Characterization of Codon Usage Patterns and Evolutionary Relationships in Partitiviruses

Abstract

This study investigated the overall sequence characteristics and codon usage patterns of Partitiviridae viruses and applied them to viruses that are part of the family Partitiviridae but are unassigned to a genus. In addition, phylogenetic analysis was performed to investigate the evolutionary relationships of viruses belonging to Partitiviridae in relation to their fungal hosts. The sequence data of the CDS region were downloaded from GenBank, including that of the conserved RdRP, capsid protein. The results showed that Botryotinia fuckeliana partitivirus 1, Beauveria bassiana partitivirus 1, Beauveria bassiana partitivirus 2, Penicillium marneffei partitivirus-1, and Aspergillus fumigatus partitivirus 2 had evolutionary relationships with Gammapartitivirus. Among them, Aspergillus fumigatus partitivirus 2 and Penicillium marneffei partitivirus-1 preferred U-ended codons similar to Gammapartitivirus in terms of codon usage patterns. In addition, Botryosphaeria dothidea virus 1 showed a different pattern from the viruses belonging to Partitiviridae in all the analysis results. This virus showed a strong bias towards the C-ended codons and the lowest ENC value among the analyzed viruses, forming a separate cluster in the phylogenetic tree. These results may help to understand the genetic diversity and evolutionary relationships of the members and tentative members of the family Partitiviridae.