Research Article Volume 6 • Issue 4 274 Efect of Natural Selection on the Codon Usage pattern of alphabaculovirus Genomes Puttatida Mahapattanakul and Patsarin Rodpothong Wongkamhang* Afliation: Mahidol International College, Mahidol University, Salaya, Nakhon-Pathom, Thailand *Corresponding author: Patsarin Rodpothong Wongkamhang, Mahidol International College, Mahidol University, Salaya, Nakhon-Pathom, Thailand. Citation: Puttatida Mahapattanakul and Patsarin Rodpothong Wongkamhang. Effect of Natural Selection on the Codon Usage pattern of alphabaculovirus Genomes. Archives of Microbiology and Immunology 6 (2022): 274-283. Received: December 09, 2022 Accepted: December 15, 2022 Published: December 24, 2022 Keywords: Codon usage, Alphabaculoviruses, Mutational bias, Natural selection Introduction The baculoviruses (family: Baculoviridae) are a group of large double- stranded DNA arthropod-specifc viruses. They can be categorized into four genera; Alphabaculovirus, Betabaculovirus, Gammabaculovirus and Deltabaculovirus. Baculoviruses can also be classifed into two types, nucleopolyhedroviruses (NPVs) and granuloviruses (GVs), based on their occlusion bodies (OBs) produced at the late stages of infection [1]. The OB is an organized structure, composed of polyhedrin, which provides stability to virions embedded within, and is responsible for virus horizontal transmission among their insect hosts [2, 3]. Genera Alphabaculovirus, Gammabaculovirus and Deltabaculovirus consist of NPVs, infecting insects belonging to the orders Lepidoptera, Hymenoptera and Diptera [4], while the genus Betabaculovirus consists of GVs and only infects lepidopteran insects. Genomes of baculoviruses range from 80–180 kbp in size, encoding 90-180 genes. There are 38 genes that are conserved across diferent genera of baculoviruses and have been assigned as "core genes", involving in viral DNA replication and packaging, transcription, architecture and assembly [6- 9, 32]. Baculoviruses confer high degree of host specifcity and insecticidal Abstract Codon usage is a refection 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 infuence 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 infuence of strong natural selection and a type of selection pressure that refects its functional conservation in DNA packaging as well as its evolutionary relation to protamine-like gene.