Salojärvi, JarkkoRambani, AditiYu, ZheGuyot , RomainStrickler, SusanLepelley, MaudWang, CuiRajaraman, SitaramRastas , PasiZheng, ChunfangMuñoz, Daniella SantosMeidanis , JoãoPaschoal , Alexandre RossiKrabbenhoft, Trevor J.Bawin, YvesWang, Zhen QinFleck , Steven J.Aussel, RudyBellanger, LaurenceCharpagne, AlineFournier, CoralieKassam, MohamedLefebvre, GregoryMétairon , SylvianeMoine, DéborahRigoreau, MichelStolte, JensHamon, PerlaCouturon, EmmanuelTranchant-Dubreuil, ChristineMukherjee , MinakshiLan, TianyingEngelhardt , JanStadler, PeterCorreia De Lemos, Samara MirezaSuzuki , Suzana IvamotoSumirat, UcuWai , Ching ManDauchot , NicolasOrozco-Arias, SimonGaravito , AndreaKiwuka, CatherineMusoli, PascalNalukenge, AnneGuichoux, ErwanReinout, HavingaSmit, MartinCarretero-Paulet, LorenzoFilho, Oliveiro GuerreiroBraghini, Masako TomaPadilha, LilianSera, Gustavo HiroshiRuttink, TomHenry, RobertMarraccini, PierreVan de Peer, YvesAndrade, AlanDomingues , DouglasGiuliano , GiovanniMueller, LukasPereira, Luiz FilipePlaisance, StephanePoncet , ValerieRombauts , StephaneSankoff, DavidAlbert, Victor A.Crouzillat , DominiqueDe Kochko , AlexandreDescombes, Patrick2025-10-082025-10-082024-04-15Salojarvi, J., Rambani, A., Yu, Z. et al. 2024, 'The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars', Nature Genetics, vol. 56, pp. 721-731. https://doi.org/10.1038/s41588-024-01695-w.1061-4036 (print)1546-1718 (online)10.1038/s41588-024-01695-whttp://hdl.handle.net/2263/104648DATA AVAILABILITY : Coffee genome assemblies are available at CoGe (https://genomevolution.org/): C. canephora: 50947; C. eugenioides: 67315; and C. arabica: 66663 (Pacbio HiFi) and 53628 (Pacbio). The genome data are also available at ORCAE (https://bioinformatics.psb.ugent.be/orcae/overview/Coara and https://bioinformatics.psb.ugent.be/gdb/coffea_arabica/). All sequencing data are available at NCBI under bioproject ID PRJNA698600, and our assemblies are accessioned there as JAZHSI000000000.1, JAZHGF000000000.1, JAZHGH000000000.1 and JAZHGG000000000.1. Genotyping data (VCF files) and syntenic alignments are available in Data Dryad: https://doi.org/10.5061/dryad.qnk98sfpt.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.en© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License.GenomePopulationDiversificationCoffea arabicaArticle