Comparative Transcriptome Analysis of Xylaria grammica Under Light and Dark Conditions Reveals Dark-Responsive Activation of a Patulin-like Locus Involved in Grammicin Biosynthesis

Xylaria grammica is an endophytic fungus that produces grammicin, a polyketide reported as a structural isomer of the mycotoxin patulin. However, the environmental regulation of grammicin production remains unclear, and the full biosynthetic pathway has not yet been completely resolved. Genome re-annotation and biosynthetic gene cluster mining revealed high secondary metabolite potential, with 92 predicted clusters spanning major biosynthetic classes. Time-series RNA sequencing under shaking dark, static dark, and continuous light conditions showed strong condition-dependent transcriptome divergence. Light-grown cultures were enriched in functions associated with stress adaptation and detoxification, including oxidoreductase- and monooxygenase-related categories, whereas static dark cultures showed broader activation of secondary metabolism-associated genes at later stages. Among the predicted biosynthetic gene clusters, a patulin-like locus in X. grammica contained homologs corresponding to most genes of the Aspergillus clavatus pat cluster from PatA to PatO, although the gene order differed. Expression profiling revealed coordinated induction of patulin-like genes after 3 days post-inoculation under dark conditions, whereas continuous light strongly repressed their transcription. Quantitative RT-PCR analysis further confirmed this darkness-dependent activation pattern. Together, with previous functional evidence showing that patK and patL are required for grammicin production, these results indicate that darkness acts as a major regulatory switch for secondary metabolism in X. grammica and support the involvement of a patulin-like locus in grammicin biosynthesis. However, the downstream tailoring steps leading to grammicin remain unresolved, and further genetic and metabolomic analyses will be required to complete pathway reconstruction.