Comparative analysis of codon usage patterns of venom gland-specific honeybee-infecting viruses in solitary hunting and social wasps

To identify the evolutionary traits of honeybee-infecting viruses (HVs), including black queen cell virus (BQCV), deformed wing virus (DWV), and Israeli acute paralysis virus (IAPV), and their adaptation patterns in the venom gland of different hosts, we conducted a comparative analysis of codon usage patterns of venom gland-specific HVs in honeybees, solitary hunting, and social wasps. The nucleotides A and U, as well as the nucleotide composition at the third position of synonymous codons (A3s and U3s), were abundantly present with high frequencies in the polyprotein region of the three HVs in Apis mellifera, solitary hunting, and social wasps. Although the three HVs exhibited a high codon adaptation index, effective number of codons and the frequencies of GC3s were observed to be high and low, respectively, indicating a low codon usage bias in the three HVs. The relative abundance of dinucleotides, nucleotide compositions, and the aromaticity of amino acids might be considered as reasons for the different codon usage patterns of the three HVs in solitary hunting and social wasps compared to A. mellifera. The result of phylogenetic analysis revealed that DWV possesses a unique evolutionary pattern compared to the lineages of Aculeate species, possibly caused by specific ecological interactions. Our study provides further insights into the evolutionary aspects of venom gland-specific HVs in Aculeate species and might contribute as fundamental information for further research on the evolution of HVs.