187 | Beyond marker genes: mitochondrial genomics as a high-resolution tool for Sporothrix schenckii molecular epidemiology

Laura Taca¹, Andrea Bonomo², Gabriele Rigano^3|4, Letterio Giuffrè¹, Orazio Romeo¹, Domenico Giosa¹ | ¹Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy; ²Department of Mathematics, University of Pavia, Italy; ³Department of Biology, University of Rome “Tor Vergata”, Rome, Italy; ⁴PhD programme in Space Science and Technology, Department of Physics, University of Trento, Italy.

Sporotrichosis is a (sub)cutaneous mycosis caused by a select group of pathogenic fungi within the genus Sporothrix. While over 60 species have been described to date, S. brasiliensis, S. schenckii, and S. globosa are the primary species associated with mammalian infections. Among these, S. schenckii exhibits the widest geographic distribution and remains the most frequently reported etiological agent globally. The rising incidence of the disease, coupled with significant genetic heterogeneity and limited genomic resources, underscores the urgent need for robust genotypic tools to enhance public health surveillance. While conserved nuclear marker genes (e.g., chitin synthase, β-tubulin, calmodulin) reliably resolve species boundaries, they often fail to capture fine-scale epidemiological or geographic structure. In contrast, fungal mitochondrial genomes are highly dynamic, exhibiting extensive structural variation driven by recombination and intron mobility, thereby providing a rich source of intraspecific genetic diversity and enhanced resolution for population-level analyses. In this study, we analyzed mitochondrial genetic polymorphism in 57 S. schenckii strains from diverse geographic regions, including Italy, Australia, South America, and North America, using raw sequencing data available from the Sequence Read Archive (SRA) database. Mitogenomes were assembled and annotated using NOVOPlasty and MFannot, while synteny and phylogenetic analyses were performed graphically using GeneView, JolyTree, and iTOL. Analysis of mitochondrial genome synteny showed that many strains cluster according to geographic location, although considerable mitochondrial diversity remains, as multiple mitotypes can be present in the same region of origin. This diversity is largely attributable to strain-specific variation in gene content, most notably the presence or absence of novel open reading frames (ORFs). Interestingly, a homing endonuclease of the LAGLIDADG family was also detected in four strains (three from Australia and one from Italy), challenging previous reports that considered this endonuclease confined to S. brasiliensis. Our results highlight the potential of mitochondrial genome analysis to reveal significant intraspecific diversity. Future studies involving larger collections of isolates, along with functional characterization of unique ORFs and mobile elements, will offer deeper insights into the evolutionary dynamics of S. schenckii and related fungal pathogens.