Hybrid genome assembly of Penicillium oxalicum UV4 delineates cryptic secondary metabolite pathways and robust lignocellulolytic potential

Abstract

Penicillium oxalicum is a saprophytic fungus well-known for its hydrolytic potential; however, little is known about its metabolic flexibility and secondary metabolite biosynthesis, especially in isolates from underrepresented areas. In this study, we sequenced the genomic DNA of Penicillium oxalicum UV4 using Illumina and Oxford Nanopore platforms, generating a high-quality hybrid genome assembly of 30.28 Mb. The genome features 7,944 predicted genes (7,747 protein-coding sequences and 197 tRNAs) and demonstrates high completeness (99.0% BUSCO). Genomic analysis revealed 40 Biosynthetic Gene Clusters (BGCs), including distant orthologs of the Alternaria phytotoxin ACT-toxin II and the mycotoxin alternariol, as well as a putative clavaric acid-like biosynthetic cluster. Further investigation revealed an expanded CAZyme repertoire comprising 150 secreted proteins, featuring an AA16 lytic polysaccharide monooxygenase and putative multi-domain architectures, such as a pectin methylesterase-polygalacturonase fusion. This comprehensive genomic profiling highlights the dynamic metabolic capacity of P. oxalicum UV4, establishing it as a highly promising candidate for bio-refining studies and the discovery of cryptic bioactive metabolites.