Rubbery taproot disease (RTD) of sugar beet was observed in Serbia for the first time in the 1960s. The disease was already described in neighbouring Bulgaria and Romania at the time, but it was associated with abiotic factors. In this study on RTD of sugar beet in its main growing area of Serbia, we provide evidence of the association between 'Ca. P. solani' (stolbur phytoplasma) infection and the occurrence of typical RTD symptomatology. 'Ca. P. solani' was identified by PCR and the sequence analyses of 16S rRNA, tuf, secY and stamp genes. In contrast, the causative agent of the syndrome “basses richesses” of sugar beet, namely, 'Ca. A. phytopathogenicus', was not detected. Sequence analysis of the stolbur strain’s tuf gene confirmed a previously reported and a new, distinct tuf stolbur genotype (named ‘tuf d’) that is prevalent in sugar beet. The sequence signature of the tuf gene as well as the one of stamp both correlate with the epidemiological cycle and reservoir plant host. This study provides knowledge that enables for the first time the differentiation of stolbur strains associated with RTD of sugar beet from closely related strains, thereby providing necessary information for further epidemiological work seeking to identify insect vectors and reservoir plant hosts. The results of this study indicate that there are differences in hybrid susceptibility. Clarifying the etiology of RTD as a long-known and economically important disease is certainly the first step towards disease management in Serbia and neighboring countries.
A recent survey in Germany revealed the wide presence of ‘Candidatus Phytoplasma ulmi’ in native elm stands. Accessions were studied for their genetic variability and phylogenetic relationship based on the conserved groEL and the variable imp gene. While the groEL sequences revealed a high intraspecific homology of more than 99%, the homology of the imp gene dropped to 71% between distantly related sequences. Twenty-nine groEL and 74 imp genotypes were distinguished based on polymorphic sites. Phylogenetic analysis of the groEL gene clustered all ‘Ca. P. ulmi’ strains and separated them from related phytoplasmas of the 16SrV group. The inferred phylogeny of the imp gene resulted in a different tree topology and separated the ‘Ca. P. ulmi’ genotypes into two clusters, one closely related to the flavescence dorée phytoplasma strain FD-D (16SrV-D), the other affiliated with the flavescence dorée phytoplasma strains FD-C and FD70 and the alder yellows phytoplasma (16SrV-C). In both phylograms, ‘Ca. P. ulmi’ genotypes from Scots elm trees formed a coherent cluster, while genotypes from European white elms and field elms grouped less strictly. The regional distribution pattern was congruent for some of the groEL and imp genotypes, but a strict linkage for all genotypes was not apparent.
The γ-proteobacterium ‘Candidatus Arsenophonus phytopathogenicus’ is assigned as the major pathogen of “Syndrome des basses richesses”, a sugar beet disease characterised by a reduction in the sugar content of taproots and biomass yield. Despite the economic impact of this bacteriosis, diagnostics for this important pathogen currently rely on end-point PCR detection. Herein, we introduce a TaqMan qPCR for diagnostics of the agent targeting genes encoding a heat shock protein of the Hsp20 family and mannose-6-phosphate isomerase. Quantitation with synthetic oligonucleotides as standard showed that the developed TaqMan qPCR assays enable the detection of up to 100 target copies. A comparison between the TaqMan qPCR and end-point PCR for ‘Ca. A. phytopathogenicus’ detection was carried out on 78 sugar beet samples from different locations in southern Germany. The newly developed assays enable the fast, reliable and sensitive detection of ‘Ca. A. phytopathogenicus’ in sugar beet.
Herein, we report the draft genome sequence of “Candidatus Phytoplasma pruni” strain ChTDIII (subgroup 16SrIII-B). The final assembly consists of 790,517 nucleotides organized in 67 contigs (minimal size, 1 kb), with a G+C content of 29.4% and encoding 672 proteins.
The <i>trans</i>-translation process is a ribosomal rescue system for stalled ribosomes processing truncated mRNA. The genes <i>ssrA</i> and <i>smpB</i> fulfil the key functions in most bacteria, but some species have either lost these genes or the function of the ribosomal rescue system is taken over by other genes. To date, the ribosomal rescue system has not been analysed in detail for the <i>Acholeplasmataceae</i>. This family, in the Mollicutes class, comprises the genus <i>Acholeplasma</i> and the provisional taxon “<i>Candidatus</i> Phytoplasma”. Despite their monophyletic origin, the two clades can be separated by traits such as not representing primary pathogens for acholeplasmas versus being phytopathogenic for the majority of phytoplasmas. Both taxa share reduced genomes, but only phytoplasma genomes are characterised by a remarkable level of instability and reduction. Despite the general relevance of the ribosomal rescue system, information is lacking on coding, the genomic context and pseudogenisation of <i>smpB</i> and <i>ssrA</i> and their possible application as a phylogenetic marker. Herein, we provide a comprehensive analysis of the ribosomal rescue system in members of <i>Acholeplasmataceae</i>. The examined <i>Acholeplasmataceae</i> genomes encode a ribosomal rescue system, which depends on tmRNA encoded by <i>ssrA</i> acting in combination with its binding protein SmpB. Conserved gene synteny is evident for <i>smpB</i>, while <i>ssrA</i> shows a less conserved genomic context. Analysis of the tmRNA sequences highlights the variability of proteolysis tag sequences and short conserved sites at the 5′- and 3′-ends. Analyses of <i>smpB</i> provided no hints regarding the coding of pseudogenes, but they did suggest its application as a phylogenetic marker of <i>Acholeplasmataceae</i> – in accordance with 16S rDNA topology. Sequence variability of <i>smpB</i> provides sufficient information for species assignment and phylogenetic analysis.
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