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.
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. Better utilization of Rutaceae plants through biotechnology. Modern biotechnological approaches majorly rely on the heterologous expression of functional proteins in different vectors; however, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays an essential role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family’s codon usage bias, followed by base mutation. In the ENC vs. CAI plot, we observed that codon usage bias in the Rutaceae family had little relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, which may provide valuable information for the genetic engineering of Rutaceae plant species in the future.
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