The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
Jarkko SalojärviOrganismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland. [email protected]Aditi RambaniBoyce Thompson Institute, Cornell University, Ithaca, NY, USAZhe YuDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, CanadaRomain GuyotDepartment of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, ColombiaSusan R. StricklerBoyce Thompson Institute, Cornell University, Ithaca, NY, USAMaud LepelleySociété des Produits Nestlé SA, Nestlé Research, Tours, FranceCui WangOrganismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, FinlandSitaram RajaramanOrganismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, FinlandPasi RastasInstitute of Biotechnology, University of Helsinki, Helsinki, FinlandChunfang ZhengDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, CanadaDaniella Santos MuñozDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, CanadaJoão MeidânisInstitute of Computing, University of Campinas, Campinas, BrazilAlexandre Rossi PaschoalDepartment of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, BrazilYves BawinPlant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, BelgiumTrevor J. KrabbenhoftDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USAZhen Qin WangDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USASteven J. FleckDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USARudy AusselCentre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, FranceLaurence BellangerSociété des Produits Nestlé SA, Nestlé Research, Tours, FranceAline CharpagneSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandCoralie FournierSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandMohamed KassamSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandGrégory LefebvreSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandSylviane MétaironSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandD MoineSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandMichel RigoreauSociété des Produits Nestlé SA, Nestlé Research, Tours, FranceJens StolteSociété des Produits Nestlé SA, Nestlé Research, Lausanne, SwitzerlandPerla HamonInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, FranceEmmanuel CouturonInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, FranceChristine Tranchant‐DubreuilInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, FranceMinakshi MukherjeeDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USATianying LanDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USAJan EngelhardtDepartment of Computer Science, University of Leipzig, Leipzig, GermanyPeter F. StadlerDepartment of Computer Science, University of Leipzig, Leipzig, GermanySamara Mireza Correia De LemosGroup of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, BrazilSuzana Ivamoto SuzukiCentro de Ciências Agrárias, Universidade Estadual de Londrina, Londrina, BrazilUcu SumiratIndonesian Coffee and Cocoa Research Institute (ICCRI), Jember, IndonesiaChing Man WaiUniversity of Illinois at Urbana-Champaign, Urbana, IL, USANicolas DauchotResearch Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, BelgiumSimón Orozco-AriasDepartment of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, ColombiaAndréa GaravitoDepartamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, ColombiaCatherine KiwukaNational Agricultural Research Organization (NARO), Entebbe, UgandaPascal MusoliNational Agricultural Research Organization (NARO), Entebbe, UgandaAnne NalukengeNational Agricultural Research Organization (NARO), Entebbe, UgandaErwan GuichouxBiodiversité Gènes & Communautés, INRA, Bordeaux, FranceHavinga ReinoutMartin SmitLorenzo Carretero‐PauletDepartamento de Biología y Geología, Universidad de Almería, Almería, SpainOliveiro Guerreiro FilhoMasako Toma BraghiniLílian PadilhaGustavo Hiroshi SeraInstituto de Desenvolvimento Rural do Paraná- IAPAR, Londrina, BrazilTom RuttinkDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, BelgiumRobert J HenryQueensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, AustraliaPierre MarracciniCIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, FranceYves Van de PeerCenter for Plant Systems Biology, VIB, Ghent, BelgiumAlan Carvalho AndradeEmbrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, BrazilDouglas Silva DominguesGroup of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, BrazilGiovanni GiulianoItalian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, ItalyLukas A. MuellerBoyce Thompson Institute, Cornell University, Ithaca, NY, USALuiz Filipe Protásio PereiraEmbrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, BrazilStéphane PlaisanceValérie PoncetInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, FranceStéphane RombautsCenter for Plant Systems Biology, VIB, Ghent, BelgiumDavid SankoffDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, CanadaVictor A. AlbertDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA. [email protected]Dominique CrouzillatSociété des Produits Nestlé SA, Nestlé Research, Tours, France. [email protected]Alexandre de KochkoInstitut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France. [email protected]Patrick DescombesSociété des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland. [email protected]
2024en
ABI
Аннотация
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.
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