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.

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.

Excessive use of chemical fertilizers deteriorates the soil environment and limits the normal growth of Arabica coffee trees. In order to identify the optimal coupling mode of chemical fertilizer application and biomass return that enhances the soil ecological environment and promotes the photosynthetic efficiency of Arabica coffee, this study investigated the impacts of three levels of inorganic fertilizers (FL: 360 kg·ha−1, FM: 720 kg·ha−1, and FH: 1080 kg·ha−1) and three types of coffee husk returning methods (CB: coffee husk biochar, CC: coffee husk compost, CA: coffee husk ash) on the soil fertility, microbial amount, enzyme activity, and photosynthetic characteristics of the Arabica coffee root zone. The entropy weight-TOPSIS method was employed to evaluate the comprehensive benefits. The results showed that FM had the biggest effect on improving soil fertility, microorganisms, and enzyme activities compared with FL and FH. Moreover, compared to CA, CC significantly increased soil organic carbon, organic matter, and total nitrogen content. CC significantly enhanced the activities of soil phosphatase and urease, respectively, by 29.84% and 96.00%, and significantly increased the amount of bacteria, fungi, and actinomycetes by 62.15%, 68.42%, and 46.21%, respectively. The net photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs) of FMCC were significantly higher than those of other treatments. The comprehensive benefit evaluation of the soil environment and photosynthetic characteristics by the entropy weight-TOPSIS method ranked FMCC first. Therefore, FMCC was the optimal coupling mode for fertilizer application and the coffee husk returning method. The findings of this study not only provide scientific guidance for fertilizing Arabica coffee but also clarify the proper approach to returning coffee husk to the field, thereby improving soil ecology and promoting green and efficient production of specialty crops.

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.