Natural Selection Shapes Codon Usage in the Autographa californica Multiple Nucleopolyhedrovirus Protein Kinase Gene

Baculoviruses are large, double-stranded DNA viruses belonging to the family Baculoviridae, known for causing lethal infections and epizootics in insect populations, particularly within the orders Lepidoptera, Diptera, and Hymenoptera. Owing to their host restriction to invertebrates, they serve as promising biocontrol agents in integrated pest management. The codon usage patterns of viruses provide critical insights into their evolutionary trajectories, gene expression regulation, and host adaptation mechanisms. Despite significant advances in baculovirus genomics, the codon usage bias (CUB) of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) protein kinase (PK) gene remains poorly characterized. In this study, PK gene sequences from AcMNPV and thirteen reference baculoviruses were retrieved from the NCBI database for comprehensive bioinformatic analysis. We assessed nucleotide composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and additional compositional indices. Our findings revealed a strong preference for G- and C-ending codons. Moreover, the results indicated that the AcMNPV PK gene has a relatively low CUB. ENC–GC3s plots, parity rule 2 bias, and neutrality analyses suggested that natural selection plays a predominant role in shaping codon usage, while mutation pressure exerts a minor effect. Correlation and correspondence analyses further supported that both selection and mutation contribute to codon bias patterns. Moreover, CAI results demonstrated the high host adaptability of the AcMNPV PK gene. This work represents the first detailed investigation of codon usage in the AcMNPV PK gene, providing new insights into its molecular evolution, expression efficiency, and host–virus interactions.