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

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Salojaervi, Jarkko ; Rambani, Aditi ; Yu, Zhe ; Guyot, Romain ; Strickler, Susan ; Lepelley, Maud ; Wang, Cui ; Rajaraman, Sitaram ; Rastas, Pasi ; Zheng, Chunfang ; Munoz, Daniella Santos ; Meidanis, Joao ; Paschoal, Alexandre Rossi ; Bawin, Yves ; Krabbenhoft, Trevor J. ; Wang, Zhen Qin ; Fleck, Steven J. ; Aussel, Rudy ; Bellanger, Laurence ; Charpagne, Aline ; Fournier, Coralie ; Kassam, Mohamed ; Lefebvre, Gregory ; Metairon, Sylviane ; Moine, Deborah ; Rigoreau, Michel ; Stolte, Jens ; Hamon, Perla ; Couturon, Emmanuel ; Tranchant-Dubreuil, Christine ; Mukherjee, Minakshi ; Lan, Tianying ; Engelhardt, Jan ; Stadler, Peter ; Correia De Lemos, Samara Mireza ; Suzuki, Suzana Ivamoto ; Sumirat, Ucu ; Wai, Ching Man ; Dauchot, Nicolas ; Orozco-Arias, Simon ; Garavito, Andrea ; Kiwuka, Catherine ; Musoli, Pascal ; Nalukenge, Anne ; Guichoux, Erwan ; Reinout, Havinga ; Smit, Martin ; Carretero-Paulet, Lorenzo ; Filho, Oliveiro Guerreiro ; Braghini, Masako Toma ; Padilha, Lilian ; Sera, Gustavo Hiroshi ; Ruttink, Tom ; Henry, Robert ; Marraccini, Pierre ; van de Peer, Yves ; Andrade, Alan ; Domingues, Douglas ; Giuliano, Giovanni ; Mueller, Lukas ; Pereira, Luiz Filipe ; Plaisance, Stephane ; Poncet, Valerie ; Rombauts, Stephane ; Sankoff, David ; Albert, Victor A. ; Crouzillat, Dominique ; de Kochko, Alexandre ; Descombes, Patrick

• Tipo de documento: Artigo Científico
• Fonte: Nature Genetics; v. 56, n. 4, p. 27-pg., 2024-04-01.

Resumo

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 similar to 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. (AU)

• Processo FAPESP: 17/01455-2 - Bases bioquímicas e moleculares da rede metabólica de diterpenos, compostos bioativos e naturais de cafeeiros
• Beneficiário: Suzana Tiemi Ivamoto
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 16/10896-0 - A sinalização do ácido hexanóico pode modular o transcriptoma, metaboloma e o desenvolvimento de patógenos no cafeeiro?
• Beneficiário: Douglas Silva Domingues
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores