Codon Usage Profiling of Chloroplast Genome in Juglandaceae

Abstract

Juglandaceae (walnut) is made up of several economically and ecologically valuable tree species. Chloroplasts, vitally important for plant growth, are also a rich source of genetic and evolutionary information. Both mutational pressure and natural selection are drivers of codon usage pattern variation among genes. Here, we studied the codon usage of Juglandaceae chloroplast genomes in order to further our understanding of the biology and evolution of this plant family. The codon usage patterns associated with the chloroplast genomes of 26 Juglandaceae samples were analyzed. Short CDS sequences (<100 amino acids) and sequencing containing internal stop codons were removed from comparative analyses. The contents of uracil (U) (31.5%–32.0%) and adenine (A) (30.0%–31.2%) of all 26 samples were higher than those of cytosine (C) (17.2%–17.7%) and guanine (G) 19.9%–20.7%. According to the neutrality and correspondence analyses, chloroplast codons tended to exhibit conserved GC content and were primarily altered by natural selection. The parity rule 2 plot analysis revealed that AU were more common than GC at the third-codon position. According to the effective number of codon (ENC) plot analysis, codon preference was driven by natural selection and protein translation, among other factors. This study represents the first examination of the codon usage characteristics of Juglandaceae plants, as revealed through the study of codon bias in 26 Juglandaceae samples.