A Symphony of Roles for Codon Usage in Fungal Genomics

Codon usage bias, or the uneven use of synonymous codons, is a universal feature of genes and genomes. Although previously considered silent, synonymous mutations can alter cellular translational and even transcriptional dynamics. Fungi have served as model organisms for many groundbreaking discoveries in codon usage. Moreover, surveys of fungi repeatedly find that selection has shaped codon usage—suggesting a functional role for synonymous sites. Here, we review how codon usage plays an active role throughout the flow of information from DNA to RNA to protein while highlighting findings from fungi. We will also discuss leveraging information encoded in fungal synonymous codon usage to address biological and phylogenetic hypotheses.