| Summary: | Light is necessary for primordium differentiation and fruiting body development for most edible fungi; however, light perception and signal transduction have only been well studied in model fungi. In this study, a hierarchical network of transcriptional response to light in <i>Cordyceps militaris</i>, one of the edible fungi, has been described on a genome-wide scale using dynamic transcriptome analysis. It was shown that light regulated the transcript of 1722 genes, making up 18% of the whole genome of <i>C. militaris</i>. Analysis of light-responsive genes in <i>C. militaris</i> identified 4 categories: immediate-early, early, late, and continuous light-responsive genes, and the gene number increased distinctly with prolonged light exposure. Light-responsive genes with distinct functional categories showed specific time-dependent regulation. The target genes of CmWC-1, the most important photoreceptor, were revealed by ChIP-seq. A total of 270 significant peaks corresponding to 427 genes were identified to be directly regulated by CmWC-1, among which 143 genes respond to light. Based on 270 ChIP-seq peaks, the binding site for CmWC-1 was identified as AAATCAGACCAC/GTGGTCTGATTT, differing from the binding site by the homolog in <i>Neurospora crassa</i>. Elucidating the mechanisms of light perception and signal transduction will be helpful for further research on the fruiting body development in edible fungi.
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