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

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Autor(es): dc.contributorNanyang Technological University-
Autor(es): dc.contributorUniversity of Helsinki-
Autor(es): dc.contributorCornell University-
Autor(es): dc.contributorUniversity of Ottawa-
Autor(es): dc.contributorUniversité de Montpellier-
Autor(es): dc.contributorUniversidad Autónoma de Manizales-
Autor(es): dc.contributorNestlé Research-
Autor(es): dc.contributorUniversidade Estadual de Campinas (UNICAMP)-
Autor(es): dc.contributorThe Federal University of Technology – Paraná (UTFPR)-
Autor(es): dc.contributorFisheries and Food (ILVO)-
Autor(es): dc.contributorUniversity at Buffalo-
Autor(es): dc.contributorAix Marseille Université-
Autor(es): dc.contributorUniversity of Leipzig-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorUniversidade Estadual de Londrina (UEL)-
Autor(es): dc.contributorIndonesian Coffee and Cocoa Research Institute (ICCRI)-
Autor(es): dc.contributorUniversity of Illinois at Urbana-Champaign-
Autor(es): dc.contributorUniversity of Namur-
Autor(es): dc.contributorUniversidad de Caldas-
Autor(es): dc.contributorNational Agricultural Research Organization (NARO)-
Autor(es): dc.contributorINRA-
Autor(es): dc.contributorHortus Botanicus Amsterdam-
Autor(es): dc.contributorUniversidad de Almería-
Autor(es): dc.contributorFazenda Santa Elisa-
Autor(es): dc.contributorEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)-
Autor(es): dc.contributorInstituto de Desenvolvimento Rural do Paraná- IAPAR-
Autor(es): dc.contributorGhent University-
Autor(es): dc.contributorUniversity of Queensland-
Autor(es): dc.contributorCIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501-
Autor(es): dc.contributorUniversity of Pretoria-
Autor(es): dc.contributorNanjing Agricultural University-
Autor(es): dc.contributorVIB-
Autor(es): dc.contributorENEA Casaccia Research Center-
Autor(es): dc.contributorVIB Nucleomics Core-
Autor(es): dc.creatorSalojärvi, Jarkko-
Autor(es): dc.creatorRambani, Aditi-
Autor(es): dc.creatorYu, Zhe-
Autor(es): dc.creatorGuyot, Romain-
Autor(es): dc.creatorStrickler, Susan-
Autor(es): dc.creatorLepelley, Maud-
Autor(es): dc.creatorWang, Cui-
Autor(es): dc.creatorRajaraman, Sitaram-
Autor(es): dc.creatorRastas, Pasi-
Autor(es): dc.creatorZheng, Chunfang-
Autor(es): dc.creatorMuñoz, Daniella Santos-
Autor(es): dc.creatorMeidanis, João-
Autor(es): dc.creatorPaschoal, Alexandre Rossi-
Autor(es): dc.creatorBawin, Yves-
Autor(es): dc.creatorKrabbenhoft, Trevor J.-
Autor(es): dc.creatorWang, Zhen Qin-
Autor(es): dc.creatorFleck, Steven J.-
Autor(es): dc.creatorAussel, Rudy-
Autor(es): dc.creatorBellanger, Laurence-
Autor(es): dc.creatorCharpagne, Aline-
Autor(es): dc.creatorFournier, Coralie-
Autor(es): dc.creatorKassam, Mohamed-
Autor(es): dc.creatorLefebvre, Gregory-
Autor(es): dc.creatorMétairon, Sylviane-
Autor(es): dc.creatorMoine, Déborah-
Autor(es): dc.creatorRigoreau, Michel-
Autor(es): dc.creatorStolte, Jens-
Autor(es): dc.creatorHamon, Perla-
Autor(es): dc.creatorCouturon, Emmanuel-
Autor(es): dc.creatorTranchant-Dubreuil, Christine-
Autor(es): dc.creatorMukherjee, Minakshi-
Autor(es): dc.creatorLan, Tianying-
Autor(es): dc.creatorEngelhardt, Jan-
Autor(es): dc.creatorStadler, Peter-
Autor(es): dc.creatorCorreia De Lemos, Samara Mireza-
Autor(es): dc.creatorSuzuki, Suzana Ivamoto-
Autor(es): dc.creatorSumirat, Ucu-
Autor(es): dc.creatorWai, Ching Man-
Autor(es): dc.creatorDauchot, Nicolas-
Autor(es): dc.creatorOrozco-Arias, Simon-
Autor(es): dc.creatorGaravito, Andrea-
Autor(es): dc.creatorKiwuka, Catherine-
Autor(es): dc.creatorMusoli, Pascal-
Autor(es): dc.creatorNalukenge, Anne-
Autor(es): dc.creatorGuichoux, Erwan-
Autor(es): dc.creatorReinout, Havinga-
Autor(es): dc.creatorSmit, Martin-
Autor(es): dc.creatorCarretero-Paulet, Lorenzo-
Autor(es): dc.creatorFilho, Oliveiro Guerreiro-
Autor(es): dc.creatorBraghini, Masako Toma-
Autor(es): dc.creatorPadilha, Lilian-
Autor(es): dc.creatorSera, Gustavo Hiroshi-
Autor(es): dc.creatorRuttink, Tom-
Autor(es): dc.creatorHenry, Robert-
Autor(es): dc.creatorMarraccini, Pierre-
Autor(es): dc.creatorVan de Peer, Yves-
Autor(es): dc.creatorAndrade, Alan-
Autor(es): dc.creatorDomingues, Douglas-
Autor(es): dc.creatorGiuliano, Giovanni-
Autor(es): dc.creatorMueller, Lukas-
Autor(es): dc.creatorPereira, Luiz Filipe-
Autor(es): dc.creatorPlaisance, Stephane-
Autor(es): dc.creatorPoncet, Valerie-
Autor(es): dc.creatorRombauts, Stephane-
Autor(es): dc.creatorSankoff, David-
Autor(es): dc.creatorAlbert, Victor A.-
Autor(es): dc.creatorCrouzillat, Dominique-
Autor(es): dc.creatorde Kochko, Alexandre-
Autor(es): dc.creatorDescombes, Patrick-
Data de aceite: dc.date.accessioned2025-08-21T18:31:44Z-
Data de disponibilização: dc.date.available2025-08-21T18:31:44Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2024-04-01-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1038/s41588-024-01695-w-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/309579-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/309579-
Descrição: dc.descriptionCoffea 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.-
Descrição: dc.descriptionSchool of Biological Sciences Nanyang Technological University-
Descrição: dc.descriptionOrganismal and Evolutionary Biology Research Programme University of Helsinki-
Descrição: dc.descriptionSingapore Centre for Environmental Life Sciences Engineering Nanyang Technological University-
Descrição: dc.descriptionBoyce Thompson Institute Cornell University-
Descrição: dc.descriptionDepartment of Mathematics and Statistics University of Ottawa-
Descrição: dc.descriptionInstitut de Recherche pour le Développement (IRD) Université de Montpellier-
Descrição: dc.descriptionDepartment of Electronics and Automation Universidad Autónoma de Manizales-
Descrição: dc.descriptionSociété des Produits Nestlé SA Nestlé Research-
Descrição: dc.descriptionInstitute of Biotechnology University of Helsinki-
Descrição: dc.descriptionInstitute of Computing University of Campinas-
Descrição: dc.descriptionDepartment of Computer Science The Federal University of Technology – Paraná (UTFPR)-
Descrição: dc.descriptionPlant Sciences Unit Flanders Research Institute for Agriculture Fisheries and Food (ILVO)-
Descrição: dc.descriptionDepartment of Biological Sciences University at Buffalo-
Descrição: dc.descriptionCentre d’Immunologie de Marseille-Luminy Aix Marseille Université-
Descrição: dc.descriptionDepartment of Computer Science University of Leipzig-
Descrição: dc.descriptionInterdisciplinary Center for Bioinformatics University of Leipzig-
Descrição: dc.descriptionGroup of Genomics and Transcriptomes in Plants São Paulo State University UNESP-
Descrição: dc.descriptionCentro de Ciências Agrárias Universidade Estadual de Londrina-
Descrição: dc.descriptionIndonesian Coffee and Cocoa Research Institute (ICCRI)-
Descrição: dc.descriptionUniversity of Illinois at Urbana-Champaign-
Descrição: dc.descriptionResearch Unit in Plant Cellular and Molecular Biology University of Namur-
Descrição: dc.descriptionDepartamento de Ciencias Biológicas Facultad de Ciencias Exactas y Naturales Universidad de Caldas-
Descrição: dc.descriptionNational Agricultural Research Organization (NARO)-
Descrição: dc.descriptionBiodiversité Gènes & amp; Communautés INRA-
Descrição: dc.descriptionHortus Botanicus Amsterdam-
Descrição: dc.descriptionDepartamento de Biología y Geología Universidad de Almería-
Descrição: dc.descriptionInstituto Agronômico (IAC) Centro de Café ‘Alcides Carvalho’ Fazenda Santa Elisa-
Descrição: dc.descriptionEmbrapa Café/Instituto Agronômico (IAC) Centro de Café ‘Alcides Carvalho’ Fazenda Santa Elisa-
Descrição: dc.descriptionInstituto de Desenvolvimento Rural do Paraná- IAPAR-
Descrição: dc.descriptionDepartment of Plant Biotechnology and Bioinformatics Ghent University-
Descrição: dc.descriptionQueensland Alliance for Agriculture and Food Innovation University of Queensland-
Descrição: dc.descriptionCIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501-
Descrição: dc.descriptionDepartment of Biochemistry Genetics and Microbiology University of Pretoria-
Descrição: dc.descriptionCollege of Horticulture Academy for Advanced Interdisciplinary Studies Nanjing Agricultural University-
Descrição: dc.descriptionCenter for Plant Systems Biology VIB-
Descrição: dc.descriptionEmbrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG-
Descrição: dc.descriptionItalian National Agency for New Technologies Energy and Sustainable Economic Development ENEA Casaccia Research Center-
Descrição: dc.descriptionEmbrapa Café/Lab. Biotecnologia Área de Melhoramento Genético-
Descrição: dc.descriptionVIB Nucleomics Core-
Descrição: dc.descriptionGroup of Genomics and Transcriptomes in Plants São Paulo State University UNESP-
Formato: dc.format721-731-
Idioma: dc.languageen-
Relação: dc.relationNature Genetics-
???dc.source???: dc.sourceScopus-
Título: dc.titleThe genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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