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

TL;DR

This study explores the genome of Cladosporium limoniforme to uncover its biosynthetic potential, focusing on conserved pathways like DHN-melanin that help the fungus survive.

Contribution

The first whole-genome analysis of C. limoniforme reveals conserved biosynthetic gene clusters and supports a metabolic streamlining hypothesis for endolichenic fungi.

Findings

C. limoniforme has 26 putative biosynthetic gene clusters, indicating untapped metabolic potential.

The metachelin C and T4HN gene clusters are highly conserved across the Cladosporium genus.

C. limoniforme retains a conserved T1PKS core but has fewer accessory genes compared to plant-pathogenic relatives.

Abstract

Background: 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 Cladosporium limoniforme have not been explored at the genomic level. Objectives: This study aimed to characterize the biosynthetic potential of C. limoniforme 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. Methods: Genome mining was performed using antiSMASH and fungiSMASH tools. Comparative genomics involved heatmap-based distribution analysis across the Cladosporium genus, synteny profiling using Clinker to assess gene order conservation, and Maximum Likelihood phylogenetic analysis of the polyketide synthase (T1PKS) domain. Results: 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 C. limoniforme retains a conserved, ancestral T1PKS core essential for stress survival, it exhibits a significant reduction in accessory genes compared to plant-pathogenic congeners. Conclusions: 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 C. limoniforme as a valuable genomic resource for future biotechnological research.

Figures