Comparative Analysis of Codon Usage Bias in Chloroplast Genomes of Ten Medicinal Species of Rutaceae

Abstract

Abstract 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.