Effect of Natural Selection on the Codon Usage pattern of alphabaculovirus Genomes

Author(s): Puttatida Mahapattanakul and Patsarin Rodpothong Wongkamhang

Codon usage is a reflection of evolutionary adaptation to environmental pressure. Codon usage pattern may be unique to species of viruses, genomes of the same species or genes within the same genome. Here, we have analyzed the overall nucleotide composition and the nucleotide composition at the three codon positions in the genomes of 6 alphabaculoviruses. The results suggest that the alphabaculovirus genomes are predominantly under an influence of a natural selection that bias toward A/T. Principle Component Analysis (PCA) based on Relative Synonymous Codon Usage (RSCU) of all Open Reading Frames (ORFs) was employed to investigate the pattern of the codon usage. The majority of the alphabaculovirus ORFs, except those of AgipMNPV, clusters at the same location in the 2-dimensional PCA plot, indicating similar RSCU indices and supporting our hypothesis that genomes of the related viruses should possess similar codon usage pattern because they share similar mechanisms of virus replication and infection, thus are subjected to the same type of evolutionary pressure. A distinct pattern of the RSCU index in the p6.9 gene, which is an outlier in the PCA plot, also demonstrates an influence of strong natural selection and a type of selection pressure that reflects its functional conservation in DNA packaging as well as its evolutionary relation to protamine-like gene.