Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'

Hodgetts, J.; Boonham, Neil; Mumford, R. A.; Harrison, N. A.; Dickinson, Matthew

doi:10.1099/ijs.0.65668-0

Cited by 208 publications

(142 citation statements)

References 31 publications

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“…Worldwide there are other reports of this phytoplasma group mainly on ornamental Cactaceae in countries such as: China (Accession # EF190970) (Wei et al, 2007;Cai et al, 2008), even in Mexico (Acc. # AF356846) (IRPCM, 2004;Leyva-López et al, 1999); UK (Aster yellows Cactus) (Lee et al, 1998) and in USA (Cactus aster yellows) (Hodgetts et al, 2008). On Opuntia crop, in USA a 16SrI-B phytoplasma subgroup was identified on a fruit of O. ficus-indica (Bertaccini et al, 2007) and this 16SrI phytoplasma group agrees with our results.…”

Section: Discussionsupporting

confidence: 81%

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New hosts of 16SrI phytoplasma group associated with edible Opuntia ficus-indica crop and its pests in Mexico

Zak¹,

Yáñez‐Morales²,

Alanis-Martínez³

et al. 2011

Afr. J. Microbiol. Res.

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In Mexico in the region of Nopaltepec in Mexico State, the edible Cactus crop, Opuntia ficus-indica is mainly cultivated for prickly pear fruit production. This crop has problems with common pests (insects, mollusks and weeds) which may serve as reservoirs and together with the named Cactus with phytoplasma-like symptoms which through the time inhibit the fruit production, and for this reason, the farmers called these Opuntia plants as Planta Macho (male plant). For molecular identification of the probably involved phytoplasma during 2005 and 2006, 38 samples of Opuntia plant tissues, fruit and some pests were collected for DNA extraction. By direct and nested PCR, 16S rRNA gene was amplified and sequenced. PCR products were analyzed by RFLP with restriction enzymes and in the sequences restriction sites were mapped. Phylogenetic analysis showed that the same phytoplasma was associated with Opuntia crop and its pests (the weeds Argemone mexicana, a grass and Lupinus sp.; a chinch bugs, Chelinidea sp. and the brown garden snail, Helix aspersa). Thus the edible Cactus crop and pests represented novel hosts of Cactus male plant Phytoplasma, and was classified as 16SrI Aster yellows group, of the species Candidatus phytoplasma asteris. This is the first report of this phytoplasma in Mexico and elsewhere.

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Section: Discussionsupporting

confidence: 81%

“…Some of these were ornamentals such as Opuntia monacantha in Lebanon (Choueiri et al, 2005); and Opuntia sp. and Zygocactus truncatus in China (Cai et al, , 2008, and on Cactus in USA (Hodgetts et al, 2008). Also in Mexico phytoplasmas were associated with ornamental cacti such as Echinopsis subdenudata and Opuntia sp.…”

Section: Introductionmentioning

confidence: 99%

New hosts of 16SrI phytoplasma group associated with edible Opuntia ficus-indica crop and its pests in Mexico

Zak¹,

Yáñez‐Morales²,

Alanis-Martínez³

et al. 2011

Afr. J. Microbiol. Res.

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“…phytoplasma associated with K. arvensis phyllody in Italy [18] and almond witches'-broom in Iran [21]. The 23S rRNA gene has not been sequenced completely for most of the phytoplasmas [10,12]. Our study of complete 23S rRNA gene sequence from TP phytoplasma showed that it has maximum identity with Jujube witches'-broom phytoplasmas of 16SrV group.…”

Section: Discussionmentioning

confidence: 94%

“…For amplification of secA gene, SecAfor1/SecArev3 (5 0 -GARATGAA AACTGGRGAAGG-3 0 /5 0 -GTTTTRGCAGTTCCTGTCAT NCC-3 0 ) phytoplasma universal primers were used [12]. PCR was also performed using 16SrIX group specific primer pair rp(IX)F2/rp(IX)R2 (5 0 -GCACAAGCTATTTTAA TGTTTACACC-3 0 /5 0 -CAAAGGGACTAAACCTAAAG-3 0 ) for amplification of a part of ribosomal protein (rp) gene.…”

Section: Isolation Of Total Dna and Pcr Amplificationmentioning

confidence: 99%

“…16S rRNA, 23S rRNA, rp and secA gene sequences were aligned with phytoplasma group/subgroup representatives available in GenBank using Clustal W [26]. Phylogenetic relationship of four isolates of TP phytoplasma with other group representative phytoplasma sequences available in GenBank were assessed based on sequences of 16S rRNA gene between primers R16F2n and R16R2, secA gene between primers SecAfor2 and SecArev3 [12], 23S rRNA gene between primers P7 and 23Srev [12], rp gene between primers rp(IX)F2 and rp(IX)R2 [19] and 16S-23S rRNA intergenic spacer region between primers P3 and P7 [12]. Sequence alignments were performed using CLUSTAL W [26].…”

Section: Phylogenetic Analysismentioning

confidence: 99%

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Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

Azadvar

2010

Indian J. Virol.

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Samples from toria plants (Brassica rapa L. subsp. dichotoma (Roxb.)) exhibiting phyllody, virescence, witches broom, extensive malformation of floral parts, formation of bladder like siliquae and flower sterility were collected from four different locations in India. Sequencing and phylogenetic analysis of the 16S rRNA, a part of 23S rRNA, partial sec A genes, rp gene and 16S-23S intergenic spacer region indicated that the phytoplasmas associated with toria phyllody (TP) symptoms were identical and belonged to 16SrIX phytoplasma Pigeon pea witches'-broom (PPWB) group. The iPhyClassifier generated virtual RFLP pattern of 1.25 kb 16S rDNA sequences indicated that TP phytoplasma belongs to 16SrIX-C phytoplasma subgroup. Complete 23S rRNA gene of TP phytoplasma had 2,787 nucleotides and is the first sequence of 16SrIX phytoplasma group. Restriction digestion of 16S rDNA and 23S rDNA PCR products has also shown that TP phytoplasmas from all the four locations in India were identical. Toria is a previously unreported host for a phytoplasma in16SrIX-C subgroup.

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“Candidatus Phytoplasma”

Harrison¹,

Gundersen‐Rindal²,

Davis³

2015

Bergey's Manual of Systematics of Archaea and Bacteria

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Phy.to.plas'ma. Gr. masc. n. phytos a plant; Gr. neut. n. plasma something formed or molded, a form. Tenericutes / Mollicutes / Acholeplasmatales / incertae Sedis ‐ Family II / “Candidatus Phytoplasma” Phytoplasmas (Sears and Kirkpatrick, 1994) are wall‐less, nutritionally fastidious, phytopathogenic prokaryotes 0.2–0.8 µm in diameter that morphologically resemble members of the Mollicutes . Sequencing of nearly full‐length PCR‐amplified 16S rRNA genes (Gundersen et al., 1994; Namba et al., 1993; Seemüller et al., 1994), combined with earlier studies (Kuske and Kirkpatrick, 1992b; Lim and Sears, 1989), provided the first comprehensive phylogeny of the organisms and showed that they constitute a unique, monophyletic clade within the Mollicutes . These organisms are most closely related to members of the genus Acholeplasma within the Anaeroplasma clade as defined by Weisburg et al. (1989). Sustained culture in cell‐free media has not yet been demonstrated for any phytoplasma. Their genome sizes have been estimated to range from 530 to 1350 kb, and the G+C content of phytoplasma DNA is about 23–30 mol%. The presence of a characteristic oligonucleotide sequence in the 16S rRNA gene, CAA GAY BAT KAT GTK TAG CYG GDC T, and standard codon usage indicate that phytoplasmas represent a distinct taxon for which the name “ Candidatus Phytoplasma” has been adopted by specialists in the molecular biology and pathogenicity of these and similar phytopathogenic organisms (IRPCM Phytoplasma/Spiroplasma Working Team – Phytoplasma Taxonomy Group, 2004). At present, the designation “ Candidatus ” must still be used for new types.

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Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'

Cited by 208 publications

References 31 publications

New hosts of 16SrI phytoplasma group associated with edible Opuntia ficus-indica crop and its pests in Mexico

New hosts of 16SrI phytoplasma group associated with edible Opuntia ficus-indica crop and its pests in Mexico

Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

“Candidatus Phytoplasma”

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