Genomic-Driven Identification of Conserved Biosynthetic Gene Clusters in Cladosporium limoniforme: The Case of the DHN-Melanin Pathway

<b>Background</b>: Endolichenic fungi represent an emerging source of bioactive secondary metabolites; however, the genomic basis of their chemical diversity remains largely poorly characterized. Specifically, the metabolic capabilities of <i>Cladosporium limoniforme</i> have not been explored at the genomic level. <b>Objectives</b>: This study aimed to characterize the biosynthetic potential of <i>C. limoniforme</i> by presenting its first whole-genome sequence and conducting a comparative analysis of its biosynthetic gene clusters (BGCs), with a specific focus on the evolutionary conservation of the DHN-melanin pathway. <b>Methods</b>: Genome mining was performed using antiSMASH and fungiSMASH tools. Comparative genomics involved heatmap-based distribution analysis across the <i>Cladosporium</i> genus, synteny profiling using Clinker to assess gene order conservation, and Maximum Likelihood phylogenetic analysis of the polyketide synthase (T1PKS) domain. <b>Results</b>: We identified 26 putative BGCs, revealing a largely untapped metabolic repertoire. Comparative analysis demonstrated a high degree of conservation for the metachelin C (siderophore) and 1,3,6,8-tetrahydroxynaphthalene (T4HN) clusters across the genus. Notably, synteny and phylogenetic analyses showed that while <i>C. limoniforme</i> retains a conserved, ancestral T1PKS core essential for stress survival, it exhibits a significant reduction in accessory genes compared to plant-pathogenic congeners. <b>Conclusions</b>: These findings support a "metabolic streamlining" hypothesis driven by the endolichenic lifestyle, where the fungus retains essential protective machinery while shedding costly accessory genes unnecessary in the buffered lichen niche. This study establishes <i>C. limoniforme</i> as a valuable genomic resource for future biotechnological research.