Genome-wide analysis of codon usage bias in Ascovirus: Insights into viral evolution and host adaptation

Ascoviruses are circular double-stranded DNA viruses that infect lepidopterans, producing large enveloped virions and causing a chronic, deadly disease with apoptosis-like cytopathology. Understanding the codon usage patterns of ascoviruses could shed light on host-virus interactions, evolutionary pressure, gene expression optimization. Nevertheless, thorough analyses of codon usage bias (CUB) within the genomes of Ascovirus (a genus in the Ascoviridae family) have yet to be conducted. Herein, a systematic analysis was performed to clarify the codon usage patterns in nine viruses of the Ascovirus genus, using their complete genomes. The results revealed a higher average nucleotide composition for A and T compared to G and C, with a preference for A/T nucleotides, particularly at the third codon position. Moreover, the results indicated that Ascovirus has a relatively low CUB. Dinucleotide composition significantly influences the codon usage patterns in Ascovirus. Further analyses, including ENC plot, neutrality plot, parity rule 2 (PR2) analysis, correspondence analysis, and correlation analysis, confirmed that mutational pressure had a more significant influence than natural selection in shaping codon usage. Codon adaptation index (CAI) analysis indicated that Ascovirus is strongly adapted to its hosts. The results of our study illustrated the codon usage patterns in Ascovirus genomes and provided essential primary data for foundational evolutionary research on these viruses.