Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Aug 9;24(1):42.
doi: 10.1186/s12863-023-01143-4.

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

Yaqi Li #  1 , Xiang Hu #  2 , Mingkun Xiao #  1 , Jiaxiong Huang  1 , Yuqiang Lou  1 , Faguang Hu  1 , Xingfei Fu  1 , Yanan Li  1 , Hongyan He  1   3 , Jinhuan Cheng  4   5
Affiliations

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

Yaqi Li et al. BMC Genom Data. .

Abstract

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.

Keywords: Chloroplast genome; Codon usage bias; Coffee; Heterologous expression.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
ENc-plot of chloroplast genomes of three Coffea species. a Coffea arabica b Coffea canephora c Coffea liberica
Fig. 2
Fig. 2
PR2-plot of chloroplast genomes of three Coffea species. a Coffea arabica b Coffea canephora c Coffea liberica
Fig. 3
Fig. 3
Neutrality plot of chloroplast genomes of three Coffea species. a Coffea arabica b Coffea canephora c Coffea liberica
Fig. 4
Fig. 4
Correspondence analysis of chloroplast genomes of three Coffea species. a Coffea arabica b Coffea canephora c Coffea liberica
Fig. 5
Fig. 5
Correlation analysis of axis 1, axis 2 and codon utilization index of chloroplast genomes of three Coffea species. a Coffea arabica b Coffea canephora c Coffea liberica. GC3s indicates the GC content at the third codon position of synonymous codons; ENc represents the effective number of codons; CAI means the codon adaptation index; Laa is defined as the total number of amino acids. * represents P < 0.05, ** represents P < 0.01
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Saud S, Salamatullah AM. Relationship between the Chemical Composition and the Biological Functions of Coffee. Molecules. 2021;26(24):7634. - PMC - PubMed
    1. Bae JH, Park JH, Im SS, Song DK. Coffee and health. Integr Med Res. 2014;3(4):189–191. - PMC - PubMed
    1. Narko T, Wibowo MS, Damayanti S, Wibowo I. Acute Toxicity Tests of Fermented Robusta Green Coffee Using Zebrafish Embryos (Danio rerio) Pharmacognosy J. 2020;12(3):485–492.
    1. Salomone F, Galvano F, Volti LG. Molecular Bases Underlying the Hepatoprotective Effects of Coffee. Nutrients. 2017;9(1):85. - PMC - PubMed
    1. Homan DJ, Mobarhan S. Coffee: good, bad, or just fun? A critical review of coffee's effects on liver enzymes. Nutr Rev. 2006;64(1):43–46. - PubMed

Publication types

LinkOut - more resources