title: An extensive analysis on the global codon usage pattern of baculoviruses.
abstract: Baculovirus-insect cell systems have been widely used over the past decades. However, few studies to date have addressed baculovirus codon usage. In this study, we calculated the effective number of codons (ENC) for all 5,842 ORFs from 42 completely sequenced baculoviruses. The results revealed that most of the baculoviruses lacked strong codon bias (ENC > 35). Exceptions were Lymantria dispar nucleopolyhedrovirus (LdMNPV) and Orgyia pseudotsugata nucleopolyhedrovirus (OpMNPV), which were found to have a strong codon bias (ENC < 35) in 20.9 and 11.8%, respectively, of their total genes. Comparisons of preferred codons based on taxonomic clades showed that the preferred codons were different in different clades, but nine codons (UUU, UAC, UUG, CAC, CAA, AAA, GUG, GAA, and AUU) were preferably adopted by most baculovirus genes. Correspondence analysis showed that the major trend in codon usage variation among all genes significantly correlated with the GC content of sequences. Analyses also suggested that the high condon bias of LdMNPV and OpMNPV were correlated with their high GC%.
authors.affiliation: State Key Laboratory of Virology, Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071, Wuhan, People's Republic of China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Jiang
authors.forename: Fei
authors.initials: F
authors.lastname: Deng
authors.forename: Hualin
authors.initials: H
authors.lastname: Wang
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Hu
mesh_terms: D016367:Baculoviridae / Q000235:genetics*; D001482:Base Composition / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D003062:Codon