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August 20, 2026Genome

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

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Authors

DCDaisy Sotero ChaconLGLaura Natalia González-GarcíaVTVitor Trinca

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Overview

Comparative genomic analysis reveals subgenome-driven diversification of biosynthetic gene clusters in allotetraploid coffee, highlighting targets for climate resilience.

Key Points

  • Characterize the organization, evolutionary dynamics, and subgenome divergence of biosynthetic gene clusters (BGCs) in Coffea arabica and its diploid progenitor species.
  • Conducted comparative genomics using standardized genome filtering, annotation, orthogroup inference, and BGC classification across Coffea arabica, Coffea eugenioides, and Coffea canephora.
  • Identified 472 BGCs containing 3,118 biosynthetic genes across 194 cluster families and integrated them into 28,280 orthogroups, with 86.4% of BGC-associated orthogroups linking to a single pathway class.
  • The C. eugenioides subgenome contributed disproportionately to 14 BGC-associated orthogroups involving flavonoid, lipid, and stress functions, compared to 2 terpene-related orthogroups from C. canephora.
  • Subgenomes exhibited substantially higher secondary metabolism gene ontology enrichment (53 and 56 enriched terms) compared to their diploid parental species (3 and 1 enriched terms).

Cite This Study

Chacon et al. (2026) studied this question.

synapsesocial.com/papers/6a86b56c8a91293e6a1ccc7fhttps://doi.org/10.1139/gen-2026-0007
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