Genome-wide characterization of invertases in Arabica coffee and its progenitors reveals putative genes involved in fruit development

Authors: FERRAZ, GABRIELA - Federal University Of Lavras; GUTIERREZ, ROBERT - Federal University Of Lavras; DE CAMPOS RUME, GABRIEL - Federal University Of Lavras; INOUE, TIAGO - Federal University Of Lavras; NOVAES, EVANDRO - Federal University Of Lavras; SALES, THAI - Federal University Of Lavras; Zhang, Dapeng; CHALFUN JUNIOR, ANTONIO - Federal University Of Lavras

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2025
Publication Date: 7/11/2025
Citation: Ferraz, G.E., Gutierrez, R.M., De Campos Rume, G., Inoue, T.Y., Novaes, E., Sales, T., Zhang, D., Chalfun Junior, A. 2025. Genome-wide characterization of invertases in Arabica coffee and its progenitors reveals putative genes involved in fruit development. Functional and Integrative Genomics. https://doi.org/10.1007/s10142-025-01662-6.
DOI: https://doi.org/10.1007/s10142-025-01662-6

Interpretive Summary: Knowledge of the key enzymes involving coffee plant growth and development is important for breeding new coffee varieties with high yield, resistance to biotic and abiotic stresses and superior bean quality. In the present study, we conducted a comprehensive analysis on Invertases gene family in three coffee species including Arabica, Robusta and a related species (C. eugenioides). A total of 65 invertase genes were identified in the three species. We found that in Arabica coffee, the invertase genes were originally derived from C. eugenioides, which is one of the parental species of Arabica coffee. Furthermore, polyploidization was found to be the primary cause of invertase gene expansion in Arabica. Our result also indicates that invertase genes were involved in coffee plant development, adaptation to biotic and abiotic stress, and hormonal responses. Moreover, we found that all invertase genes were expressed at different stages of fruit development. This study provides the groundwork for future functional analysis of invertase genes in coffee, which will contribute to an improved understanding of disease resistance, tolerance to abiotic stresses, and fruit chemical composition. This information will be used by coffee growers and coffee breeders to design crop management practice and for the breeding of new coffee varieties.

Technical Abstract: Invertases are crucial enzymes in plants as they involve plant development and stress response, biosynthetic processes and hydrolysis of sucrose into glucose and fructose. However, few genes of invertases have been characterized in Coffea species, and their relationship with coffee plant development is not well understood. In the present study, a genome-wide analyses combining proteomic characterization, chromosome mapping, phylogenetic analysis, and tissue-specific expression was conducted on three Coffea species (C. arabica, C. canephora and C. eugenioides) to gain insight into the Invertase gene family in coffee. A total of 65 invertase genes were identified in C. arabica (CaINV), C. canephora (CcINV) and C. eugenioides (CeINV) through proteomics analysis. Polyploidization was found the primary cause of the expansion of CaINV genes. Synteny analysis, along with chromosomal mapping, suggested that the CaINV genes are originally derived from C. eugenioides. The cis-acting elements indicated that invertase genes involved coffee plant growth and development, adaptation to biotic and abiotic stress, and hormonal response. Transcriptome analyses showed that, except for the neutral/alkaline invertase gene CaN/AINV1, all invertase genes of C. arabica and C. canephora were expressed at different stages of coffee fruit development. This study provides the groundwork for future functional analysis of invertase genes in coffee, which will contribute to improved understanding in disease resistance, tolerance to abiotic stresses, and fruit chemical composition.