Chromosome-level assembly and phylophenetic insights of <i>Cladosporium oxysporum</i> A3.I.1, a fungus with the ability to degrade polyurethane polymers

Notwithstanding the ecological significance of the Cladosporium genus, which includes several cosmopolitan fungi reported as saprobes, plant pathogens, and causes of allergic and cutaneous diseases in humans, only 41 genomes have been reported. Here, we report the genome of a polyurethane (PU)-degrading fungus initially identified as Cladosporium tenuissimum A3.I.1. PU is a plastic material widely used as mattress foams, building insulation, protective sealants, and fabrics, that is highly resistant to degradation and barely recycled, hence its waste remains in the environment for hundreds of years. After sequencing its genome using three different techniques-Illumina, PacBio SMRT RSII, and Hi-C-and performing different bioinformatic analyses, the A3.I.1 species placement was reassessed. This analysis provides the first high-quality chromosome-level genome assembly, with 33,552,215 bp, a genome coverage of 58.7X, a contig N50 of 1,881,040 bp, and a GC content of 53%. Assembly scaffolding with Proximo Hi-C revealed 19 scaffolds, corresponding to the total number of haploid chromosomes. The phylophenetic analysis supports its re-classification as Cladosporium oxysporum strain A3.I.1, refining its taxonomic placement. When comparing A3.I.1 against the reference genome of Cladosporium oxysporum strain AAAS_A1, 693,670 single-nucleotide variants, 18,623 insertions, and 18,687 deletions were uncovered in the A3.I.1 genome. Gene prediction using FunGAP identified 13,115 protein-coding genes, 121 tRNA genes, and 69 rRNA genes. This genomic resource provides valuable insights into environmental resilience research and supports the emerging role of C. oxysporum A3.I.1 as a PU degrader. It also opens new venues for the development of sustainable biorecycling processes.