A study on the codon usage bias of arenavirus common genes

Abstract

Introduction:The Arenaviridae family consists of the genera Mammarenavirus, Reptarenavirus,Hartmanivirus, Antennavirus and Innmovirus. The codon usage bias between thedifferent genera has not yet been studied comparatively.Methods: Weretrieved the arenavirus genome sequences from public databases and usedbioinformatics tools to compare the codon usage bias between the differentgenera for the GPC, NP and L proteins, common to all arenaviruses.Results anddiscussion: Hartmaniviruses show a larger codon usage bias, which can bepartially explained by mutational bias. Patterns of relative use of synonymouscodons were maintained within genera, with individual genera differing in theirpreference for the third nucleotide position in synonymous codons. Of the threeproteins examined, the ARN polymerase L protein exhibited a slightly strongercodon usage bias, but overall, the patterns were repeated between genera forthe three proteins examined. Our results suggest that codon usage pattern biasin arenaviruses is influenced by selection pressure and to a lesser extent bymutational selection.