학술논문
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
Document Type
Original Paper
Author
Salojärvi, Jarkko; Rambani, Aditi; Yu, Zhe; Guyot, Romain; Strickler, Susan; Lepelley, Maud; Wang, Cui; Rajaraman, Sitaram; Rastas, Pasi; Zheng, Chunfang; Muñoz, Daniella Santos; Meidanis, João; 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; Métairon, Sylviane; Moine, Déborah; 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
Source
Nature Genetics. 56(4):721-731
Subject
Language
English
ISSN
1061-4036
1546-1718
1546-1718
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.
Chromosome-level genome assemblies of allotetraploid Coffea arabica and representatives of its diploid progenitors, Coffeaeugenioides and Coffeacanephora, provide insights into Arabica’s diversification history.
Chromosome-level genome assemblies of allotetraploid Coffea arabica and representatives of its diploid progenitors, Coffeaeugenioides and Coffeacanephora, provide insights into Arabica’s diversification history.