title: The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.
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.
authors.affiliation: 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.
authors.forename: France
authors.initials: F
authors.lastname: Denoeud
authors.affiliation: Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Carretero-Paulet
authors.affiliation: 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.
authors.forename: Alexis
authors.initials: A
authors.lastname: Dereeper
authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Gaëtan
authors.initials: G
authors.lastname: Droc
authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
authors.affiliation: Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Pietrella
authors.affiliation: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: Chunfang
authors.initials: C
authors.lastname: Zheng
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: 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.
authors.forename: François
authors.initials: F
authors.lastname: Anthony
authors.affiliation: Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
authors.forename: Giuseppe
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authors.lastname: Aprea
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Bento
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Bernard
authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Bocs
authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Campa
authors.affiliation: 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.
authors.forename: Alberto
authors.initials: A
authors.lastname: Cenci
authors.affiliation: 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.
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Combes
authors.affiliation: Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Crouzillat
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Da Silva
authors.affiliation: ENEA Trisaia Research Center, 75026 Rotondella, Italy.
authors.forename: Loretta
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authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: De Bellis
authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Dussert
authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Olivier
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authors.lastname: Garsmeur
authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Thomas
authors.initials: T
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authors.affiliation: Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
authors.forename: Valentin
authors.initials: V
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authors.affiliation: 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.
authors.forename: Katharina
authors.initials: K
authors.lastname: Jahn
authors.affiliation: 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.
authors.forename: Véronique
authors.initials: V
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authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Joët
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: 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.
authors.forename: Tianying
authors.initials: T
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authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Julie
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authors.lastname: Leclercq
authors.affiliation: Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
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authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Leroy
authors.affiliation: 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.
authors.forename: Lei-Ting
authors.initials: LT
authors.lastname: Li
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Librado
authors.affiliation: ENEA Trisaia Research Center, 75026 Rotondella, Italy.
authors.forename: Loredana
authors.initials: L
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authors.affiliation: 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.
authors.forename: Adriana
authors.initials: A
authors.lastname: Muñoz
authors.affiliation: Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
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authors.affiliation: Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy.
authors.forename: Alberto
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authors.affiliation: ENEA Trisaia Research Center, 75026 Rotondella, Italy.
authors.forename: Gaetano
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authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Valérie
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authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
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authors.affiliation: Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia.
authors.lastname: Priyono
authors.affiliation: Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
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authors.affiliation: Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
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authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Christine
authors.initials: C
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authors.affiliation: 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.
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.affiliation: 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.
authors.forename: Qiong
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authors.affiliation: 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.
authors.forename: Alan C
authors.initials: AC
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authors.affiliation: CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Argout
authors.affiliation: CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Bertrand
authors.affiliation: IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
authors.affiliation: Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Graziosi
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia.
authors.forename: Robert J
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authors.affiliation: Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India.
authors.lastname: Jayarama
authors.affiliation: 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.
authors.forename: Ray
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authors.affiliation: Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA.
authors.forename: Chifumi
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authors.affiliation: BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Rounsley
authors.affiliation: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: David
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authors.lastname: Sankoff
authors.affiliation: Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
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authors.affiliation: 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.
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
authors.affiliation: 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.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: 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.
authors.forename: Philippe
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authors.lastname: Lashermes
mesh_terms: D002110:Caffeine / Q000096:biosynthesis / Q000235:genetics*; D040503:Coffea / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D008780:Methyltransferases / Q000235:genetics / Q000502:physiology*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000502:physiology*
chemical_list: D010940:Plant Proteins; D002110:Caffeine; D008780:Methyltransferases