Coffea Comparative Genomics Reveals Subgenome-Associated Expansion and Diversification of Biosynthetic Gene Clusters

Biosynthetic gene clusters (BGCs) are important for plant specialized metabolism, but remain poorly characterized in coffee. Given Brazil’s importance in coffee production, we performed a comparative genomic analysis of BGCs across the allotetraploid Coffea arabica and its diploid progenitors C. eugenioides and C. canephora. Using standardized genome filtering, annotation, orthogroup inference, and cluster classification, we identified 472 BGCs comprising 3,118 biosynthetic genes, which were grouped into 194 cluster families and integrated with 28,280 orthogroups. Of these, 7,091 orthogroups were shared across all species; Coffea canephora and subgenomes shared 10,923, while Coffea eugenioides and subgenomes shared 11,446. Most BGC-associated orthogroups (86.4%) link to a single pathway class. BGC-associated genes form a highly structured yet lineage-dynamic component of the Coffea pangenome. C. eugenioides and its derived subgenomes in Arabica contributed disproportionately to 14 BGC-associated orthogroups, including flavonoid-, lipid-, and stress-related functions. In contrast, C. canephora derivatives contributed only two terpene-related orthogroups. The parental species showed fewer secondary metabolism-related enriched GO terms (3 and 1) than their subgenomes (53 and 56). Species-specific rearrangements, expansions, and subgenome retention indicate that hybridization and polyploidy shaped BGC diversification. These results advance understanding of specialized metabolism in Coffea and identify targets for coffee improvement and climate resilience.