ABSTRACT Coffea arabica , an allotetraploid hybrid of C. eugenioides and C. canephora , is the source of approximately 60% of coffee products worldwide. Cultivated accessions have undergone several population bottlenecks resulting in low genetic diversity. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora . The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, which show a mosaic pattern of dominance, similar to other polyploid crop species. Resequencing of 39 wild and cultivated accessions suggests a founding polyploidy event ∼610,000 years ago, followed by several subsequent bottlenecks, including a population split ∼30.5 kya and a period of migration between Arabica populations until ∼8.9 kya. Analysis of lines historically introgressed with C. canephora highlights loci that may contribute to their superior pathogen resistance and lay the groundwork for future genomics-based breeding of C. arabica .

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars