Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes SummaryVerticillium longisporum, a soil-borne pathogenic fungus, causes vascular disease in oilseed rape (Brassica napus). We proposed that plant microRNAs (miRNAs) are involved in the plant-V. longisporum interaction.To identify oilseed rape miRNAs, we deep-sequenced two small RNA libraries made from V. longisporum infected/noninfected roots and employed Brassica rapa and Brassica oleracea genomes as references for miRNA prediction and characterization.We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to the AA and CC genomes, respectively. Microsynteny analysis with the conserved miRNAs and their flanking protein coding sequences revealed 137 AA-CC genome syntenic miRNA pairs and 61 AA and 42 CC genome-unique miRNAs. Sixtytwo miRNAs were responsive to the V. longisporum infection. We present data for specific interactions and simultaneously reciprocal changes in the expression levels of the miRNAs and their targets in the infected roots. We demonstrate that miRNAs are involved in the plant-fungus interaction and that miRNA168-Argonaute 1 (AGO1) expression modulation might act as a key regulatory module in a compatible plant-V. longisporum interaction.Our results suggest that V. longisporum may have evolved a virulence mechanism by interference with plant miRNAs to reprogram plant gene expression and achieve infection.

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Fusarium head blight (FHB) is one of the most important diseases of wheat, causing yield losses and mycotoxin contamination of harvested grain. A complex of different toxigenic Fusarium species is responsible for FHB and the composition and predominance of species within the FHB complex are determined by meteorological and agronomic factors. In this study, grain of three different susceptible winter wheat cultivars from seven locations in northern Germany were analysed within a five-year survey from 2013 to 2017 by quantifying DNA amounts of different species within the Fusarium community as well as deoxynivalenol (DON) and zearalenone (ZEA) concentrations. Several Fusarium species co-occur in wheat grain samples in all years and cultivars. F. graminearum was the most prevalent species, followed by F. culmorum, F. avenaceum and F. poae, while F. tricinctum and F. langsethiae played only a subordinate role in the FHB complex in terms of DNA amounts. In all cultivars, a comparable year-specific quantitative occurrence of the six detected species and mycotoxin concentrations were found, but with decreased DNA amounts and mycotoxin concentrations in the more tolerant cultivars, especially in years with higher disease pressure. In all years, similar percentages of DNA amounts of the six species to the total Fusarium DNA amount of all detected species were found between the three cultivars for each species, with F. graminearum being the most dominant species. Differences in DNA amounts and DON and ZEA concentrations between growing seasons depended mainly on moisture factors during flowering of wheat, while high precipitation and relative humidity were the crucial meteorological factors for infection of wheat grain by Fusarium. Highly positive correlations were found between the meteorological variables precipitation and relative humidity and DNA amounts of F. graminearum, DON and ZEA concentrations during flowering, whereas the corresponding correlations were much weaker several days before (heading) and after flowering (early and late milk stage).