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

Coffea arabica, an allotetraploid hybrid of C.
eugenioides and C. canephora, is the source of
approximately 60% of coffee products worldwide, and its cultivated
accessions have undergone several population bottlenecks. 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, with no obvious global
subgenome dominance. We find evidence for a founding polyploidy event
350,000-610,000 years ago, followed by several pre-domestication
bottlenecks, resulting in narrow genetic variation. A split between wild
accessions and cultivar progenitors occurred ∼30.5 kya, followed by a
period of migration between the two populations. Analysis of modern
varieties, including lines historically introgressed with C.
canephora, highlights their breeding histories and loci that may
contribute to pathogen resistance, laying the groundwork for future
genomics-based breeding of C. arabica.