Comparative genome-wide characterization and evolutionary insights into the AP2/ERF gene family in three Coffea species (C. canephora, C. eugenioides, and C. arabica)

Authors: Park, Sunchung; Ahn, Ezekiel; Zhang, Dapeng; Meinhardt, Lyndel

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2025
Publication Date: 7/11/2025
Citation: Park, S., Ahn, E.J., Zhang, D., Meinhardt, L.W. 2025. Comparative genome-wide characterization and evolutionary insights into the AP2/ERF gene family in three Coffea species (C. canephora, C. eugenioides, and C. arabica). BMC Genomics. 26:653. https://doi.org/10.1186/s12864-025-11850-0.
DOI: https://doi.org/10.1186/s12864-025-11850-0

Interpretive Summary: Coffee farming is under threat from various environmental problems like diseases and rising temperatures. These issues can reduce coffee yields and quality, which is a big concern for farmers and the global coffee supply. To tackle these challenges, it's essential to understand the genetic makeup of coffee plants that helps them survive and thrive in tough conditions. One key group of genes, known as the AP2/ERF family, plays a vital role in how coffee plants grow and respond to stress, but we haven't fully explored how these genes work in the main types of coffee plants: Robusta and Arabica coffee. In our study, we closely examined the entire genetic blueprint of three coffee species to identify and analyze the AP2/ERF genes. We found 453 of these important genes, making up about 0.45% of all the genes. By mapping where these genes are located on the coffee plant chromosomes and comparing them across the different species, we saw that these genes are highly similar between the coffee species. We also discovered that many of these AP2/ERF genes have been duplicated over time, which has helped expand this gene family. About 16% of the AP2/ERF genes are duplicates, and the extent of duplications varies between the different coffee species. For example, genes linked to fighting diseases and those helping the plant handle temperature changes show variation. This suggests that each type of coffee has developed its own strategies to cope with specific environmental challenges. The characterization of the AP2/ERF gene family and its evolutionary dynamics in coffee species provides critical insights into the genetic basis of environmental adaptability. By identifying specific subgroups associated with disease resistance and temperature tolerance, this research highlights potential genetic targets for breeding programs aimed at enhancing climate resilience in coffee crops. Consequently, these findings support the development of sustainable coffee production strategies, ensuring the industry's viability in the face of global environmental challenges. This research will be used by researchers, plant breeders, germplasm curators, and coffee producers to aid the coffee industry and consumers.

Technical Abstract: The AP2/ERF transcription factor family plays a crucial role in plant development and adaptability to environmental stresses, characterized by the AP2 DNA-binding domain and including subfamilies such as ERF, AP2, and RAV. Leveraging recent genome resources for Coffea canephora (Robusta coffee), Coffea arabica, and Coffea eugenioides, we conducted a comprehensive genome-wide characterization and evolutionary analysis of the AP2/ERF family in these species. In total, we identified 453 AP2/ERF genes across the three species, representing 0.48% of protein-coding genes. Chromosomal mapping and synteny analysis revealed high conservation among the three species, consistent with their close evolutionary relationships. As observed in many plant species, gene duplication played a significant role in expansion of this family, with duplications accounting for 16% of this family. Subgroup IX, associated with disease resistance, showed significant variation between two parental species and their descendant subgenomes in C. arabica, suggesting possible lineage-specific gene loss or expansion. Subgroup III, linked to temperature tolerance, also displayed distinct expansion patterns among the coffee species, highlighting adaptive responses to environmental pressures. These lineage-specific differences in subgroup composition underscored the evolutionary dynamics of the AP2/ERF family in response to environmental pressures, providing potential candidates for development of climate-resilient coffee cultivars. This research provides a foundation for breeding programs aimed at enhancing the resilience in coffee crops, supporting sustainable production in the face of global climate change.