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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 63, Issue Pt_10

Evaluation of the DNA-dependent RNA polymerase β-subunit gene () for phytoplasma classification and phylogeny Free

Abstract

Phytoplasmas are classified into 16Sr groups and subgroups and ‘ ’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘ ’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene () exists as a single copy in the phytoplasma genome, we explored the use of for phytoplasma classification and phylogenetic analysis. We sequenced a clover phyllody (CPh) phytoplasma genetic locus containing ribosomal protein genes, a complete gene and a partial gene encoding the β′-subunit of DpRp. Primers and reaction conditions were designed for PCR-mediated amplification of gene fragments from diverse phytoplasmas. The gene sequences from phytoplasmas classified in groups 16SrI, 16SrII, 16SrIII, 16SrX and 16SrXII were subjected to sequence similarity and phylogenetic analyses. The gene sequences were more variable than 16S rRNA gene sequences, more clearly distinguishing among phytoplasma lineages. Phylogenetic trees based on 16S rRNA and gene sequences had similar topologies, and branch lengths in the tree facilitated distinctions among closely related phytoplasmas. Virtual RFLP analysis of gene sequences also improved distinctions among closely related lineages. The results indicate that the gene provides a useful additional marker for phytoplasma classification that should facilitate studies of disease aetiology and epidemiology.

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2013-10-01
2024-04-19
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Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny
Int J Syst Evol Microbiol 63, 3904 (2013); https://doi.org/10.1099/ijs.0.051912-0
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