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Science (New York, N.Y.)
Sep 05, 2014;345 (6201): 1181-4.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

France Denoeud, Lorenzo Carretero-Paulet, Alexis Dereeper, Gaëtan Droc, Romain Guyot, Marco Pietrella, Chunfang Zheng, Adriana Alberti, François Anthony, Giuseppe Aprea, Jean-Marc Aury, Pascal Bento, Maria Bernard, Stéphanie Bocs, Claudine Campa, Alberto Cenci, Marie-Christine Combes, Dominique Crouzillat, Corinne Da Silva, Loretta Daddiego, Fabien De Bellis, Stéphane Dussert, Olivier Garsmeur, Thomas Gayraud, Valentin Guignon, Katharina Jahn, Véronique Jamilloux, Thierry Joët, Karine Labadie, Tianying Lan, Julie Leclercq, Maud Lepelley, Thierry Leroy, Lei-Ting Li, Pablo Librado, Loredana Lopez, Adriana Muñoz, Benjamin Noel, Alberto Pallavicini, Gaetano Perrotta, Valérie Poncet, David Pot, Michel Rigoreau, Mathieu Rouard, Julio Rozas, Christine Tranchant-Dubreuil, Robert VanBuren, Qiong Zhang, Alan C Andrade, Xavier Argout, Benoît Bertrand, Alexandre de Kochko, Giorgio Graziosi, Robert J Henry, Ray Ming, Chifumi Nagai, Steve Rounsley, David Sankoff, Giovanni Giuliano, Victor A Albert, Patrick Wincker, Philippe Lashermes
Author Information
  1. France Denoeud: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
  2. Lorenzo Carretero-Paulet: Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA.
  3. Alexis Dereeper: Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.
  4. Gaëtan Droc: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  5. Romain Guyot: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  6. Marco Pietrella: Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
  7. Chunfang Zheng: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada.
  8. Adriana Alberti: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  9. François Anthony: Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.
  10. Giuseppe Aprea: Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
  11. Jean-Marc Aury: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  12. Pascal Bento: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  13. Maria Bernard: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  14. Stéphanie Bocs: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  15. Claudine Campa: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  16. Alberto Cenci: Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
  17. Marie-Christine Combes: Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.
  18. Dominique Crouzillat: Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
  19. Corinne Da Silva: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  20. Loretta Daddiego: ENEA Trisaia Research Center, 75026 Rotondella, Italy.
  21. Fabien De Bellis: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  22. Stéphane Dussert: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  23. Olivier Garsmeur: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  24. Thomas Gayraud: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  25. Valentin Guignon: Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
  26. Katharina Jahn: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universität Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany.
  27. Véronique Jamilloux: Institut National de la Recherche Agronomique (INRA), Unité de Recherches en Génomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France.
  28. Thierry Joët: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  29. Karine Labadie: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  30. Tianying Lan: Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China.
  31. Julie Leclercq: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  32. Maud Lepelley: Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
  33. Thierry Leroy: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  34. Lei-Ting Li: Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  35. Pablo Librado: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain.
  36. Loredana Lopez: ENEA Trisaia Research Center, 75026 Rotondella, Italy.
  37. Adriana Muñoz: Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada.
  38. Benjamin Noel: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
  39. Alberto Pallavicini: Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy.
  40. Gaetano Perrotta: ENEA Trisaia Research Center, 75026 Rotondella, Italy.
  41. Valérie Poncet: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  42. David Pot: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  43. Priyono: Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia.
  44. Michel Rigoreau: Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
  45. Mathieu Rouard: Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
  46. Julio Rozas: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain.
  47. Christine Tranchant-Dubreuil: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  48. Robert VanBuren: Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  49. Qiong Zhang: Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  50. Alan C Andrade: Laboratório de Genética Molecular, Núcleo de Biotecnologia (NTBio), Embrapa Recursos Genéticos e Biotecnologia, Final Av. W/5 Norte, Parque Estação Biológia, Brasília-DF 70770-917, Brazil.
  51. Xavier Argout: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
  52. Benoît Bertrand: CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  53. Alexandre de Kochko: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
  54. Giorgio Graziosi: Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy.
  55. Robert J Henry: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia.
  56. Jayarama: Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India.
  57. Ray Ming: Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  58. Chifumi Nagai: Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA.
  59. Steve Rounsley: BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA.
  60. David Sankoff: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada.
  61. Giovanni Giuliano: Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
  62. Victor A Albert: Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.
  63. Patrick Wincker: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.
  64. Philippe Lashermes: Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.
PMID: 25190796 DOI: 10.1126/science.1255274

Abstract

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

MeSH Term

Caffeine
Coffea
Evolution, Molecular
Genome, Plant
Methyltransferases
Phylogeny
Plant Proteins

Chemicals

Plant Proteins
Caffeine
Methyltransferases
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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