Evaluations on the effects of phenylpyrrole fungicides in Botrytis cinerea by RNA-Seq transcriptome analysis

The use of synthetic fungicides is still very common for the management of grey mould caused by Botrytis cinerea. However, mode of action and resistance mechanism in the target pathogen for several fungicides, including the phenylpyrrole fludioxonil, are not completely understood. Whole transcriptional changes caused by the exposure to different concentrations of fludioxonil (EC50 and EC75) in two strains of the pathogen, one sensitive and one resistant to fludioxonil, were investigated using Illumina sequencing and RNASeq analysis to identify affected genes and metabolic processes. Overall, about 930 differentially expressed transcripts (DETs; Fold change ≥ |6| and RPKM ≥ 5) were identified in each strain comparing fludioxonil-exposed versus the unexposed colonies. Comprehensive functional enrichment analysis showed that redox processes were associated to up- and down-regulated DETs, while biosynthesis of secondary metabolites and cell wall and surface proteins were strictly related with the up-regulated ones. Membrane-lipid metabolic processes were up-regulated in the sensitive strain and downregulated in the resistant strain. Fungal growth as well as regulation and signalling, transmembrane transport, response to stress and protein metabolism were more frequently related to down-regulated DETs. Among transcripts associated with transport and regulation, the mrr1 gene, encoding the transcription factor responsible for Multi-Drug Resistance type 1 (MDR1)-related atrB overexpression, was up-regulated in the fludioxonil-resistant strain. The results provide new knowledge that might be useful to plan novel sustainable disease management strategies, increasingly oriented to preserve effectiveness of chemicals and minimize environmental impact.