Sequence and RFLP analysis of the elongation factor Tu gene used in differentiation and classification of phytoplasmas

Schneider, Bernd; Gibb, Karen S.

doi:10.1099/00221287-143-10-3381

Cited by 204 publications

(174 citation statements)

References 35 publications

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“…Approximately 15 groups (putative species) of phytoplasmas and several sub-groups have been delineated on the basis of differences in 16s rDNA sequences (Gundersen et al, 1994;Lee et al, 1993b;Namba et al, 1993;Schneider et al, 1995b;Seemuller et al, 1994). This delineation is supported by sequence differences in ribosomal protein genes (Gundersen et al, 1994;Lee et al, 1998) and the gene encoding elongation factor Tu (Schneider et al, 1997). Several of the groups were previously known from DNA-DNA hybridization data (Lee et al, 1990(Lee et al, , 1991(Lee et al, , 1993aNakashima et al, 1993).…”

Section: Introductionmentioning

confidence: 49%

The phytoplasma associated with ash yellows and lilac witches'-broom: ‘Candidatus Phytoplasma fraxini’

Griffiths

Sinclair

Smart

et al. 1999

International Journal of Systematic and Evolutionary Microbiology

107

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Phytoplasmas associated with the plant diseases ash yellows (Ashy, occurring in fraxinus) and lilac witches'-broom (LWB, occurring in Syringa) represent a putative species-level taxon. Phytoplasmal DNA from 19 ash or lilac sources across the known geographic range of Ashy (71-113 OW) was examined to determine if Ashy and LWB phytoplasmas are a coherent group, if variability exists in both conserved and anonymous DNA, and if variability in 16s rDNA is related to host or geographic origin. The 165 rRNA gene and the 16S-235 spacer were amplified using primer pair PWP7 and analysed using 15 restriction enzymes. RFLPs were detected in digests obtained with A M , Hhal or Taql, for a total of four RFLP profile types. Sequencing of the amplimers from strains AshYIT, AshY3, Ashy5 and LWB3 (which represent the four 16s rDNA RFLP profile types) revealed only three positions in the 16s rRNA gene and one position in the 16S-23s spacer a t which differences occurred; these were single nucleotide substitutions. Sequence homology between any two strains was >99-8%. A portion of a ribosomal protein operon, amplified with primer pair rpFI/Rl from each of the four strains noted above, was analysed with six restriction enzymes, resulting in the detection of two RFLP profiles with MseI. Southern analysis, utilizing two non-specif ic probes from other phytoplasma groups, revealed three RFLP profile types in anonymous chromosomal DNA of strains representing the four 16s rDNA genotypes. Two strains, Ashy3 and LWB3, had unique combinations of characters in the various assays. On the basis of RFLP profiles, the strains from the other plants sampled comprised two groups. The grouping was not clearly related to host or geographic origin. The genome size of strain Ashy3 was estimated from PFGE data to be 645 kbp. Phylogenetic analysis of a 1423 bp 165 rDNA sequence from strains AshYIT, AshY3, Ashy5 and LWB3, together with sequences from 14 other mollicutes archived in GenBank, produced a tree on which the Ashy and LWB strains clustered as a discrete group, consistent with previous analyses utilizing only type strain AshYIT. Thus, the Ashy phytoplasma group is coherent but heterogeneous. The name 'Candidatus Phytoplasma fraxini ' is proposed for this group.

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Section: Introductionmentioning

confidence: 49%

The phytoplasma associated with ash yellows and lilac witches'-broom: ‘Candidatus Phytoplasma fraxini’

Griffiths

Sinclair

Smart

et al. 1999

International Journal of Systematic and Evolutionary Microbiology

107

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“…A congruent amount of results has already been produced in recent years, showing that phytoplasma strains that have <97?5 % similarity in their 16S rRNA gene sequence actually represent different organisms, on the basis of phylogenetic analysis based on 16S rRNA gene sequences (Namba et al, 1993b;Gundersen et al, 1994;Seemüller et al, 1994Seemüller et al, , 1998Tymon et al, 1998;Lee et al, 2000), 16S-23S rRNA gene spacer sequences , 23S rRNA gene sequences (Guo et al, 1998), ribosomal protein gene sequences (Jomantiene et al, 1998;Lee et al, 1998), transcription factor Tu gene (Schneider et al, 1997a), restriction analysis of the same genes (Schneider et al, , 1997aVibio et al, 1996;Lee et al, 1998), RFLP of total DNA with chromosomal probes (Lee & Davis, 1988;Bertaccini et al, 1990;Harrison et al, 1991Harrison et al, , 1992Hibben et al, 1991;Kuske et al, 1991;Lee et al, 1991Lee et al, , 1992aLee et al, , b, 1993aDaire et al, 1992;Davis et al, 1992a, b;Ahrens et al, 1993;Mäurer et al, 1993;Chen et al, 1994;Griffiths et al, 1994;Davis & Sinclair, 1998) and biological properties, such as insect vector specificity (Tsai, 1979;Shiomi & Sugiura, 1984;Kirkpatrick, 1992).…”

Section: Species Belonging To 'Ca Phytoplasma'mentioning

confidence: 99%

‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects

Group¹

2004

International Journal of Systematic and Evolutionary Microbiology

541

135

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The trivial name ‘phytoplasma’ has been adopted to collectively name wall-less, non-helical prokaryotes that colonize plant phloem and insects, which were formerly known as mycoplasma-like organisms. Although phytoplasmas have not yet been cultivated in vitro, phylogenetic analyses based on various conserved genes have shown that they represent a distinct, monophyletic clade within the class Mollicutes. It is proposed here to accommodate phytoplasmas within the novel genus ‘Candidatus (Ca.) Phytoplasma’. Given the diversity within ‘Ca. Phytoplasma’, several subtaxa are needed to accommodate organisms that share <97·5 % similarity among their 16S rRNA gene sequences. This report describes the properties of ‘Ca. Phytoplasma’, a taxon that includes the species ‘Ca. Phytoplasma aurantifolia’ (the prokaryote associated with witches'-broom disease of small-fruited acid lime), ‘Ca. Phytoplasma australiense’ (associated with Australian grapevine yellows), ‘Ca. Phytoplasma fraxini’ (associated with ash yellows), ‘Ca. Phytoplasma japonicum’ (associated with Japanese hydrangea phyllody), ‘Ca. Phytoplasma brasiliense’ (associated with hibiscus witches'-broom in Brazil), ‘Ca. Phytoplasma castaneae’ (associated with chestnut witches'-broom in Korea), ‘Ca. Phytoplasma asteris' (associated with aster yellows), ‘Ca. Phytoplasma mali’ (associated with apple proliferation), ‘Ca. Phytoplasma phoenicium’ (associated with almond lethal disease), ‘Ca. Phytoplasma trifolii’ (associated with clover proliferation), ‘Ca. Phytoplasma cynodontis' (associated with Bermuda grass white leaf), ‘Ca. Phytoplasma ziziphi’ (associated with jujube witches'-broom), ‘Ca. Phytoplasma oryzae’ (associated with rice yellow dwarf) and six species-level taxa for which the Candidatus species designation has not yet been formally proposed (for the phytoplasmas associated with X-disease of peach, grapevine flavescence dorée, Central American coconut lethal yellows, Tanzanian lethal decline of coconut, Nigerian lethal decline of coconut and loofah witches'-broom, respectively). Additional species are needed to accommodate organisms that, despite their 16S rRNA gene sequence being >97·5 % similar to those of other ‘Ca. Phytoplasma’ species, are characterized by distinctive biological, phytopathological and genetic properties. These include ‘Ca. Phytoplasma pyri’ (associated with pear decline), ‘Ca. Phytoplasma prunorum’ (associated with European stone fruit yellows), ‘Ca. Phytoplasma spartii’ (associated with spartium witches'-broom), ‘Ca. Phytoplasma rhamni’ (associated with buckthorn witches'-broom), ‘Ca. Phytoplasma allocasuarinae’ (associated with allocasuarina yellows), ‘Ca. Phytoplasma ulmi’ (associated with elm yellows) and an additional taxon for the stolbur phytoplasma. Conversely, some organisms, despite their 16S rRNA gene sequence being <97·5 % similar to that of any other ‘Ca. Phytoplasma’ species, are not presently described as Candidatus species, due to their poor overall characterization.

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“…Symptomatic and asymptomatic samples were also screened using the fTufAy and rTufAy primers according to Schneider et al (1997). These primers amplify the Tu elongation factor (tuf) gene of phytoplasmas assigned to the aster yellows and stolbur groups, which includes Ca.…”

Section: Screening For Phytoplasmas and Rickettsia-like-organismsmentioning

confidence: 99%

“…The PCR reactions were prepared according to Schneider et al (1997) and subjected to 35 cycles of 95 • C / 1 min; 55 • C / 1 min and 72 • C / 1.5 min. One microlitre of undiluted DNA or DNA diluted 1 : 10 or 1 : 50 in water was used as DNA template in PCR.…”

Section: Screening For Phytoplasmas and Rickettsia-like-organismsmentioning

confidence: 99%

Plant hosts of the phytoplasmas and rickettsia-like-organisms associated with strawberry lethal yellows and green petal diseases

Streten

Herrington²,

Hutton³

et al. 2005

Austral. Plant Pathol.

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Abstract. Candidatus Phytoplasma australiense (Ca. P. australiense) is associated with the plant diseases strawberry lethal yellows (SLY), strawberry green petal (SGP), papaya dieback (PDB), Australian grapevine yellows (AGY) and Phormium yellow leaf (PYL; New Zealand). Strawberry lethal yellows disease is also associated with a rickettsia-like-organism (RLO) or infrequently with the tomato big bud (TBB) phytoplasma, the latter being associated with a wide range of plant diseases throughout Australia. In contrast, the RLO has been identified only in association with SLY disease, and Ca. P. australiense has been detected only in a limited number of plant host species. The aim of this study was to identify plant hosts that are possible reservoirs of Ca. P. australiense and the SLY RLO. Thirty-one plant species from south-east Queensland were observed with disease between 2001 and 2003 and, of these, 18 species tested positive using phytoplasma-specific primers. The RLO was detected in diseased Jacksonia scoparia and Modiola caroliniana samples collected at Stanthorpe. The TBB phytoplasma was detected in 16 different plant species and Ca. P. australiense Australian grapevine yellows strain was detected in six species. The TBB phytoplasma was detected in plants collected at Nambour, Stanthorpe, Warwick and Brisbane. Ca. P. australiense was detected in plants collected at Nambour, Stanthorpe, Gatton and Allora. All four phytoplasmas were detected in diseased Gomphocarpus physocarpus plants collected at Toowoomba, Allora, Nambour and Gatton. These results indicated that the vector(s) of Ca. P. australiense are distributed throughout south-east Queensland and the diversity of phytoplasmas detected in G. physocarpus suggests it is a feeding source for phytoplasma insect vectors or it has a broad susceptibility to a range of phytoplasmas.

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Sequence and RFLP analysis of the elongation factor Tu gene used in differentiation and classification of phytoplasmas

Cited by 204 publications

References 35 publications

The phytoplasma associated with ash yellows and lilac witches'-broom: ‘Candidatus Phytoplasma fraxini’

The phytoplasma associated with ash yellows and lilac witches'-broom: ‘Candidatus Phytoplasma fraxini’

‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects

Plant hosts of the phytoplasmas and rickettsia-like-organisms associated with strawberry lethal yellows and green petal diseases

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