Jacquat, A. G. | bioRxiv Science

bioRxiv2026

Novel RNA viruses reveal a complex mycovirome in the smut fungus Thecaphora thlaspeos

Mycoviruses are widespread in fungi, yet their diversity and host associations remain poorly explored in many lineages, including smut fungi. Here, we report the discovery of the first eight novel RNA viruses infecting the Brassicaceae-associated smut fungus Thecaphora thlaspeos. Using transcriptomic datasets derived from fungal mycelium and host plant controls, we identified dsRNA viral genomes supported by consistent read abundance, high genome coverage, and codon usage patterns closely matching those of the fungal host. All genomes are monosegmented and bicistronic, encoding capsid protein and polymerase genes in compact arrangements. Genome annotation and phylogenetic analyses based on the predicted RNA polymerase classified these viruses within the genera Totivirus and Eimeriavirus. Comparative analyses across fungal strains revealed intraspecific variation in virome composition, suggesting that host genetic background may influence viral community structure and that multiple dsRNA infection is common. Together, these findings expand the known diversity of mycoviruses in Ustilaginomycotina and identify T. thlaspeos as a host of a complex RNA virome. This work establishes a foundation for future studies on virus prevalence, transmission, and potential impacts on fungal biology and plant pathogenesis.

microbiology↗

bioRxiv2024

Long-distance gene flow and recombination shape the evolutionary history of a maize pathogen

The evolutionary history of crop pathogens is shaped by a complex interaction of natural and anthropogenic factors. The ascomycete fungus Colletotrichum graminicola causes maize anthracnose. The disease can result in significant yield losses and is also an important model for genetic studies. We conducted a comprehensive investigation into the evolutionary genomics of C. graminicola using a collection of 212 isolates from 17 countries. Genomic analyses supported the existence of three geographically isolated genetic lineages, with a significant pattern of isolation by distance. We identified two distinct gene flow patterns, driven by short and long-distance dispersion, likely resulting from the natural spread of the pathogen and the exchange of contaminated seeds. We present evidence of genetic introgression between lineages, suggesting a long history of recombination. We identified significant recombination events coalescing at distinct points in time, with the North American lineage displaying evidence of most ancient recombination. Demographic modeling indicated that North America is an intermediate between Brazil, Europe and an ancestral, unsampled source population, hypothesized to be Mesoamerican. Our analyses revealed that the global genomic structure of C. graminicola is shaped by geographic differentiation driven by long-distance migration and a long history of recombination and introgression. We show historical relationships among these lineages, identifying a potential route for fungal spread, with the North American population emerging ancestrally, followed sequentially by the Brazilian and European populations. Our research indicates that the European lineage is more virulent, which has implications for the potential emergence of new outbreaks of maize anthracnose in Europe.

genomics↗