Nanopore sequencing as a proof of concept for antifungal resistance in Cladosporium cladosporioides from banana

Controlling phytopathogenic fungi is essential for maintaining food safety and reducing postharvest losses. However, the extensive use of antifungal agents such as Imazalil has promoted the emergence of resistant strains, creating new challenges for agricultural systems. This study presents a proof-of-concept application of Oxford Nanopore Technologies (ONT) sequencing to identify antifungal-resistant fungal isolates from banana epicarp. The most resistant isolate, identified as Cladosporium cladosporioides, was able to grow at concentrations up to 300 ppm of Imazalil, suggesting a possible adaptive response. Transcriptomic analysis revealed expression of ENO1 and ENO2, genes linked to metabolic activity and general stress responses, though not directly associated with antifungal resistance. Due to limited sequencing depth, RNA quality constraints, and reduced analytical resolution, these findings should be interpreted with caution. Nonetheless, the results demonstrate the exploratory potential of ONT-based sequencing for preliminary molecular assessments in agricultural fungal pathogens and underscore the need for more comprehensive studies.