Lineage-specific genomic signatures in Coffea identified through comparative gene family evolution

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

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2026
Publication Date: 5/9/2026
Citation: Park, S., Ahn, E.J., Oh, S., Zhang, D., Meinhardt, L.W. 2026. Lineage-specific genomic signatures in Coffea identified through comparative gene family evolution. Tree Genetics and Genomes. 16. Article 1632888. https://doi.org/10.1007/s11295-026-01738-9.
DOI: https://doi.org/10.1007/s11295-026-01738-9

Interpretive Summary: Coffee is a critical crop that supports the livelihoods of over 100 million small-scale farmers globally. However, the most widely grown species, Coffea arabica, has limited genetic diversity, making it more vulnerable to environmental stresses, diseases, and pests. Although researchers have recently sequenced the genomes of several coffee species, we still don’t fully understand which makes each species unique or how we can use that knowledge to improve coffee crops. To address this, we compared the genes of 24 plant species, including three coffee species, to identify unique genetic traits in coffee. We used advanced computational tools to find genes that are either specific to coffee or have expanded over time—especially those related to disease resistance, flavor compounds, and adaptability to environmental conditions like shade and altitude. Our study uncovered over 2,000 gene families that could play important roles in making coffee more resilient and flavorful. Some of these genes help the plant fight off diseases, while others are linked to the rich taste and aroma we associate with a good cup of coffee. These discoveries give plant breeders new tools to develop stronger, tastier, and more sustainable coffee varieties—ensuring better crops for farmers.

Technical Abstract: Coffee is among the most widely consumed beverages worldwide, with diverse Coffea species displaying a broad spectrum of flavors and agronomically important traits. While genome assemblies for several coffee species have recently become available, comparative gnomonic analyses remain underutilized in harnessing this information for crop improvement. In this study, we conducted comprehensive orthology and gene family evolution analyses across 24 plant species–including three Coffea species (C. arabica, C. canephora, and C. eugenioides), twelve Lamiales, and eight Solanales–to identify lineage-specific genomic features associated with adaptation and coffee quality traits. Using OrthoFinder in conjunction with gene family evolution models (CAFE5 and COUNT), we identified 2,159 orthogroups that are either specific to Coffea or have undergone significant expansion or contraction. Disease-resistance genes were the most prominent among rapidly expanded gene families, reflecting ongoing evolutionary arms race with pathogens. We also observed asymmetric patterns of gene family evolution, including contraction of light and ethylene signaling gene families in C. canephora, contrasted by their expansion in C. arabica and C. eugenioides, which may contribute to their adaptation to shaded, high-altitude environments. Further analysis using COUNT identified twelve Coffea-specific gene family expansions associated with secondary metabolite biosynthesis, including key enzymes for caffeine and chlorogenic acid production. Our comprehensive catalog of lineage-specific orthogroups, supported by functional enrichment and phylogenetic analyses, provides a valuable genomic resource to guide functional validation studies and support breeding programs focused on enhancing stress resilience, disease resistance, and cup quality in cultivated coffee.