Comparative genomics of Coffea species highlights expansion of gene families linked to adaptation and secondary metabolism

Coffee is among the most widely consumed beverages worldwide, with diverse Coffea species displaying a broad spectrum of flavors and important agronomic traits. Despite recent advances in genomics and the availability of assembled coffee genomes, comparative genomic analyses remain underutilized 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 1,552 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 support breeding programs focused on enhancing stress resilience, disease resistance, and cup quality in cultivated coffee.