Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea 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 thousand years ago, 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.

阿拉比卡咖啡 ( Coffea arabica ) 是咖啡豆 (Coffea eugenioides)和中果咖啡 (Coffea canephora)的异源四倍体杂交种，是全球约 60% 的咖啡产品的来源，其栽培品种经历了数次种群瓶颈。我们展示了二单倍体阿拉比卡种质及其二倍体祖先C. eugenioides和C. canephora的现代代表的染色体水平组装。这三个物种在二倍体亲本和后代亚基因组之间表现出很大程度上保守的基因组结构，没有明显的全局亚基因组优势。我们找到了 350,000-610,000 年前多倍体事件的证据，随后出现了几个驯化前的瓶颈，导致了狭窄的遗传变异。大约 30500 年前，野生种和品种祖先之间发生了分裂，随后两个种群之间出现了一段迁徙时期。对现代品种（包括历史上用C. canephora渗入的品系）的分析，突出了它们的育种历史和可能有助于病原体抗性的位点，为未来基于基因组学的阿拉比卡咖啡育种奠定了基础。