The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
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 accessi...
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| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/179450 |
| _version_ | 1826110469212995584 |
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| 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 |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences 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 |
| author_sort | Salojärvi, Jarkko |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T02:34:56Z |
| format | Journal Article |
| id | ntu-10356/179450 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:34:56Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1794502024-08-05T15:31:59Z The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars 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 School of Biological Sciences Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) Medicine, Health and Life Sciences Coffea arabica Plant genome 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. Nanyang Technological University Published version Funding was provided from the Academy of Finland (decisions 318288 and 329441) and a Nanyang Technological University start-up grant (J. Salojärvi); Ecos-Nord grant no. C21MA01 and STIC-AmSud grant no. 21-STIC-13 (R.G. and S.O.-A.); the Academy of Finland, grant no. 343656 (P.R.); NAPI Bioinformática from Fundação Araucária and TELearning Project 2021–22 (grant no. 21-STIC-13) from STIC-AmSud (A.R.P.); Research Foundation – Flanders (FWO, grant no. G056517N) (Y.B.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant no. 833522) and Ghent University (Methusalem funding, grant no. BOF.MET.2021.0005.01) (Y.V.d.P.); the Horizon Europe program, PRO-GRACE project (grant no. 101094738) (G.G.); INCT-Café-CNPq/Fapemig (A.A.); São Paulo State Research Foundation (FAPESP), grant nos. 2016/10896-0 and 2017/01455-2 (D.D. and S.M.C.L.); NSERC and the Canada Research Chairs programs (D.S.); the United States National Science Foundation grant nos. 1442190 and 2030871 (V.A.A.); and Nestlé Research (P.D.). 2024-07-31T08:25:48Z 2024-07-31T08:25:48Z 2024 Journal Article Salojärvi, J., Rambani, A., Yu, Z., Guyot, R., Strickler, S., Lepelley, M., Wang, C., Rajaraman, S., Rastas, P., Zheng, C., Muñoz, D. S., Meidanis, J., Paschoal, A. R., Bawin, Y., Krabbenhoft, T. J., Wang, Z. Q., Fleck, S. J., Aussel, R., Bellanger, L., ...Descombes, P. (2024). The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature Genetics, 56(4), 721-731. https://dx.doi.org/10.1038/s41588-024-01695-w 1061-4036 https://hdl.handle.net/10356/179450 10.1038/s41588-024-01695-w 38622339 2-s2.0-85190413075 4 56 721 731 en NTU SUG Nature Genetics © 2024 The Author(s). Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons. org/licenses/by/4.0/ application/pdf |
| spellingShingle | Medicine, Health and Life Sciences Coffea arabica Plant genome 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 The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars |
| title | The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars |
| title_full | The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars |
| title_fullStr | The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars |
| title_full_unstemmed | The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars |
| title_short | The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars |
| title_sort | genome and population genomics of allopolyploid coffea arabica reveal the diversification history of modern coffee cultivars |
| topic | Medicine, Health and Life Sciences Coffea arabica Plant genome |
| url | https://hdl.handle.net/10356/179450 |
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