FUSARIUM MUSAE AND FUSARIUM VERTICILLIOIDES CROSS-KINGDOM PATHOGENS: GENOMICS AND DIAGNOSTIC INNOVATION

Fusarium species comprise a diverse group of filamentous fungi that include major plant pathogens, food contaminants, and opportunistic human pathogens. Among them, transkingdom species capable of infecting both plants and humans represent an emerging challenge within the One Health framework. Fusarium musae exemplifies this dual ecological behavior, acting as the causal agent of postharvest banana crown rot while increasingly being reported in human infections. Despite its growing relevance, the biology, genomic diversity, and mechanisms underlying host adaptation in F. musae remain insufficiently characterized, and available genomic resources have been largely restricted to plant-derived isolates. Moreover, the widespread use of azole antifungals in both agricultural and clinical settings has further intensified this concern, as the shared modes of action of these compounds contribute to the emergence of resistant strains and may facilitate cross-environment adaptation. This PhD research addressed these knowledge gaps by integrating genomics, comparative analyses, and diagnostic tool development to investigate mechanisms of host adaptation in F. musae and its closely related species Fusarium. verticillioides. In Chapter I, sixteen F. musae isolates obtained from both plant and human sources were sequenced and annotated, substantially expanding the genomic representation of the species. This dataset enabled the first comparative assessment of genomic diversity across ecological origins, providing insights into intraspecific variability and establishing a foundation for investigating traits potentially associated with transkingdom pathogenicity. Chapter II focused on the generation of a high-quality reference genome through hybrid assembly combining long and short read sequencing technologies, followed by RNA-Seq–guided annotation refinement. Beyond improving genome completeness and annotation accuracy, this work contributed methodological advances for manual genome curation in filamentous fungi, addressing common challenges associated with fragmented assemblies. In Chapter III, comparative genomic analyses were extended to F. verticillioides, including the sequencing and characterization of clinical isolates for the first time. Structural and functional analyses of CYP51 paralogs revealed candidate genetic determinants linked to azole resistance, providing novel insights into antifungal adaptation mechanisms and highlighting evolutionary pathways relevant to both agricultural and clinical environments within the F. fujikuroi species complex. Finally, Chapter IV translated genomic knowledge into practical diagnostic applications. Comparative mitochondrial genomics enabled the identification of species-specific markers used to design PCR assays capable of discriminating F. musae and F. verticillioides through direct amplicon-based detection. In parallel, volatile organic compound profiling using an electronic nose system demonstrated the feasibility of rapid, non-destructive species identification based on metabolic signatures, establishing a complementary phenotypic diagnostic approach. Collectively, this thesis provides the first integrated genomic and diagnostic framework for F. musae, significantly expanding available genomic resources, improving understanding of fungal transkingdom pathogenicity, and delivering accessible tools for accurate species identification. By bridging fundamental genomics with applied diagnostics, this work supports improved surveillance, risk assessment, and management strategies across agricultural and clinical contexts, contributing to proactive One Health approaches for emerging fungal pathogens.