Identification and characterization of a novel negative-sense RNA virus infecting Fusarium commune, a fungus causing tobacco root rot

The fungal genus Fusarium includes several pathogenic species of significant agricultural importance for tobacco cultivation. In this study, we characterized a novel mycovirus, designated "Fusarium commune mononegavirus 1" (FcMV1), isolated from Fusarium commune strain JF-46. The bipartite genome of FcMV1 comprises two negative-sense RNA segments: RNA1 (6,443 nt) and RNA2 (6,301 nt). RNA1 contains a single open reading frame (ORF1, position nt 102–6098) encoding a 224.5-kDa polyprotein with two conserved functional domains: an RNA-dependent RNA polymerase (RdRp) and a mononegavirus mRNA-capping region V. RNA2 has seven putative ORFs (ORF2-ORF8), with ORF6 predicted to encode a nucleocapsid protein, while the remaining ORFs encode hypothetical proteins of unknown function. A multiple sequence alignment revealed 53.5% identity between the FcMV1 polyprotein and its counterpart in Trichoderma harzianum mononegavirus 2, with the nucleocapsid protein showing 33.4% sequence identity. A phylogenetic tree based on RdRp sequences, constructed using the maximum-likelihood method, positioned FcMV1 within a clade with members of the genus Plasmopamonavirus of the family Mymonaviridae. This is the first report of a negative-sense RNA mycovirus infecting F. commune, expanding our understanding of mycovirus diversity in phytopathogenic fungi.