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

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.

Optimizing drip fertigation at different periods to improve yield, volatile compounds and cup quality of Arabica coffee.

How to improve and regulate coffee bean yield and quality through split fertilization in the whole life cycle of coffee is still unclear and deserves further study. A field experiment of 5-year-old Arabica coffee trees was conducted for 2 consecutive years from 2020 to 2022. The fertilizer (750 kg ha-1 year-1, N-P2O5-K2O:20%-20%-20%) was split in three times at early flowering (FL), the berry expansion (BE), and the berry ripening (BR). Taking equal fertilization throughout the growth cycle (FL250BE250BR250) as the control check, variable fertilizations including FL150BE250BR350, FL150BE350BR250, FL250BE150BR350, FL250BE350BR150, FL350BE150BR250, and FL350BE250BR150. Leaf net photosynthetic rate (A net), stomatal conductance (g s), transpiration rate (T r), leaf water use efficiency (LWUE), carboxylation efficiency (CE), partial factor productivity of fertilizer (PFP), bean yield, crop water use efficiency (WUE), bean nutrients, volatile compounds and cup quality, and the correlation of nutrients with volatile compounds and cup quality was evaluated. FL350BE250BR150 had the maximum A net and g s, followed by FL250BE350BR150. The highest dry bean yield and WUE were obtained from FL250BE350BR150, which increased by 8.86% and 8.47% compared with FL250BE250BR250 in two-year average. The ash, total sugar, fat, protein, caffeine and chlorogenic acid in FL250BE350BR150 were 6.47%, 9.48%, 3.60%, 14.02%, 4.85% and 15.42% higher than FL250BE250BR250. Cluster analysis indicated FL150BE350BR250, FL250BE350BR150, FL350BE150BR250 and FL350BE250BR150 under medium roasted degree increased pyrazines, esters, ketones and furans, FL150BE350BR250 and FL250BE350BR150 under dark roasted degree increased ketones and furans. The aroma, flavor, acidity and overall score of medium roasted coffee were higher than dark roasted coffee, while the body score of dark roasted coffee was higher than medium roasted coffee. The nutrient contents were correlated with the volatile compounds and cup quality. TOPSIS indicated that FL250BE350BR150 was the optimal fertilization mode in the xerothermic regions. The obtained optimum fertilization mode can provide a scientific basis for coffee fertilization optimization and management.

Simultaneous analysis of the oxidation of solvent-extracted and cold-pressed green coffee oil during accelerated storage using 1H NMR and 13C NMR spectroscopy.

Green coffee oil (GCO) extracted from green coffee beans, is known for its antioxidant and anticancer properties, and has been increasingly utilised in cosmetic and other consumer products. However, lipid oxidation of GCO fatty acid components during storage may be harmful to human health, and there remains a need to understand the evolution of GCO chemical component oxidation. In this study, proton nuclear magnetic resonance (1H and 13C NMR) spectroscopy was used to investigate the oxidation status of solvent-extracted and cold-pressed GCO under accelerated storage conditions. Results show that the signal intensity of oxidation products gradually increased with increasing oxidation time, while unsaturated fatty acid signals gradually weakened. Five different types of GCO extracts were clustered according to their properties, except for minor overlapping in the two-dimensional plane of the principal component analysis. Partial least squares-least analysis results demonstrate that oxidation products (δ = 7.8-10.3 ppm), unsaturated fatty acids (δ = 5.28-5.42 ppm), and linoleic acid (δ = 2.70-2.85 ppm) in 1H NMR can be used as characteristic indicators of GCO oxidation levels. Furthermore, the kinetics curves of unsaturated fatty acids, linoleic, and linolenic acyl groups all fit an exponential equation with high coefficients of GCO for 36 days under accelerated storage conditions. Our results show that the current NMR system is a fast, easy-operated and convenient tool for the oxidation process monitoring and quality control of GCO.

Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes.

BACKGROUND: The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quality are yet largely unknown in peaberry. A transcriptome analysis was performed by using peaberry and regular coffee beans in this study. RESULTS: The result of phenotypic analysis stated a difference in the physical attributes of both coffee beans. In addition, transcriptome analysis revealed low genetic differences. Only 139 differentially expressed genes were detected in which 54 genes exhibited up-regulation and 85 showed down-regulations in peaberry beans compared to regular beans. The majority of differentially expressed genes had functional annotation with cell wall modification, lipid binding, protein binding, oxidoreductase activity, and transmembrane transportation. Many fold lower expression of Ca25840-PMEs1, Ca30827-PMEs2, Ca30828-PMEs3, Ca25839-PMEs4, Ca36469-PGs. and Ca03656-Csl genes annotated with cell wall modification might play a critical role to develop different bean shape patterns in Arabica. The ERECTA family genes Ca15802-ERL1, Ca99619-ERL2, Ca07439-ERL3, Ca97226-ERL4, Ca89747-ERL5, Ca07056-ERL6, Ca01141-ERL7, and Ca32419-ERL8 along lipid metabolic pathway genes Ca06708-ACOX1, Ca29177-ACOX2, Ca01563-ACOX3, Ca34321-CPFA1, and Ca36201-CPFA2 are predicted to regulate different shaped bean development. In addition, flavonoid biosynthesis correlated genes Ca03809-F3H, Ca95013-CYP75A1, and Ca42029-CYP75A2 probably help to generate rarely formed peaberry beans. CONCLUSION: Our results provide molecular insights into the formation of peaberry. The data resources will be important to identify candidate genes correlated with the different bean shape patterns in Arabica.

Enhanced Electrochemical Performance of Aprotic Li-CO2 Batteries with a Ruthenium-Complex-Based Mobile Catalyst.

Li-CO2 batteries are regarded as next-generation high-energy-density electrochemical devices. However, the greatest challenge arises from the formation of the discharge product, Li2 CO3 , which would accumulate and deactivate heterogenous catalysts to cause huge polarization. Herein, Ru(bpy)3 Cl2 was employed as a solution-phase catalyst for Li-CO2 batteries and proved to be the most effective one screened so far. Spectroscopy and electrochemical analyses elucidate that the RuII center could interact with both CO2 and amorphous Li2 C2 O4 intermediate, thus promoting electroreduction process and delaying carbonate transformation. As a result, the charge potential is reduced to 3.86 V and over 60 discharge/charge cycles are achieved with a fixed capacity of 1000 mAh g-1 at a current density of 300 mA g-1 . Our work provides a new avenue to improve the electrochemical performance of Li-CO2 batteries with efficient mobile catalysts.