Kube, Michael

ABSTRACT The complete genome of “ Candidatus Phytoplasma solani” GOE was obtained from the infected vector Pentastiridius leporinus by single-molecule real-time sequencing. This 16SrXII-P phytoplasma is associated with the economically important sugar beet disease “syndrome basses richesses.” The genome sequence is an essential resource for diagnosis and understanding pathogen–host interaction.

ABSTRACT The complete genome of “ Candidatus Phytoplasma fraxini” AshY1, originating from Fraxinus americana in North America, was assembled using long reads from single-molecule real-time sequencing technology. The chromosome of 598 kb provides insights into the effector repertoire of a phytopathogenic bacterium from the 16SrVII phytoplasma group.

Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon ‘Candidatus Phytoplasma asteris’ were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of ‘Ca. P. asteris’ and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.

Two phloem-limited pathogens, ‘Candidatus Arsenophonus phytopathogenicus’ and ‘Candidatus Phytoplasma solani’, threaten sugar beet production in France, Switzerland, and Germany. Previous studies of these pathogens in Germany had focused on its western and southern regions, leaving a knowledge gap about eastern Germany. Despite their importance, this study is the first to investigate phytoplasmas in sugar beet in Saxony-Anhalt, Germany. A phytoplasma strain related to ‘Ca. P. solani’ is found predominant in Saxony-Anhalt, unlike in France, where ‘Ca. P. solani’ has a minor role compared with ‘Ca. A. phytopathogenicus’. The phytoplasma strain infecting sugar beet in Saxony-Anhalt was classified into a new subgroup designated as 16SrXII-P. The multilocus sequence analysis (MLSA) of nonribosomal genes of the novel phytoplasma strain showed that it is significantly different from the reference and all previously reported ‘Ca. P. solani’ strains including the strain from western Germany. Analyses of sugar beet samples from previous years confirmed the presence of the 16SrXII-P strain in sugar beet as early as 2020 and also in Bavaria in southern Germany. Based on 16S rDNA analysis, ‘Ca. A. phytopathogenicus’ in Saxony-Anhalt is identical to strains in sugar beet in other parts of Germany and France, as well as to a strain in potato from Germany. The presence and prevalence of two phytoplasmas in sugar beet in Germany suggest that more attention should be directed toward understanding phytoplasma infection in sugar beet in this country.

Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, phyllody, and virescence. The recently published genome of ‘Ca. P. rubi’ RS enabled a comprehensive genomic comparison to the complete genomes of 16SrV phytoplasmas, comprising strains of the flavescence dorée-associated phytoplasma CH and two ‘Candidatus Phytoplasma ziziphi’ strains. Besides the typical transporters and metabolic features of phytoplasmas, the phosphorolysis of sucrose and the utilization of the carboxylic acid L-lactate became apparent for the 16SrV-group. With respect to the effector repertoire and the encoded immunodominant membrane proteins involved in host colonization, the group revealed conserved features that comprise the variable membrane proteins A and B. However, SAP11- and SAP54 orthologs were limited to ‘Ca. P. rubi’ RS and ‘Ca. P. ziziphi’. Genome-sequence-based phylogenetic analysis supports the close relationship of these genomes relative to alder yellows phytoplasmas. The analyses supported the impact of the mobilome on phytoplasma evolution but also highlighted that there is the possibility of identifying phytoplasmas with a larger metabolic repertoire in the future.

The phytoplasma “ Candidatus Phytoplasma rubi” is associated with Rubus stunt disease. The complete genome was determined by assembling Oxford Nanopore Technologies system-derived long reads, with short-read polishing with Illumina reads. The genome of strain RS, from Germany, is organized in one circular chromosome with a length of 762 kb.

The genus ‘Candidatus Phytoplasma’ was proposed to accommodate cell wall-less bacteria that are molecularly and biochemically incompletely characterized, and colonize plant phloem and insect vector tissues. This provisional classification is highly relevant due to its application in epidemiological and ecological studies, mainly aimed at keeping the severe phytoplasma plant diseases under control worldwide. Given the increasing discovery of molecular diversity within the genus ‘Ca. Phytoplasma’, the proposed guidelines were revised and clarified to accommodate those ‘Ca. Phytoplasma’ species strains sharing >98.65 % sequence identity of their full or nearly full 16S rRNA gene sequences, obtained with at least twofold coverage of the sequence, compared with those of the reference strain of such species. Strains sharing <98.65 % sequence identity with the reference strain but >98.65 % with other strain(s) within the same ‘Ca. Phytoplasma’ species should be considered related strains to that ‘Ca. Phytoplasma’ species. The guidelines herein, keep the original published reference strains. However, to improve ‘Ca. Phytoplasma’ species assignment, complementary strains are suggested as an alternative to the reference strains. This will be implemented when only a partial 16S rRNA gene and/or a few other genes have been sequenced, or the strain is no longer available for further molecular characterization. Lists of ‘Ca. Phytoplasma’ species and alternative reference strains described are reported. For new ‘Ca. Phytoplasma’ species that will be assigned with identity ≥98.65 % of their 16S rRNA gene sequences, a threshold of 95 % genome-wide average nucleotide identity is suggested. When the whole genome sequences are unavailable, two among conserved housekeeping genes could be used. There are 49 officially published ‘Candidatus Phytoplasma’ species, including ‘Ca. P. cocostanzaniae’ and ‘Ca. P. palmae’ described in this manuscript.

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.

Rubbery taproot disease of sugar beet (RTD), associated with ‘Candidatus Phytoplasma solani’, appeared in 2020 on an epidemic scale in northern Serbia and southern Slovakia, situated at opposite edges of the Pannonian Plain. In the affected locations where the disease was assessed, symptomatic sugar beets were analysed for phytoplasma infection. Additionally, multilocus sequence analyses of ‘Ca. P. solani’ strains on epidemiologically informative marker genes (tuf, stamp and vmp1) were performed. Symptomatic sugar beets from other countries of the Pannonian Plain (Croatia, Hungary and Austria), one sample from Germany, and red beets from Serbia were included in the analyses. ‘Ca. P. solani’ was detected in sugar beet in all assessed countries, as well as in red beet. Molecular analyses revealed the high genetic variability of ‘Ca. P. solani’ with the presence of all four tuf-types (a, b1, b2 and d), 14 stamp genotypes (seven new) and five vmp1 profiles (one new). The most common multilocus genotype in Serbia, Slovakia, Croatia, and Hungary was dSTOLg (tuf-d/STOL/V2-TA). It was dominant on sites with epidemic RTD outbreaks in the Pannonian Plain and in several sugar beet fields with non-epidemic RTD occurrence suggesting the prevalence of a particular epidemiological pathway during the epidemic’s phases.