Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2012
Publication Date: 2/1/2013
Publication URL: http://handle.nal.usda.gov/10113/57467
Citation: Davis, R.E., Zhao, Y., Dally, E.L., Lee, I., Jomantiene, R., Douglas, S.M. 2013. 'Candidatus Phytoplasmas pruni', a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes. International Journal of Systematic and Evolutionary Microbiology. 63:766-776. Interpretive Summary: X-disease is one of the most damaging diseases known in peach and other stone fruit trees, in which it causes causes heavy losses in fruit crops. X-disease has been attributed to infection by a phytoplasma, a tiny bacterium that has no cell wall, is spread by sap-sucking insects, and cannot be isolated like other bacteria and grown in the laboratory. There is need to obtain precise molecular markers for identification and classification of the X-disease phytoplasma to aid the design of appropriate disease control measures and to enable quarantine measures that effectively prevent spread of the disease. Using molecular methods to study specific genes, we found that the X-disease phytoplasma represents a previously undescribed species level lineage, for which we have proposed the designation, ‘Candidatus Phytoplasma pruni’. Our results provide molecular markers by which the X-disease phytoplasma may be detected and identified, benefitting measures to control the disease, as well as aiding implementation of quarantine measures to prevent its spread. Such measures will aid the cause of food security and sustainable production of a valued source of nutritious fruit. This report will be of interest to diagnostics laboratories, research scientists, farmers, and quarantine agencies internationally. By molecularly characterizing the cause of disease in an important fruit crop, the work immediately impacts efforts to attain sustainable agricultural systems.
Technical Abstract: X-disease is one of the most serious diseases known in peach (Prunus persica). Based on RFLP analysis of 16S rRNA gene sequences, peach X-disease phytoplasma strains from eastern and western United States and eastern Canada were classified in 16S rDNA RFLP group 16SrIII, subgroup A. Phylogenetic analyses of 16S rRNA gene sequences revealed that the X-disease phytoplasma strains formed a distinct subclade within the phytoplasma clade and supported the hypothesis that they represent a lineage distinct from those of previously described ‘Candidatus Phytoplasma’ species. Nucleotide sequence alignments revealed that all studied X-disease phytoplasma strains shared less than 97.5 % similarity of 16S rDNA with previously described ‘Candidatus Phytoplasma’ species. Based on unique properties of DNA, we propose recognition of X-disease phytoplasma strain PX11CT1R as representative of a novel taxon, ‘Candidatus Phytoplasma pruni’. Results from nucleotide and phylogenetic analyses of secY and ribosomal protein (rp) gene sequences provided additional molecular markers of the ‘Ca. Phytoplasma pruni’ lineage. We propose that the term ‘Candidatus Phytoplasma pruni’ be applied to phytoplasma strains whose 16S rRNA gene sequences contain the oligonucleotide sequences of unique regions that are designated in the formally published description of the species. Such strains include X-disease phytoplasma and - within the tolerance of a single base difference in one unique sequence - peach rosette, peach red suture, and little peach phytoplasmas. We further propose that secY, rp, and other genetic loci from the reference strain of a species, and where possible oligonucleotide sequences of unique regions of those genes that distinguish species within a given 16Sr group, be incorporated in amended descriptions and as part of future descriptions of ‘Candidatus Phytoplasma’ species.