Diversity and Evolution of RNA Recognition Motifs: A Case Study on the Utility of RdRp in the phylum Duplornaviricota

Viruses possess specific conserved regions known as RNA recognition motifs, which are shared within taxonomic groups. Applying these to the Baltimore virus classification system, there are genes/proteins that serve as biomarkers for each of the seven groups. Mutations in conserved sequence regions can have a significant impact on the function of a virus, especially if these conserved regions are part of a major protein. In this study, we analyzed the RdRp gene, known to be a representative RRM of RNA viruses, from viruses of five families (Alternaviridae, Chrysoviridae, Totiviridae, Sedoreoviridae, and Spinareoviridae) within the phylum Duplornaviricota. Data were retrieved from the NCBI non-redundant (nr) database (https://www.ncbi.nlm.nih.gov/protein) applying a cut-off of 300 amino acids in length. RdRp protein sequences were aligned using PROMALS3D, and PhyML (v3.0) was used for phylogenetic analysis. In the next step, we utilized the officially provided ICTV taxonomy and bioinformatics tools to assign the phylogenetic position of RdRp. Although this analysis focused solely on RdRp, it can be concluded that using this gene as a marker may be sufficient for taxonomic assignment. Subsequent analyses will target DNA viruses and RT viruses to perform a more comprehensive assessment. This extensive analysis aims to validate the usefulness of marker genes in the overall viral taxonomy.