Sex prepares the plant pathogenic fungus Botrytis cinerea for host invasion

Botrytis cinerea is a plant pathogenic ascomycete producing apothecia as sexual fruiting bodies. We used RNAseq to analyse expression profiles in sclerotia, three stages of apothecium development (primordia, full grown stipe, apothecial disk), and mature ascospores. Very pure tissue samples of the five developmental stages could be isolated and transcriptional changes between successive developmental stages were analysed. Changes were observed in the expression levels of as many as 15 secondary metabolite gene clusters, in different stages. The most profound overall changes in transcript profiles were at the initiation of sexual development (transition from sclerotia to primordia, >2500 differentially expressed genes) and even more so, at the completion of sexual reproduction in the mature ascospores: 1424 genes were upregulated and 2485 genes were downregulated in ascospores as compared to mature apothecial disks. Among the genes upregulated in ascospores were many genes encoding virulence factors (plant cell wall hydrolases, proteinases, multidrug efflux ABC transporters, superoxide dismutase, phytoalexin-oxidising laccase, an oxalic acid biosynthetic enzyme), several hexose transporters and a number of signal transduction components known to be involved in virulence. These observations clearly suggest that ascospores are transcriptionally primed for infection already prior to their arrival on host plants. Strikingly, the large transcriptional changes at the initiation and the completion of the sexual cycle often affected numerous clusters of genes (not only genes in secondary metabolite clusters), rather than genes randomly dispersed through the genome. Sexual development also coincided with changes in the expression of several genes potentially involved in chromatin organization (C-5 cytosine methylase, several histone acetyltransferases, dicer-like protein), suggesting an epigenetic regulation of gene expression during the sexual cycle.