Viral diversity and interconnected host associations in fungi and plants with agricultural relevance

Mycoviruses, viruses that infect fungi, constitute a vast and largely unexplored component of the global viosphere. While they encompass diverse genome types, including double-stranded (dsRNA), single-stranded positive-sense (+ssRNA), negative-sense (-ssRNA), and single-stranded DNA (ssDNA), the majority are RNA viruses. Advances in high-throughput sequencing (HTS) have expanded our understanding of viral diversity, revealing an increasing number of novel viral sequences. This thesis investigates the diversity, ecology, and evolutionary dynamics of viruses associated with phytopathogenic fungi, and explores their relationship with plant-infecting viruses (phytoviruses). Using RNAHTS, the mycoviromes of Sclerotinia sclerotiorum and Hemileia vastatrix, as well as the virome of eucalyptus plants, were characterized, revealing high viral diversity of viruses within the fungal hosts, encompassing multiple families and diverse genomic configurations. Notably, viral sequences were also detected in the plant tissue, motivating an in-depth exploration of potential cross-kingdom associations. Complementary in silico analyses of fungal- and plant-associated viral metadata from the NCBI Virus database demonstrated that mycovirus diversity can be influenced by host ecology, with phytopathogenic fungi serving as a reservoir for plant virus-infecting viruses. Viral genera were found to be shared between fungi and plants, providing evidence for cross-kingdom viral occurrence. These findings suggest that intimate fungus-plant interactions, particularly in pathogenic contexts, act as ecological bridges that may facilitate viral host shifts and persistence across the kingdoms Fungi and Plantae. Altogether, this thesis highlights the ecological and evolutionary significance of fungal hosts as hubs of viral diversity and offers new insights into the interconnected nature of viral communities relevant to agriculture. Keywords: phytopathogen fungi; RNA-seq; viruses