Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.

Allelopathy is a plant-plant interaction in which an allelopathic plant negatively affects the growth of neighboring plants. Induction of oxidative stress is a common reaction to environmental stress; however, the molecular pathways between allelopathy and oxidative stress are not well understood. In this study, we analyzed the effects of 1 % and 10 % aqueous rhizome extracts of two highly invasive plants, Japanese knotweed (Fallopia japonica) and Bohemian knotweed (Fallopia × bohemica), on the growth, morphology, metabolome, and transcriptome of 3-day-old radish (Raphanus sativus) seedlings. Fallopia extracts decreased root biomass by up to 70 % and affected root morphology. Several genes associated with root hair formation were downregulated, resulting in decreased or completely blocked root hair development. Based on the differential gene expression, we propose a model of how Fallopia extracts affect radish root hair development. The extracts also induced several genes associated with the glutathione-ascorbate cycle, including glutathione peroxidases, ascorbate peroxidase, dehydroascorbate reductase, and catalase. Treated radish roots exhibited disturbed homeostasis of reactive oxygen species and oxidative stress, as indicated by the increased content of proline, total glutathione, and total cysteine, and the decreased content of total ascorbate. Both Fallopia extracts exhibited phytotoxic potential; however, the F. × bohemica extract caused more severe changes in radish seedlings than the F. japonica extract. Overall, our findings reveal that Fallopia extracts decrease root growth and root hair development, induce oxidative stress, and alter the expression of genes related to hormones and ROS homeostasis. As such, they provide new insights into the mechanisms underlying the invasiveness and allelopathic effects of Fallopia.