Transcriptional Changes in Potato Sprouts upon Interaction with Rhizoctonia solani Indicate Pathogen-Induced Interference in the Defence Pathways of Potato.

Rhizoctonia solani is the causer of black scurf disease on potatoes and is responsible for high economical losses in global agriculture. In order to increase the limited knowledge of the plants' molecular response to this pathogen, we inoculated potatoes with R. solani AG3-PT isolate Ben3 and carried out RNA sequencing with total RNA extracted from potato sprouts at three and eight days post inoculation (dpi). In this dual RNA-sequencing experiment, the necrotrophic lifestyle of R. solani AG3-PT during early phases of interaction with its host has already been characterised. Here the potato plants' comprehensive transcriptional response to inoculation with R. solani AG3 was evaluated for the first time based on significantly different expressed plant genes extracted with DESeq analysis. Overall, 1640 genes were differentially expressed, comparing control (-Rs) and with R. solani AG3-PT isolate Ben3 inoculated plants (+Rs). Genes involved in the production of anti-fungal proteins and secondary metabolites with antifungal properties were significantly up regulated upon inoculation with R. solani. Gene ontology (GO) terms involved in the regulation of hormone levels (i.e., ethylene (ET) and jasmonic acid (JA) at 3 dpi and salicylic acid (SA) and JA response pathways at 8 dpi) were significantly enriched. Contrastingly, the GO term "response to abiotic stimulus" was down regulated at both time points analysed. These results may support future breeding efforts toward the development of cultivars with higher resistance level to black scurf disease or the development of new control strategies.

Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3.

The basidiomycetes fungus Rhizoctonia solani AG3 is responsible for black scurf disease on potato and occurs in each potato growing area world-wide. In this study, the draft genome sequence of the black scurf pathogen R. solani AG3-PT isolate Ben3 is presented. The genome sequence of R. solani AG3-PT isolate Ben3 consists of 1385 scaffolds. These scaffolds amount to a size of approx. 51 Mb. Considering coverage analyses of contigs, the size of the diploid genome was estimated to correspond to 116 Mb. Gene prediction by applying AUGUSTUS (3.2.1.) resulted in 12,567 identified genes. Based on automatic annotation using GenDBE, genes potentially encoding cellulases and enzymes involved in secondary metabolite synthesis were identified in the R. solani AG3-PT isolate Ben3 genome. Comparative analyses including the R. solani AG3 isolate Rhs1AP, also originating from potato, revealed first insights into core genes shared by both isolates and unique determinants of each isolate.

Does Constitutive Expression of Defense-Related Genes and Salicylic Acid Concentrations Correlate with Field Resistance of Potato to Black Scurf Disease?

Black scurf disease on potato caused by Rhizoctonia solani AG3 occurs worldwide and is difficult to control. The use of potato cultivars resistant to black scurf disease could be part of an integrated control strategy. Currently, the degree of resistance is based on symptom assessment in the field, but molecular measures could provide a more efficient screening method. We hypothesized that the degree of field resistance to black scurf disease in potato cultivars is associated with defense-related gene expression levels and salicylic acid (SA) concentration. Cultivars with a moderate and severe appearance of disease symptoms on tubers were selected and cultivated in the same field. In addition, experiments were conducted under controlled conditions in an axenic in vitro culture and in a sand culture to analyze the constitutive expression of defense-related genes and SA concentration. The more resistant cultivars did not show significantly higher constitutive expression levels of defense-related genes. Moreover, the level of free SA was increased in the more resistant cultivars only in the roots of the plantlets grown in the sand culture. These results indicate that neither expression levels of defense-related genes nor the amount of SA in potato plants can be used as reliable predictors of the field resistance of potato genotypes to black scurf disease.

Capsicum Leaves under Stress: Using Multi-Omics Analysis to Detect Abiotic Stress Network of Secondary Metabolism in Two Species.

The plant kingdom contains an enormous diversity of bioactive compounds which regulate plant growth and defends against biotic and abiotic stress. Some of these compounds, like flavonoids, have properties which are health supporting and relevant for industrial use. Many of these valuable compounds are synthesized in various pepper (Capsicum sp.) tissues. Further, a huge amount of biomass residual remains from pepper production after harvest, which provides an important opportunity to extract these metabolites and optimize the utilization of crops. Moreover, abiotic stresses induce the synthesis of such metabolites as a defense mechanism. Two different Capsicum species were therefore exposed to chilling temperature (24/18 ℃ vs. 18/12 ℃), to salinity (200 mM NaCl), or a combination thereof for 1, 7 and 14 days to investigate the effect of these stresses on the metabolome and transcriptome profiles of their leaves. Both profiles in both species responded to all stresses with an increase over time. All stresses resulted in repression of photosynthesis genes. Stress involving chilling temperature induced secondary metabolism whereas stresses involving salt repressed cell wall modification and solute transport. The metabolome analysis annotated putatively many health stimulating flavonoids (apigetrin, rutin, kaempferol, luteolin and quercetin) in the Capsicum biomass residuals, which were induced in response to salinity, chilling temperature or a combination thereof, and supported by related structural genes of the secondary metabolism in the network analysis.

Impact of Moderate Cold and Salt Stress on the Accumulation of Antioxidant Flavonoids in the Leaves of Two Capsicum Cultivars.

The horticultural production of bell peppers generates large quantities of residual biomass. Abiotic stress stimulates the production of protective flavonoids, so the deliberate application of stress to the plants after fruit harvest could provide a strategy to valorize horticultural residuals by increasing flavonoid concentrations, facilitating their industrial extraction. Here we exposed two Capsicum cultivars, a chilli and a bell pepper, to cold and salt stress and combinations thereof to determine their valorization potential. Noninvasive image-based phenotyping and multiparametric fluorescence measurements indicated that all stress treatments inhibited plant growth and reduced the leaf chlorophyll fluorescence index, with the chilli cultivar showing greater sensitivity. The fluorescence-based FLAV index allowed the noninvasive assessment of foliar luteolin glycosides. High-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis showed that moderate cold increased the levels of two foliar antioxidant luteolin glycosides in both cultivars, with bell pepper containing the highest amounts (induced to maximum 5.5 mg g-1 DW cynaroside and 37.0 mg g-1 DW graveobioside A) after combined stress treatment. These data confirm the potential of abiotic stress for the valorization of residual leaf biomass to enhance the industrial extraction of antioxidant and bioactive flavonoids.

Genome Analyses of the Less Aggressive Rhizoctonia solani AG1-IB Isolates 1/2/21 and O8/2 Compared to the Reference AG1-IB Isolate 7/3/14.

Rhizoctonia solani AG1-IB of the phylum Basidiomycota is known as phytopathogenic fungus affecting various economically important crops, such as bean, rice, soybean, figs, cabbage and lettuce. The isolates 1/2/21 and O8/2 of the anastomosis group AG1-IB originating from lettuce plants with bottom rot symptoms represent two less aggressive R. solani isolates, as confirmed in a pathogenicity test on lettuce. They were deeply sequenced on the Illumina MiSeq system applying the mate-pair and paired-end mode to establish their genome sequences. Assemblies of obtained sequences resulted in 2092 and 1492 scaffolds, respectively, for isolate 1/2/21 and O8/2, amounting to a size of approximately 43 Mb for each isolate. Gene prediction by applying AUGUSTUS (v. 3.2.1.) yielded 12,827 and 12,973 identified genes, respectively. Based on automatic functional annotation, genes potentially encoding cellulases and enzymes involved in secondary metabolite synthesis were identified in the AG1-IB genomes. The annotated genome sequences of the less aggressive AG1-IB isolates were compared with the isolate 7/3/14, which is highly aggressive on lettuce and other vegetable crops such as bean, cabbage and carrot. This analysis revealed the first insights into core genes of AG1-IB isolates and unique determinants of each genome that may explain the different aggressiveness levels of the strains.

Necrotrophic lifestyle of Rhizoctonia solani AG3-PT during interaction with its host plant potato as revealed by transcriptome analysis.

The soil-borne pathogen Rhizoctonia solani infects a broad range of plants worldwide and is responsible for significant crop losses. Rhizoctonia solani AG3-PT attacks germinating potato sprouts underground while molecular responses during interaction are unknown. To gain insights into processes induced in the fungus especially at early stage of interaction, transcriptional activity was compared between growth of mycelium in liquid culture and the growing fungus in interaction with potato sprouts using RNA-sequencing. Genes coding for enzymes with diverse hydrolase activities were strongly differentially expressed, however with remarkably dissimilar time response. While at 3 dpi, expression of genes coding for peptidases was predominantly induced, strongest induction was found for genes encoding hydrolases acting on cell wall components at 8 dpi. Several genes with unknown function were also differentially expressed, thus assuming putative roles as effectors to support host colonization. In summary, the presented analysis characterizes the necrotrophic lifestyle of R. solani AG3-PT during early interaction with its host.