Integrated Transcriptomics and Metabolomics Data Reveal Principal Metabolites and Biosynthesis Genes in Penicillium polonicum

ABSTRACT

A previously isolated strain of Penicillium polonicum exhibited antagonistic activity against the oomycete plant pathogen Pythium aphanidermatum through the production of penicillic acid. Using integrated transcriptomic and metabolomic analyses, we attempted to identify the metabolites and the putative biosynthetic machinery in P. polonicum . A comparison of 2‐day and 7‐day cultures resulted in identification of transcripts associated with secondary metabolism. Gene enrichment analysis identified genes that are related to transmembrane transport, biosynthesis of lactones, polyketides, mycotoxins, organic cyclic compounds, and other secondary metabolites. RT‐qPCR validation were consistent with both upregulated and downregulated transcripts identified in the RNAseq dataset. Since most of the major metabolites produced by this fungus are polyketides, five upregulated and one downregulated polyketide synthase (PKS) genes were further examined. All these six genes are part of secondary metabolite biosynthesis gene clusters. Among them, the PKS gene PENPOL_c005G03784 showed the highest fold overexpression, while PENPOL_c008G04807 was downregulated. Metabolite profiling using LC‐MS/MS analysis confirmed the presence of seven major secondary metabolites, with penicillic acid being the most abundant. One of the gene clusters identified is an orthologue of the Aspergillus westerdijikae penicillic acid cluster. Further studies are required to establish gene‐metabolite relationship in P. polonicum , a prolific producer of secondary metabolites.