Molecular characterization of genes in the GP41 region of baculoviruses and phylogenetic analysis based upon GP41 and polyhedrin genes

A newly sequenced Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) gp41 gene was used to reconstruct the phylogeny for gp41 by comparison with Autographa californica MNPV, Bombyx mori MNPV, Helicoverpa zea single nucleopolyhedrovirus (SNPV), Lymantria dispar MNPV, Orgyia pseudotsugata MNPV and Spodoptera frugiperda MNPV. The 3.5 kb fragment of the AgMNPV gp41 region not only contained the gp41 gene but also three other open reading frames that had significant homology with the very late factor (vlf-1) of baculoviruses, AcMNPV ORF78, AcMNPV ORF79, and one partial open reading frame homologous to AcMNPV ORF81. The reconstructed phylogenetic tree of baculovirus gp41 genes compared with the polyhedrin gene tree produced similar topologies. Two other phylogenetic trees were reconstructed based on either combined gp41 and polyhedrin nucleotide sequences (total evidence) or combined evolutionary histories of both genes (strict consensus tree). The former had an identical tree topology as the gp41 gene tree alone, and the latter lost resolution in the branch of AcMNPV and BmMNPV. Mutation rate analysis showed the gp41 gene had a higher nucleotide substitution rate than the polyhedrin gene, implying that the polyhedrin gene may have a different selection constraint than the gp41 gene. Both genes have nonsynonymous/synonymous substitution values close to 0.1, similar to other DNA viruses.