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Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

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

Author information

1
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
Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA.
3
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
CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France.
5
IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
6
Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy.
7
Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada.
8
Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France.
9
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.
10
Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France.
11
ENEA Trisaia Research Center, 75026 Rotondella, Italy.
12
Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
13
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.
14
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.
15
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.
16
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.
17
Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain.
18
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.
19
Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy.
20
Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia.
21
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.
22
CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France.
23
Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy.
24
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia.
25
Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India.
26
Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA.
27
BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA.
28
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.
29
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.
30
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.

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.

Comment in

PMID:
25190796
DOI:
10.1126/science.1255274
[Indexed for MEDLINE]
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