ArticleNature genetics2024
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.
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Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46citing papers in PubMed
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46 citing papers in PubMed.
- Subgenome-Resolved Analysis and Regulatory Divergence of UDP-Glycosyltransferases in AllotetraploidGenes · 2026Article
- Contrasting regulation of protein-coding genes and lncRNA homeologs in allotetraploid Coffea arabica.Planta · 2026Article
- Cell-Specific Expression and Cellular Compartmental Regulation in Camptothecin Biosynthesis.Plant biotechnology journal · 2026Article
- CoalMiner: a coalescent model generator forbioRxiv : the preprint server for biology · 2026Article
- Genome‑wide analysis of the CaWRKY transcription factors reveals CaWRKY28 as a candidate gene for cold tolerance breeding in Coffea arabica L.BMC plant biology · 2026Article
- Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.Food chemistry. Molecular sciences · 2026Article
- Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus.Scientific reports · 2026Article
- Main characteristic metabolites with xanthine oxidase inhibitory activities from YunnanFood chemistry: X · 2026Article
- The Late Quaternary climate impact on the genome of the woodland strawberry (Fragaria vesca), a perennial herb.Communications biology · 2026Article
- Genetic diversity and population structure ofFrontiers in plant science · 2026Article
- What you plant may not be what you bought: morphological and genetic discordance in specialtyFrontiers in plant science · 2026Article
- Tracing the Evolutionary Dynamics and the Transcriptional Partitioning of Terpene Synthase Gene Family inBioinformatics and biology insights · 2026Article
- Machine-learning-based analysis of host-depletedBioinformatics advances · 2026Article
- Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressedFrontiers in plant science · 2026Article
- FFrontiers in plant science · 2026Review
- Production and trade of specialty coffee in Brazil.Scientific reports · 2025Article
- A Near Telomere-To-Telomere Genome Assembly of Coffea arabica (Mundo Novo) Provides Insights Into Its Secondary Metabolism.Molecular ecology resources · 2025Article
- Genome-Wide Analysis Reveals Chitinases as Putative Defense-Related Proteins Against Fungi in the Genomes ofPlants (Basel, Switzerland) · 2025Article
- A chromosome-level Mitragyna parvifolia genome unveils spirooxindole alkaloid diversification and mitraphylline biosynthesis.The Plant cell · 2025Article
- The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches.Microorganisms · 2025Article
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Authors and funding
69 authors.
Jarkko SalojärviSchool of Biological Sciences, Nanyang Technological University, Singapore, Singapore. jarkko@ntu.edu.sg.ORCID http://orcid.org/0000-0002-4096-6278
Aditi Rambani *Boyce Thompson Institute, Cornell University, Ithaca, NY, USA.
Zhe Yu *Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
Romain Guyot *Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.ORCID http://orcid.org/0000-0002-7016-7485
Susan Strickler *Boyce Thompson Institute, Cornell University, Ithaca, NY, USA.
Maud LepelleySociété des Produits Nestlé SA, Nestlé Research, Tours, France.
Cui WangOrganismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.ORCID http://orcid.org/0000-0003-2916-3922
Sitaram RajaramanOrganismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.ORCID http://orcid.org/0000-0001-5171-3578
Pasi RastasInstitute of Biotechnology, University of Helsinki, Helsinki, Finland.ORCID http://orcid.org/0000-0003-2768-1339
Chunfang ZhengDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
Daniella Santos MuñozDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
João MeidanisInstitute of Computing, University of Campinas, Campinas, Brazil.ORCID http://orcid.org/0000-0001-7878-4990
Alexandre Rossi PaschoalDepartment of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Brazil.ORCID http://orcid.org/0000-0002-8887-0582
Yves BawinPlant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium.
Trevor J KrabbenhoftDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-7680-5169
Zhen Qin WangDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
Steven J FleckDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA.ORCID http://orcid.org/0000-0001-5370-2258
Rudy AusselSociété des Produits Nestlé SA, Nestlé Research, Tours, France.
Laurence BellangerSociété des Produits Nestlé SA, Nestlé Research, Tours, France.
Aline CharpagneSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
Coralie FournierSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.ORCID http://orcid.org/0000-0002-7310-0227
Mohamed KassamSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
Gregory LefebvreSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
Sylviane MétaironSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.ORCID http://orcid.org/0000-0003-2434-8733
Déborah MoineSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
Michel RigoreauSociété des Produits Nestlé SA, Nestlé Research, Tours, France.
Jens StolteSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
Perla HamonInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
Emmanuel CouturonInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
Christine Tranchant-DubreuilInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
Minakshi MukherjeeDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-5172-838X
Tianying LanDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
Jan EngelhardtDepartment of Computer Science, University of Leipzig, Leipzig, Germany.ORCID http://orcid.org/0000-0003-4934-2135
Peter StadlerDepartment of Computer Science, University of Leipzig, Leipzig, Germany.ORCID http://orcid.org/0000-0002-5016-5191
Samara Mireza Correia De LemosGroup of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil.ORCID http://orcid.org/0000-0003-3484-1943
Suzana Ivamoto SuzukiCentro de Ciências Agrárias, Universidade Estadual de Londrina, Londrina, Brazil.ORCID http://orcid.org/0000-0001-7078-5809
Ucu SumiratIndonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia.
Ching Man WaiUniversity of Illinois at Urbana-Champaign, Urbana, IL, USA.ORCID http://orcid.org/0000-0002-2913-5721
Nicolas DauchotResearch Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, Belgium.ORCID http://orcid.org/0000-0001-8766-0498
Simon Orozco-AriasDepartment of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia.ORCID http://orcid.org/0000-0001-5991-8770
Andrea GaravitoDepartamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia.ORCID http://orcid.org/0000-0002-0864-8608
Catherine KiwukaNational Agricultural Research Organization (NARO), Entebbe, Uganda.
Pascal MusoliNational Agricultural Research Organization (NARO), Entebbe, Uganda.
Anne NalukengeNational Agricultural Research Organization (NARO), Entebbe, Uganda.
Erwan GuichouxBiodiversité Gènes & Communautés, INRA, Bordeaux, France.
Havinga ReinoutHortus Botanicus Amsterdam, Amsterdam, the Netherlands.
Martin SmitHortus Botanicus Amsterdam, Amsterdam, the Netherlands.
Lorenzo Carretero-PauletDepartamento de Biología y Geología, Universidad de Almería, Almería, Spain.
Oliveiro Guerreiro FilhoInstituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil.ORCID http://orcid.org/0000-0002-8228-2886
Masako Toma BraghiniInstituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil.
Lilian PadilhaEmbrapa Café/Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil.ORCID http://orcid.org/0000-0002-2204-6793
Gustavo Hiroshi SeraInstituto de Desenvolvimento Rural do Paraná- IAPAR, Londrina, Brazil.
Tom RuttinkPlant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium.ORCID http://orcid.org/0000-0002-1012-9399
Robert HenryQueensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia.
Pierre MarracciniCIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, France.ORCID http://orcid.org/0000-0001-7637-6811
Yves Van de PeerDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.ORCID http://orcid.org/0000-0003-4327-3730
Alan AndradeEmbrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, Brazil.ORCID http://orcid.org/0000-0001-7128-3472
Douglas DominguesGroup of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil.ORCID http://orcid.org/0000-0002-1290-0853
Giovanni GiulianoItalian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, Italy.ORCID http://orcid.org/0000-0002-2486-0510
Lukas MuellerBoyce Thompson Institute, Cornell University, Ithaca, NY, USA.
Luiz Filipe PereiraEmbrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, Brazil.
Stephane PlaisanceVIB Nucleomics Core, Leuven, Belgium.ORCID http://orcid.org/0000-0002-1651-241X
Valerie PoncetInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.ORCID http://orcid.org/0000-0002-1099-2846
Stephane RombautsDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.ORCID http://orcid.org/0000-0002-3985-4981
David SankoffDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.ORCID http://orcid.org/0000-0001-8415-5189
Victor A AlbertDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA. vaalbert@buffalo.edu.ORCID http://orcid.org/0000-0002-0262-826X
Dominique CrouzillatSociété des Produits Nestlé SA, Nestlé Research, Tours, France. dcrouzillat@gmail.com.ORCID http://orcid.org/0009-0000-3369-0173
Alexandre de KochkoInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France. alexandre.dekochko@gmail.com.ORCID http://orcid.org/0000-0001-9212-3195
Patrick DescombesSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland. patrick.descombes@rd.nestle.com.ORCID http://orcid.org/0000-0002-1274-247X
Funding
Academy of Finland (Suomen Akatemia) 343656Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders) G056517NNSF | Directorate for Biological Sciences (BIO) 1442190NSF | Directorate for Biological Sciences (BIO) 2030871Universitair Ziekenhuis Gent (Ghent University Hospital) BOF.MET.2021.0005.01
Abstract
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.
Indexed as
CoffeaCoffeeGenome, PlantMetagenomicsPlant BreedingCoffee
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