Mycoviruses-mediated compensation function: Mycoviruses induce hypovirulence and enhances host-dependent anifungal VOC production in a phytopathogenic fungus

<p dir="ltr">The 3D structures of the RNA-dependent RNA polymerase (RdRP) (shu_RdRP_2419-3331_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb) and the protease (shu_pro_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb) of the mycovirus Sclerotinia sclerotiorum ascoshuvirus 1 (SsAShV1) were predicted using AlphaFold 2. Subsequently, the predicted viral protein structures were aligned against the virus-specific BFVD database and the PDB database using the 3Di/AA alignment mode of Foldseek (<a href="https://search.foldseek.com/search" rel="noreferrer" target="_blank">https://search.foldseek.com/search</a>). Multiple structural alignments and visualizations were performed using UCSF ChimeraX software.</p><p dir="ltr">For the phylogenetic analysis of SsAShV1, the viral protein sequences were aligned using the L-INS-i method in MAFFT 7.0 (RdRP_domain_trim2end_reorder.afa). The aligned sequences were then trimmed with trimAl 1.2 (RdRP_domain_trim2end_reorder_clipped.afa), and a maximum likelihood phylogenetic tree was constructed using IQ-TREE 2.2.6 (RdRP_domain_trim2end_reorder_clipped.treefile). Branch support values were calculated based on 1000 bootstrap replicates. The phylogenetic tree was finally visualized and annotated using the Evolview online platform (<a href="https://www.evolgenius.info/evolview/#/treeview" rel="noreferrer" target="_blank">https://www.evolgenius.info/evolview/#/treeview</a>).</p>