An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

Abstract

Abstract Background Chloroplast genome has the characteristic of small genome size and low rate of mutation and recombination, which has been used in plant phylogeny, molecular evolution, and pedigree geography, normally. Codon usage bias is an important evolutionary feature of organisms, plays a crucial role in the study of species evolution, gene function and foreign gene expression. Coffee is extremely important in the world's tropical agricultural economy, international trade and human daily life. Studying the codon usage bias of coffee genome is of great significance to guide the subsequent coffee research work, such as the selection of efficient heterologous expression system required for coffee genetic transformation. Results The findings demonstrated a high degree of utilization pattern commonality among the three coffee genome codons. The three types of coffee had identical base chemical compositions, high A/T content, low G/C content, and A/T ends were favored for codons in all three types of coffee. The three types of coffee contained 30 high frequency codons, 96.67% of which were codons with the A/T ending. The ideal codons totaled fourteen. Natural selection was the primary impacting force, as seen by the findings of the ENc-GC3s mapping, PR2 analysis, and neutral analysis, which revealed that the three coffee codon utilization patterns were driven by a variety of mechanisms. The most effective heterologous expression receptor for the three coffee genes was tobacco, which could be employed in Arabidopsis thaliana, Nicotiana tabacum, Escherichia coli, and Saccharomyces cerevisiae. Conclusion This study demonstrates how the three coffee genomes' codon use patterns are remarkably similar and primarily influenced by natural selection. Understanding the gene expression properties of coffee and investigating the laws governing its genetic evolution are made possible by the study on the preference of the three coffee codons. The study's findings can help foreign genes express themselves more effectively and serve as a foundation for future coffee evolution guidelines.