FgHtf1 regulates global gene expression towards aerial mycelium and conidiophore formation in the cereal fungal pathogen Fusarium graminearum

The homeobox gene family of transcription factors (HTF) control many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF (FgHtf1) regulates conidia morphology in the plant pathogenic Fusarium graminearum. This study investigates the mechanism of FgHtf1-mediated regulation and identifies putative FgHtf1 target genes by chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1 were identified. Subsequent motif prediction analysis identified two DNA binding motifs TAAT and CTTGT. Among the FgHtf1 target genes included FgHTF1 itself and several important conidiation related genes (e.g. FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-PKA-Msn2/4 and Ca2+-calcineurin-Crz1 pathways. Taken together, these results suggest that in addition to auto-regulation, FgHtf1 also controls global gene expression, and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation related genes. IMPORTANCE The homeobox gene family of transcription factors is known to be involved in development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of Homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum. In this study, we have identified FgHtf1-controlled target genes and binding motifs. We found that besides auto-regulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCon7 and other conidiation related-genes.