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Lilac (Syringa sp.) Hosts a New ‘Candidatus Phytoplasma pruni’-related Strain in Utah: Ribosomal RNA and secY Genes Distinguish the Phytoplasma from Previously Described Lineages

    Authors and Affiliations
    • R. E. Davis
    • E. L. Dally
    • Y. Zhao , USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD 20705
    • S. V. Thomson
    • C. Nischwitz , Department of Biology, Utah State University, Logan 84322.

      A decline in lilac (Syringa sp.) has been observed in Utah for over 25 years. Symptoms initially included leaf chlorosis, mosaic, and rolling, and diseased plants eventually died over a period of 2 to 3 years. Attempts over several years did not result in consistent isolation or detection of any bacterial, fungal, or viral pathogen. Samples for this study were taken from plants in a row of 15 diseased lilacs in Cache County, Utah. Polymerase chain reaction assays (PCRs) for amplification of ribosomal (r) RNA gene sequences (rDNA) (primers, P1/16S-SR) and secY genomic regions [nested primers, L15F1A(III)/MapR1A(III) followed by SecYF1(III)/SecYR1(III)] (Davis et al. 2013) were used to assess possible association of a phytoplasma with the disease, lilac decline (LlcDec). DNA for use as PCR template was separately extracted from excised veins of symptomatic leaves collected from two symptomatic plants. Amplicons of rDNA were of predicted sizes, indicating possible phytoplasmal infection in both plants; nucleotide sequencing confirmed that the amplicons were derived from a phytoplasma. The rDNA and secY sequences, respectively, were mutually identical for the phytoplasma strains (designated LlcDec1 and LlcDec2) detected in the two plants. The nucleotide sequences determined for the amplified 1.5-kbp rDNA and 1.7-kbp secY genomic regions were deposited in GenBank under Accession Nos. KP877578 and KP877579 (rDNAs) and KP877580 and KP877581 (secY regions). LlcDec phytoplasma was classified, using iPhyClassifier (Zhao et al. 2009), as a member of group 16SrIII. The 16S rDNA virtual RFLP patterns were most similar to those of subgroup 16SrIII-A (‘Candidatus Phytoplasma pruni’), but the MseI RFLP pattern differed, indicating strain LlcDec represents a variant subgroup lineage, 16SrIII-A*. Strains LlcDec1 and LlcDec2 shared 99.7% nucleotide sequence identity with ‘Ca. Phytoplasma pruni’ (rrnA, Accession No. JQ044393), but differed from ‘Ca. Phytoplasma pruni’ by a single nucleotide in each of three 16S rRNA gene regions corresponding to unique signature sequences in the original description of ‘Ca. Phytoplasma pruni’ (Davis et al. 2013). Accordingly, strains LlcDec1 and LlcDec2 are referred to as ‘Ca. Phytoplasma pruni’-related strains. The deduced amino acid sequences of SecY protein translocase from the LlcDec strains differed from that of ‘Ca. Phytoplasma pruni’ (Accession No. AEY80160) by two residues (at positions 90, P [proline in LlcDec]→S [serine in ‘Ca. Phytoplasma pruni’]; and 167, I [isoleucine in LlcDec]→V [valine in ‘Ca. Phytoplasma pruni’]). Phylogenetic analyses of 16S rDNA and SecY amino acid sequences indicated that LlcDec phytoplasma represents a distinct lineage closely related to ‘Ca. Phytoplasma pruni’. Although lilac can be infected by a ‘Ca. Phytoplasma pruni’-related strain (as we have found in this study), ‘Ca. Phytoplasma fraxini’ (Hibben et al. 1991), ‘Ca. Phytoplasma pruni’ (Green et al. 2015), and a ‘Ca. Phytoplasma asteris’-related strain (Jomantiene et al. 2011), the symptoms associated with infection by the ‘Ca. Phytoplasma pruni’-related strain reported here differ from those associated with infection of lilac by the other phytoplasmas.