Integrated Omics-Based Discovery of Novel Genes, Secondary Metabolites Clusters, and Small Molecules in Penicillium spp. with Disparate Fungal Isolates

<p><em>Penicillium expansum</em> is a ubiquitous postharvest pathogen of pome fruit that causes blue mold decay of apple fruit while another member of the genus, <em>P. chrysogenum</em>,<em> </em>is a well-studied saprophyte used for antibiotic and small molecule production. While these two fungi have been investigated individually, the recent discovery of <em>P. chrysogenum </em>hindering <em>P. expansum</em> apple fruit infection has not been well studied. To shed light on this interaction between the two species, we conducted a comparative transcriptomic, metabolomic, and genomic study. Global transcriptional and metabolomic outputs were disparate between the species, nearly identical for the <em>P. chrysogenum </em>isolates, and different between <em>P. expansum </em>isolates. Further, the two <em>P. chrysogenum</em> genomes revealed secondary metabolite gene clusters that differed from <em>P. expansum</em>. This included the absence of an intact patulin gene cluster in <em>P. chrysogenum</em>, which corroborates the metabolomic data regarding the species’ inability to produce patulin. Additionally, <em>P. expansum </em>virulence gene homologues were identified in <em>P. chrysogenum </em>and were similarly transcriptionally regulated <em>in vitro</em>. Molecules with potential antimicrobial activity, and phytohormones like indole-3-acetic acid (IAA), were detected for the first time in <em>P. expansum</em> while pharmacological compounds like the well-studied antibiotic penicillin G were identified in <em>P. chrysogenum</em> culture supernatants. Our findings provide new omics-based resources that enable the study of small molecule production of interest, the potential of <em>Penicillium</em>-derived antimicrobials for postharvest decay control, and <em>P.</em> <em>expansum’s</em> metabolites roles in host-pathogen interactions. </p>