16SrXXIX-16SrXXXIX). However, it is noteworthy that no new phytoplasmas have been identified in groups 16SrXXIII-16SrXXVIII during the past 15 years. This suggests that the phytoplasmas belonging to these groups may be rare or the sequences representing these groups contain errors. In addition, the researchers also noted that several pairs of strains share high sequence identity, but very low RFLP similarity coefficients. Such discrepancy might be caused by indels or sequencing errors that occurred within restriction enzyme recognition sites.

    3. Phytoplasma Identification: Detection, Diagnostics and Characterization

    The early identification and diagnosis of phytoplasmas and phytoplasmal diseases are vital for the formulation and implementation of rapid control measures. This not only thwarts the further spread of disease and reduce direct economic losses from plant death/damage, but also prevents delays and restrictions on the import and export of plant materials. Plants infected by phytoplasmas often exhibit remarkable symptoms. These symptoms include virescence (flower petals turning green), phyllody (leafy flowers), cauliflower-like inflorescence (repetitive initiation of inflorescence meristems), and witches’-broom (excessive shoot proliferation) [94][95]. In addition to these characteristic symptoms, phytoplasma infection can also induce some general symptoms seen in diseases caused by various other plant pathogens. Such general symptoms include leaf discoloration (such as purple leaves and leaf yellowing), little leaf, stem fasciation, and stunting [94][95][96]. Furthermore, asymptomatic phytoplasma infections were reported as well [97].
    As phytoplasmas cannot be cultured in vitro, the routine culture-dependent metrics and characteristics for bacterial identification (morphological observation, biochemical assay, serotyping and antibiotic inhibition/resistance pattern assessment) cannot be employed. Phytoplasma detection and characterization heavily rely on the molecular diagnostic techniques. With the rapid development of molecular diagnostic techniques, a variety of fast, sensitive, and cost effective phytoplasma detection methods have emerged, ranging from PCR, nested PCR, real time PCR, droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) to CRISPR-based detection methods. These methods are devised based on highly conserved gene sequences of phytoplasmas, namely 16S rRNA gene, rp gene, SecY gene and tuf gene, etc. [26][98][99][100][101][102][103][104].
    Currently, the most widely adopted procedure for the phytoplasma identification and further classification includes the following steps: (i) PCR or nested PCR amplification of phytoplasma DNA using universal primers of 16S rRNA gene, for example, P1, P7, P1A, P7A, 16S-SR, 16RF2n, and R16R2 [56][99][105][106]; (ii) Sequencing of PCR amplicons (direct sequencing or sequencing after amplicon cloning); and (iii) Sequence analysis using iPhyClassifier, classifying the phytoplasma strain under study to existing 16Sr group/subgroup and assigning (relating) the strain to previously named Candidatus Phytoplasma species. Results from the last step also offer opportunities for establishing new groups/subgroups and discovering novel Candidatus Phytoplasma species.
    MLSA-based classification schemes have been established in many bacteria, but not yet implemented in non-culturable phytoplasmas. However, this does not affect MLSA as a very effective method for phytoplasma diversity studies and fine differentiation of closely related phytoplasmas. For example, MLSA-based approach revealed the genetic diversity of apple proliferation phytoplasmas [107]; in addition, 16S rRNA, rp, and secY genes based MLSA characterization also indicated azalea little leaf phytoplasmas represented a distinct lineage within 16SrI group [108].

    References

    1. Kämpfer, P.; Glaeser, S.P. Prokaryotic taxonomy in the sequencing era–the polyphasic approach revisited. Environ. Microbiol. 2012, 14, 291–317.
    2. Rosselló-Mora, R.; Amann, R. The species concept for prokaryotes. FEMS Microbiol. Rev. 2001, 25, 39–67.
    3. Chiykowski, L.N. Clover phyllody virus in Canada and its transmission. Can. J. Bot. 1962, 40, 397–404.
    4. Freitag, J.H. Interaction and mutual suppression among three strains of aster yellows virus. Virology 1964, 24, 401–413.
    5. Granados, R.R.; Chapman, R.K. Identification of some new aster yellows virus strains and their transmission by aster leafhopper Macrosteles fascifrons. Phytopathology 1968, 58, 1685.
    6. Chiykowski, L.N.; Sinha, R.C. Differentiation of MLO diseases by means of symptomatology and vector transmission. In Recent advances in mycoplasmology. In Proceedings of the 7th congress of the International Organization for Mycoplasmology, Baden near Vienna, Austria, 2–9 June 1988; Gustav Fischer Verlag: Baden near Vienna, Austria, 1990; pp. 280–287.
    7. McCoy, R.E.; Caudwell, A.; Chang, C.G.; Chen, T.A.; Chiykowski, L.N.; Cousin, M.T.; De Leeuw, G.D.; Golino, D.A.; Hacke, K.J.; Kirkpatrick, B.C.; et al. Mycoplasmalike organisms. Mycoplasmas 1989, 5, 545–568.
    8. Stackebrandt, E.; GOEBEL, B.M. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 1994, 44, 846–849.
    9. Stephen, J.R.; McCaig, A.E.; Smith, Z.; Prosser, J.I.; Embley, T.M. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 1996, 62, 4147–4154.
    10. Drancourt, M.; Bollet, C.; Carlioz, A.; Martelin, R.; Gayral, J.P.; Raoult, D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 2000, 38, 3623–3630.
    11. Moore, E.R.; Krüger, A.S.; Hauben, L.; Seal, S.E.; De Baere, R.; De Wachter, R.; Timmis, K.N.; Swings, J. 16S rRNA gene sequence analyses and inter-and intrageneric relationships of Xanthomonas species and Stenotrophomonas maltophilia. FEMS Microbiol. Lett. 1997, 151, 145–153.
    12. Woo, P.C.; Lau, S.K.; Teng, J.L.; Tse, H.; Yuen, K.Y. Then and now: Use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin. Microbiol. Infect. 2008, 14, 908–934.
    13. Oren, A.; Garrity, G.M. Valid publication of the names of forty-two phyla of prokaryotes. Int. J. Syst. Evol. Microbiol. 2021, 71, 005056.
    14. Murray, R.G.E.; Sneath, P.H.A.; Mair, N.S.; Sharpe, M.E. Kingdom Procaryotae. Bergey’s Man. Syst. Bacteriol. 1984, 1, 34–36.
    15. Gasparich, G.E.; Bertaccini, A.; Zhao, Y. Candidatus Phytoplasma. In Bergey’s Manual of Systematics of Archaea and Bacteria; Trujillo, M.E., Dedysh, S., DeVos, P., Hedlund, B., Kämpfer, P., Rainey, F.A., Whitman, W.B., Eds.; John Wiley & Sons, Inc.: Hoboken, NJ, USA, 2020.
    16. Murray, R.G.E.; Schleifer, K.H. Taxonomic notes: A proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Evol. Microbiol. 1994, 44, 174–176.
    17. Oren, A. A plea for linguistic accuracy–also for Candidatus taxa. Int. J. Syst. Evol. Microbiol. 2017, 67, 1085–1094.
    18. IRPCM Phytoplasma/Spiroplasma Working Team–Phytoplasma Taxonomy Group. ‘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.
    19. Severin, H.H. Infection of perennial delphiniums by California-aster-yellows virus. Hilgardia 1942, 14, 411–440.
    20. Black, L.M. Transmission of plant viruses by cicadellids. In Advances in Virus Research; Academic Press: Cambridge, MA, USA, 1953; Volume 1, pp. 69–89.
    21. Doi, Y.; Teranaka, M.; Yora, K.; Asuyama, H. 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. 1967, 33, 259–266.
    22. Lim, P.O.; Sears, B.B. 16S rRNA sequence indicates that plant-pathogenic mycoplasmalike organisms are evolutionarily distinct from animal mycoplasmas. J. Bacteriol. 1989, 171, 5901–5906.
    23. International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Mollicutes. Minutes of the Interim Meetings, 1 and 2 August, 1992, Ames, Iowa. Int. J. Syst. Bacteriol. 1993, 43, 394–397.
    24. Oshima, K.; Kakizawa, S.; Nishigawa, H.; Jung, H.Y.; Wei, W.; Suzuki, S.; Arashida, R.; Nakata, D.; Miyata, S.; Ugaki, M.; et al. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat. Genet. 2004, 36, 27–29.
    25. Kirkpatrick, B.C.; Stenger, D.C.; Morris, T.J.; Purcell, A.H. Cloning and detection of DNA from a nonculturable plant pathogenic mycoplasma-like organism. Science 1987, 238, 197–200.
    26. Lee, I.M.; Bertaccini, A.; Vibio, M.; Gundersen, D.E. Detection of multiple phytoplasmas in perennial fruit trees with decline symptoms in Italy. Phytopathology 1995, 85, 728–735.
    27. Zhao, Y.; Wei, W.; Lee, M.; Shao, J.; Suo, X.; Davis, R.E. 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 Pt 10, 2582.
    28. Kirdat, K.; Tiwarekar, B.; Thorat, V.; Sathe, S.; Shouche, Y.; Yadav, A. ‘Candidatus Phytoplasma sacchari’, a novel taxon-associated with Sugarcane Grassy Shoot (SCGS) disease. Int. J. Syst. Evol. Microbiol. 2021, 71, 004591.
    29. Bertaccini, A.; Arocha-Rosete, Y.; Contaldo, N.; Duduk, B.; Fiore, N.; Montano, H.G.; Kube, M.; Kuo, C.H.; Martini, M.; Oshima, K.; et al. Revision of the ‘Candidatus Phytoplasma’species description guidelines. Int. J. Syst. Evol. Microbiol. 2022, 72, 005353.
    30. Schildkraut, C.L.; Marmur, J.; Doty, P. The formation of hybrid DNA molecules and their use in studies of DNA homologies. J. Mol. Biol. 1961, 3, 595–617, IN15–IN16.
    31. Woese, C.R.; Fox, G.E. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA 1977, 74, 5088–5090.
    32. Wayne, L.G.; Brenner, D.J.; Colwell, R.R.; Grimont, P.A.D.; Kandler, O.; Krichevsky, M.I.; Moore, L.H.; Moore, W.E.C.; Murray, R.G.E.; Stackebrandt, E.S.M.P.; et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 1987, 37, 463–464.
    33. Hillis, D.M.; Dixon, M.T. Ribosomal DNA: Molecular evolution and phylogenetic inference. Q Rev. Biol. 1991, 66, 411–453.
    34. Hugenholtz, P.; Chuvochina, M.; Oren, A.; Parks, D.H.; Soo, R.M. Prokaryotic taxonomy and nomenclature in the age of big sequence data. ISME J. 2021, 15, 1879–1892.
    35. Stackebrandt, E.; Frederiksen, W.; Garrity, G.M.; Grimont, P.A.; Kämpfer, P.; Maiden, M.C.; Nesme, X.; Rosselló-Mora, R.; Swings, J.; Trüper, H.G.; et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 2002, 52, 1043–1047.
    36. Auch, A.F.; von Jan, M.; Klenk, H.P.; Göker, M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic. Sci. 2010, 2, 117–134.
    37. Baron, E.J. Classification. In Medical Microbiology, 4th ed.; Baron, S., Ed.; University of Texas Medical Branch at Galveston: Galveston, TX, USA, 1996; Chapter 3. Available online: https://www.ncbi.nlm.nih.gov/books/NBK8406/ (accessed on 6 June 2022).
    38. Kirkpatrick, B.C. Strategies for characterizing plant pathogenic mycoplasma-like organisms and their effects on plants. Plant-Microbe Interact. USA 1989.
    39. Davis, R.E.; Lee, I.; Dally, E.L.; Dewitt, N.; Douglas, S.M. Cloned nucleic acid hybridization probes in detection and classification of mycoplasmalike organisms (MLOs). In Proceedings of the VII International Symposium on Virus Diseases of Ornamental Plants, Sanremo, Italy, 29 May–2 June 1988; Volume 234, pp. 115–122.
    40. Zhao, Y.; Wei, W.; Davis, R.E.; Lee, I.-M. Recent advances in 16S rRNA gene-based phytoplasma differ-entiation, classification and taxonomy. In Phytoplasmas: Genomes, Plant Hosts and Vector; Weintraub, P., Jones, P., Eds.; CABI Publishing: Wallingford, UK, 2010; pp. 64–92.
    41. Lee, I.M.; Gundersen-Rindal, D.E.; Davis, R.E.; Bartoszyk, I.M. Revised classification scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int. J. Syst. Evol. Microbiol. 2010, 48, 1153–1169.
    42. Marcone, C.; Ragozzino, A.; Seemüller, E. Detection of Bermuda grass white leaf disease in Italy and characterization of the associated phytoplasma by RFLP analysis. Plant Dis. 1997, 81, 862–866.
    43. Pérez-López, E.; Luna-Rodríguez, M.; Olivier, C.Y.; Dumonceaux, T.J. The underestimated diversity of phytoplasmas in Latin America. Int. J. Syst. Evol. Microbiol. 2016, 66, 492–513.
    44. Fernandez, F.D.; Meneguzzi, N.G.; Guzman, F.A.; Kirschbaum, D.S.; Conci, V.C.; Nome, C.F.; Conci, L.R. Detection and identification of a novel 16SrXIII subgroup phytoplasma associated with strawberry red leaf disease in Argentina. Int. J. Syst. Evol. Microbiol. 2015, 65 Pt 8, 2741–2747.
    45. Nejat, N.; Vadamalai, G. Diagnostic techniques for detection of phytoplasma diseases: Past and present. J. Plant Dis. Prot. 2013, 120, 16–25.
    46. Lee, I.-M.; Davis, R.E.; Gundersen-Rindal, D.E. Phytoplasma: Phytopathogenic mollicutes. Annu. Rev. Microbiol. 2000, 54, 221–255.
    47. Wei, W.; Davis, R.E.; Lee, 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.
    48. Wei, W.; Lee, M.; Davis, R.E.; Suo, X.; Zhao, Y. Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int. J. Syst. Evol. Microbiol. 2008, 58, 2368–2377.
    49. Edel, V. Use of PCR and RFLP in fungal systematics. In Chemical Fungal Taxonomy; CRC Press: Boca Raton, FL, USA, 2020; pp. 51–76.
    50. Claussen, M.; Schmidt, S. Differentiation of Basidiobolus s isolates: RFLP of a diagnostic PCR amplicon matches sequence-based classification and growth temperature preferences. J. Fungi 2021, 7, 110.
    51. Silvester, R.; Alexander, D.; Antony, A.C.; Hatha, M. GroEL PCR-RFLP–an efficient tool to discriminate closely related pathogenic Vibrio species. Microb. Pathog. 2017, 105, 196–200.
    52. Lee, I.M.; Gundersen-Rindal, D.E.; Davis, R.E.; Bottner, K.D.; Marcone, C.; Seemüller, E. ‘Candidatus Phytoplasma asteris’, a novel phytoplasma taxon associated with aster yellows and related diseases. Int. J. Syst. Evol. Microbiol. 2004, 54, 1037–1048.
    53. Arocha, Y.; Antesana, O.; Montellano, E.; Franco, P.; Plata, G.; Jones, P. ‘Candidatus Phytoplasma lycopersici’, a phytoplasma associated with ‘hoja de perejil’ disease in Bolivia. Int. J. Syst. Evol. Microbiol. 2007, 57, 1704–1710.
    54. White, D.T.; Blackall, L.L.; Scott, P.T.; Walsh, K.B. Phylogenetic positions of phytoplasmas associated with dieback, yellow crinkle and mosaic diseases of papaya, and their proposed inclusion in ‘Candidatus Phytoplasma australiense’ and a new taxon, ‘Candidatus Phytoplasma australasia’. Int. J. Syst. Evol. Microbiol. 1998, 48, 941–951.
    55. Davis, R.E.; Zhao, Y.; Dally, E.L.; Lee, M.; Jomantiene, R.; Douglas, S.M. ‘Candidatus Phytoplasma pruni’, a novel taxon associated with X-disease of stone fruits, Prunus s: Multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes. Int. J. Syst. Evol. Microbiol. 2013, 63 Pt 2, 766–776.
    56. Lee, M.; Martini, M.; Marcone, C.; Zhu, S.F. 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. 2004, 54, 337–347.
    57. Jung, H.Y.; Sawayanagi, T.; Kakizawa, S.; Nishigawa, H.; Wei, W.; Oshima, K.; Miyata, S.I.; Ugaki, M.; Hibi, T.; Namba, S. ‘Candidatus Phytoplasma ziziphi’, a novel phytoplasma taxon associated with jujube witches’-broom disease. Int. J. Syst. Evol. Microbiol. 2003, 53, 1037–1041.
    58. Malembic-Maher, S.; Salar, P.; Filippin, L.; Carle, P.; Angelini, E.; Foissac, X. Genetic diversity of European phytoplasmas of the 16SrV taxonomic group and proposal of ‘Candidatus Phytoplasma rubi’. Int. J. Syst. Evol. Microbiol. 2011, 61, 2129–2134.
    59. Win, N.K.K.; Lee, S.Y.; Bertaccini, A.; Namba, S.; Jung, H.Y. ‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora. Int. J. Syst. Evol. Microbiol. 2013, 63 Pt 2, 636–640.
    60. Hiruki, C.; Wang, K. Clover proliferation phytoplasma: ‘Candidatus Phytoplasma trifolii’. Int. J. Syst. Evol. Microbiol. 2004, 54, 1349–1353.
    61. Davis, R.E.; Zhao, Y.; Dally, E.L.; Jomantiene, R.; Lee, M.; Wei, W.; Kitajima, E.W. ‘Candidatus Phytoplasma sudamericanum’, a novel taxon, and strain PassWB-Br4, a new subgroup 16SrIII-V phytoplasma, from diseased passion fruit (Passiflora edulis f. flavicarpa Deg.). Int. J. Syst. Evol. Microbiol. 2012, 62 Pt 4, 984–989.
    62. Griffiths, H.M.; Sinclair, W.A.; Smart, C.D.; Davis, R.E. The phytoplasma associated with ash yellows and lilac witches’-broom: ‘Candidatus Phytoplasma fraxini’. Int. J. Syst. Evol. Microbiol. 1999, 49, 1605–1614.
    63. Davis, R.E.; Zhao, Y.; Wei, W.; Dally, E.L.; Lee, M. ‘Candidatus Phytoplasma luffae’, a novel taxon associated with witches’ broom disease of loofah, Luffa aegyptica Mill. Int. J. Syst. Evol. Microbiol. 1999, 67, 3127–3133.
    64. Verdin, E.; Salar, P.; Danet, J.L.; Choueiri, E.; Jreijiri, F.; El Zammar, S.; Gelie, B.; Bove, J.M.; Garnier, M. ‘Candidatus Phytoplasma phoenicium’sp. nov., a novel phytoplasma associated with an emerging lethal disease of almond trees in Lebanon and Iran. Int. J. Syst. Evol. Microbiol. 2003, 53, 833–838.
    65. Seemüller, E.; Schneider, B. ‘Candidatus Phytoplasma mali’, ‘Candidatus Phytoplasma pyri’and ‘Candidatus Phytoplasma prunorum’, the causal agents of apple proliferation, pear decline and European stone fruit yellows, respectively. Int. J. Syst. Evol. Microbiol. 2004, 54, 1217–1226.
    66. Marcone, C.; Gibb, K.S.; Streten, C.; Schneider, B. ‘Candidatus Phytoplasma spartii’, ‘Candidatus Phytoplasma rhamni’ and ‘Candidatus Phytoplasma allocasuarinae’, respectively associated with spartium witches’-broom, buckthorn witches’-broom and allocasuarina yellows diseases. Int. J. Syst. Evol. Microbiol. 2004, 54, 1025–1029.
    67. Jung, H.Y.; Sawayanagi, T.; Wongkaew, P.; Kakizawa, S.; Nishigawa, H.; Wei, W.; Oshima, K.; Miyata, S.I.; Ugaki, M.; Hibi, T.; et al. ‘Candidatus Phytoplasma oryzae’, a novel phytoplasma taxon associated with wheat yellow dwarf disease. Int. J. Syst. Evol. Microbiol. 2003, 53, 1925–1929.
    68. Šafárŏvá, D.; Zemanek, T.; Valova, P.; Navratil, M. ‘Candidatus Phytoplasma cirsii’, a novel taxon from creeping thistle . Int. J. Syst. Evol. Microbiol. 2016, 66, 1745–1753.
    69. Davis, R.E.; Dally, E.L.; Gundersen, D.E.; Lee, I.-M.; Habili, N. “Candidatus Phytoplasma australiense,” a new phytoplasma taxon associated with Australian grapevine yellows. Int. J. Syst. Bacteriol. 1997, 47, 262–269.
    70. Sawayanagi, T.; Horikoshi, N.; Kanehira, T.; Shinohara, M.; Bertaccini, A.; Cousin, M.T.; Hiruki, C.; Namba, S. ‘Candidatus Phytoplasma japonicum’, a new phytoplasma taxon associated with Japanese Hydrangea phyllody. Int. J. Syst. Evol. Microbiol. 1999, 49, 1275–1285.
    71. Valiunas, D.; Staniulis, J.; Davis, R.E. ‘Candidatus Phytoplasma fragariae’, a novel phytoplasma taxon discovered in yellows diseased strawberry, Fragaria× ananassa. Int. J. Syst. Evol. Microbiol. 1999, 56, 277–281.
    72. Quaglino, F.; Zhao, Y.; Casati, P.; Bulgari, D.; Bianco, P.A.; Wei, W.; Davis, R.E. ‘Candidatus Phytoplasma solani’, a novel taxon associated with stolbur-and bois noir-related diseases of plants. Int. J. Syst. Evol. Microbiol. 2013, 63 Pt 8, 2879–2894.
    73. Martini, M.; Marcone, C.; Mitrović, J.; Maixner, M.; Delić, D.; Myrta, A.; Ermacora, P.; Bertaccini, A.; Duduk, B. ‘Candidatus Phytoplasma convolvuli’, a new phytoplasma taxon associated with bindweed yellows in four European countries. Int. J. Syst. Evol. Microbiol. 2012, 62 Pt 12, 2910–2915.
    74. Davis, R.E.; Harrison, N.A.; Zhao, Y.; Wei, W.; Dally, E.L. ‘Candidatus Phytoplasma hispanicum’, a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus. Int. J. Syst. Evol. Microbiol. 2016, 66, 3463–3467.
    75. Fernández, F.D.; Galdeano, E.; Kornowski, M.V.; Arneodo, J.D.; Conci, L.R. Description of ‘Candidatus Phytoplasma meliae’, a phytoplasma associated with Chinaberry (Melia azedarach L.) yellowing in South America. Int. J. Syst. Evol. Microbiol. 2016, 66, 5244–5251.
    76. Marcone, C.; Schneider, B.; Seemüller, E. ‘Candidatus Phytoplasma cynodontis’, the phytoplasma associated with Bermuda grass white leaf disease. Int. J. Syst. Evol. Microbiol. 2004, 54, 1077–1082.
    77. Montano, H.G.; Davis, R.E.; Dally, E.L.; Hogenhout, S.; Pimentel, J.P.; Brioso, P.S. ‘Candidatus Phytoplasma brasiliense’, a new phytoplasma taxon associated with hibiscus witches’ broom disease. Int. J. Syst. Evol. Microbiol. 2001, 51, 1109–1118.
    78. Arocha, Y.; Lopez, M.; Pinol, B.; Fernandez, M.; Picornell, B.; Almeida, R.; Palenzuela, I.; Wilson, M.R.; Jones, P. ‘Candidatus Phytoplasma graminis’ and ‘Candidatus Phytoplasma caricae’, two novel phytoplasmas associated with diseases of sugarcane, weeds and papaya in Cuba. Int. J. Syst. Evol. Microbiol. 2005, 55, 2451–2463.
    79. Lee, M.; Bottner, K.D.; Secor, G.; Rivera-Varas, V. ‘Candidatus Phytoplasma americanum’, a phytoplasma associated with a potato purple top wilt disease complex. Int. J. Syst. Evol. Microbiol. 2005, 56, 1593–1597.
    80. Jung, H.Y.; Sawayanagi, T.; Kakizawa, S.; Nishigawa, H.; Miyata, S.I.; Oshima, K.; Ugaki, M.; Lee, J.T.; Hibi, T.; Namba, S. ‘Candidatus Phytoplasma castaneae’, a novel phytoplasma taxon associated with chestnut witches’ broom disease. Int. J. Syst. Evol. Microbiol. 2002, 52, 1543–1549.
    81. Schneider, B.; Torres, E.; Martín, M.P.; Schröder, M.; Behnke, H.D.; Seemüller, E. ‘Candidatus Phytoplasma pini’, a novel taxon from Pinus silvestris and Pinus halepensis. Int. J. Syst. Evol. Microbiol. 2005, 55, 303–307.
    82. Harrison, N.A.; Davis, R.E.; Oropeza, C.; Helmick, E.E.; Narvaez, M.; Eden-Green, S.; Dollet, M.; Dickinson, M. ‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique. Int. J. Syst. Evol. Microbiol. 2014, 64 Pt 6, 1890–1899.
    83. Al-Saady, N.A.; Khan, A.J.; Calari, A.; Al-Subhi, A.M.; Bertaccini, A. ‘Candidatus Phytoplasma omanense’, associated with witches’-broom of Cassia italica (Mill.) Spreng. in Oman. Int. J. Syst. Evol. Microbiol. 2008, 58, 461–466.
    84. Zhao, Y.; Sun, Q.; Wei, W.; Davis, R.E.; Wu, W.; Liu, Q. ‘Candidatus Phytoplasma tamaricis’, a novel taxon discovered in witches’-broom-diseased salt cedar (Tamarix chinensis Lour.). Int. J. Syst. Evol. Microbiol. 2009, 59, 2496–2504.
    85. Lee, I.M.; Bottner-Parker, K.D.; Zhao, Y.; Villalobos, W.; Moreira, L. ‘Candidatus Phytoplasma costaricanum’, a novel phytoplasma associated with an emerging disease in soybean (Glycine max). Int. J. Syst. Evol. Microbiol. 2011, 61, 2822–2826.
    86. Nejat, N.; Vadamalai, G.; Davis, R.E.; Harrison, N.A.; Sijam, K.; Dickinson, M.; Abdullah, S.N.A.; Zhao, Y. ‘Candidatus Phytoplasma malaysianum’, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus). Int. J. Syst. Evol. Microbiol. 2013, 63 Pt 2, 540–548.
    87. Naderali, N.; Nejat, N.; Vadamalai, G.; Davis, R.E.; Wei, W.; Harrison, N.A.; Kong, L.; Kadir, J.; Tan, Y.H.; Zhao, Y. ‘Candidatus Phytoplasma wodyetiae’, a new taxon associated with yellow decline disease of foxtail palm (Wodyetia bifurcata) in Malaysia. Int. J. Syst. Evol. Microbiol. 2017, 67, 3765–3772.
    88. Jardim, B.R.; Kinoti, W.M.; Tran-Nguyen, L.T.; Gambley, C.; Rodoni, B.; Constable, F.E. ‘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, ijsem004589.
    89. Miyazaki, A.; Shigaki, T.; Koinuma, H.; Iwabuchi, N.; Rauka, G.B.; Kembu, A.; Saul, J.; Watanabe, K.; Nijo, T.; Maejima, K.; et al. ‘Candidatus Phytoplasma noviguineense’, a novel taxon associated with Bogia coconut syndrome and banana wilt disease on the island of New Guinea. Int. J. Syst. Evol. Microbiol. 2018, 68, 170–175.
    90. Jones, L.M.; Pease, B.; Perkins, S.L.; Constable, F.E.; Kinoti, W.M.; Warmington, D.; Allgood, B.; Powell, S.; Taylor, P.; Pearce, C.; et al. ‘Candidatus Phytoplasma dypsidis’, a novel taxon associated with a lethal wilt disease of palms in Australia. Int. J. Syst. Evol. Microbiol. 2021, 71, 004818.
    91. Zhao, Y.; Wei, W.; Davis, R.E.; Lee, M.; Bottner-Parker, K.D. The agent associated with blue dwarf disease in wheat represents a new phytoplasma taxon, ‘Candidatus Phytoplasma tritici’. Int. J. Syst. Evol. Microbiol. 2021, 71, 004604.
    92. Zreik, L.; Carle, P.; Bove, J.M.; 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.
    93. Zhao, Y.; Davis, R.E. 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. 2021, 66, 2121–2123.
    94. MacLean, A.M.; Sugio, A.; Makarova, O.V.; Findlay, K.C.; Grieve, V.M.; Tóth, R.; Nicolaisen, M.; Hogenhout, S.A. Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants. Plant Physiol. 2011, 157, 831–841.
    95. Wei, W.; Davis, R.E.; Nuss, D.L.; Zhao, Y. Phytoplasmal infection derails genetically preprogrammed meristem fate and alters plant architecture. Proc. Natl. Acad. Sci. USA 2013, 110, 19149–19154.
    96. Wu, W.; Cai, H.; Wei, W.; Davis, R.E.; Lee, I.M.; Chen, H.; Zhao, Y. Identification of two new phylogenetically distant phytoplasmas from S enna surattensis plants exhibiting stem fasciation and shoot proliferation symptoms. Ann. Appl. Biol. 2012, 160, 25–34.
    97. Zwolińska, A.; Krawczyk, K.; Borodynko-Filas, N.; Pospieszny, H. Non-crop sources of Rapeseed Phyllody phytoplasma (‘Candidatus Phytoplasma asteris’: 16SrI-B and 16SrI-(B/L)L), and closely related strains. Crop Prot. 2019, 119, 59–68.
    98. Lee, I.M.; Hammond, R.W.; Davis, R.E.; Gundersen, D.E. Universal amplification and analysis of pathogen 16S rDNA for classification and identification of mycoplasmalike organisms. Phytopathology 1993, 83, 834–842.
    99. Gundersen, D.E.; Lee, I.-M. Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathol. Mediterr. 1996, 35, 114–151.
    100. Christensen, N.M.; Nicolaisen, M.; Hansen, M.; Schulz, A. Distribution of phytoplasmas in infected plants as revealed by real-time PCR and bioimaging. Mol. Plant-Microbe Interact. 1993, 17, 1175–1184.
    101. Wei, W.; Kakizawa, S.; Suzuki, S.; Jung, H.Y.; Nishigawa, H.; Miyata, S.; Oshima, K.; Ugaki, M.; Hibi, T.; Namba, S. In planta dynamic analysis of onion yellows phytoplasma using localized inoculation by insect transmission. Phytopathology 2004, 94, 244–250.
    102. Mehle, N.; Dreo, T.; Ravnikar, M. Quantitative analysis of “flavescence doreé” phytoplasma with droplet digital PCR. Phytopathogenic Mollicutes 2014, 4, 9–15.
    103. Dickinson, M. Loop-mediated isothermal amplification (LAMP) for detection of phytoplasmas in the field. In Plant Pathology; Humana Press: New York, NY, USA, 2015; pp. 99–111.
    104. Wheatley, M.S.; Wang, Q.; Wei, W.; Bottner-Parker, K.D.; Zhao, Y.; Yang, Y. Cas12a-based diagnostics for potato purple top disease complex associated with infection by ‘Candidatus Phytoplasma trifolii’-related strains. Plant Dis. 2022, PDIS09212119RE.
    105. Deng, S.J.; Hiruki, C. Amplification of 16S ribosomal-RNA genes from culturable and nonculturable Mollicutes. J. Microbiol. Methods 1991, 14, 53–61.
    106. Schneider, B.; Seemüller, E.; Smart, C.D.; Kirkpatrick, B.C. Phylogenic classification of plant pathogenic mycoplasmalike organisms or phytoplasmas. In Molecular and Diagnostic Procedures in Mycoplasmology; Razin, I.R., Tully, J.G., Eds.; Academic Press: San Diego, CA, USA, 1995; pp. 369–380.
    107. Casati, P.; Quaglino, F.; Stern, A.R.; Tedeschi, R.; Alma, A.; Bianco, P.A. Multiple gene analyses reveal extensive genetic diversity among ‘Candidatus Phytoplasma mali’populations. Ann. Appl. Biol. 2011, 158, 257–266.
    108. Wei, W.; Cai, H.; Jiang, Y.; Lee, I.M.; Davis, R.E.; Ding, Y.; Yuan, E.; Chen, H.; Zhao, Y. A new phytoplasma associated with little leaf disease in azalea: Multilocus sequence characterization reveals a distinct lineage within the aster yellows phytoplasma group. Ann. Appl. Biol. 2011, 158, 318–330.
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      Wei, W.; Zhao, Y. Phytoplasma Taxonomy. Encyclopedia. Available online: https://encyclopedia.pub/entry/26680 (accessed on 07 February 2023).
      Wei W, Zhao Y. Phytoplasma Taxonomy. Encyclopedia. Available at: https://encyclopedia.pub/entry/26680. Accessed February 07, 2023.
      Wei, Wei, Yan Zhao. "Phytoplasma Taxonomy," Encyclopedia, https://encyclopedia.pub/entry/26680 (accessed February 07, 2023).
      Wei, W., & Zhao, Y. (2022, August 30). Phytoplasma Taxonomy. In Encyclopedia. https://encyclopedia.pub/entry/26680
      Wei, Wei and Yan Zhao. ''Phytoplasma Taxonomy.'' Encyclopedia. Web. 30 August, 2022.
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