Genomics of thermally pathogenic dimorphic human fungi: From the mitochondrion to the pangenome

The genomics of human pathogenic thermally dimorphic fungi has advanced significantly thanks to international initiatives such as the 1000 Fungal Genomes Project, which has reported a wide range of complete genomes in public repositories. This has driven the genomic characterization of genera such as Histoplasma, Paracoccidioides, and Sporothrix, including clinically relevant Colombian isolates. Genomic studies have revealed key aspects of their diversity, evolution, and host adaptation, while enabling comparative analyses based on orthologous genes that highlight both conservation and divergence among lineages. Beyond their description, the availability of complete genomes has had direct applications in diagnostics through systematic comparison algorithms that identify unique genomic regions serving as highly specific molecular targets. This has facilitated the design and validation of innovative PCR assays for the above-mentioned genera, overcoming the limitations of traditional candidate-gene approaches. In Colombia, significant challenges remain, including the limited availability of clinical isolates, biosafety requirements, and difficulties in timely diagnosis. In this context, we aimed to analyze the current state of assembled genomes of these dimorphic fungi available in public databases for Colombia and their use in the development of highly specific molecular diagnostic tools.