Insights into the factors affecting synonymous codon usage bias in the coat protein of soil-borne sugar beet-infecting viruses

Synonymous codon usage patterns (CUP) indicate a series of evolutionary changes that influence viral survival rates and fitness. As viral coat protein (CP) genes evolve more rapidly, they pro-vide a strong incentive to study the genetic diversity and evolutionary changes of viruses based on CP genes. In this study, CP sequences were analyzed using different bioinformatic approaches. Nucleotide composition and relative synonymous codon usage (RSCU) analysis indicates mutation bias and prefers A/U ended codon. The Parity rule 2 (PR2) and the effective number of codon (ENC) plots showed the dominant role of mutation in CUP of CP genes. Host relatedness in terms of codon usage was analyzed, with codon adaptation index (CAI), and similarity index (SiD) calculations; indicating that during the evolution of these viruses, sugar beet has a greater impact on the beet black scorch virus (BBSV) rather than beet necrotic yellow vein virus (BNYVV). In addition, Polymyxa betae has a more profound effect on shaping RSCU patterns of BNYVV. As P. betae and Olpidium brassica are the natural reservoir and host for soil-borne viruses infecting sugar beet, it makes sense that the virus has evolved its genomic proper-ties to a steady level to better adjust to its primary host's condition. The principal component (PCA) plot indicated that BNYVV and beet soil-borne virus (BSBV) have originated from the Old World, whereas BBSV separated into three diverged groups, what is in accordance with phylogenetic groups. This research is the first study of codon usage analysis of beet soil-borne viruses and increases our knowledge about the mechanisms that support codon usage and their evolution.