Background The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation. Results Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes. Conclusion This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.
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.
Here, we report the complete chloroplast genome of Pittosporum brevicalyx. The genome is 153,388 bp in size, which is comprised of a large single-copy (LSC) region of 84,724 bp, a small single-copy (SSC) region of 18,716 bp, and two inverted repeat (IR) regions of 24,974 bp. The overall GC content of the plastome was 38.3%. The new sequence comprised 127 unique genes, including 82 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis showed that P.brevicalyx was close to Pittosporum kerrii and Pittosporum eugenioides. These data may providing useful information for phyletic evolution of P.brevicalyx within the Pittosporaceae family.
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