Codon usage in nucleopolyhedroviruses

Phylogenetic analyses based on baculovirus polyhedrin nucleotide and amino acid sequences revealed two major nucleopolyhedrovirus (NPV) clades, design ated Group I and Group II. Subsequent phylogenetic analyses have revealed t hree Group II subclades, designated A, B and C. Variations in amino acid fr equencies determine the extent of dissimilarity for divergent but structura lly and functionally conserved genes and therefore significantly influence the analysis of phylogenetic relationships. Hence, it is important to consi der variations in amino acid codon usage. The Genome Hypothesis postulates that genes in any given genome use the same coding pattern with respect to synonymous codons and that genes in phylogenetically related species genera lly show the same pattern of codon usage. We have examined codon usage in s ix genes from six NPVs and found that: (1) there is significant variation i n codon use by genes within the same virus genome; (2) there is significant variation in the codon usage of homologous genes encoded by different NPVs ; (3) there is no correlation between the level of gene expression and codo n bias in NPVs; (4) there is no correlation between gene length and codon b ias in NPVs; and (5) that while codon use bias appears to be conserved betw een viruses that are closely related phylogenetically, the patterns of codo n usage also appear to be a direct function of the GC-content of the virus- encoded genes.