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; Priyono; 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; Jayarama; Ray Ming; Chifumi Nagai; Steve Rounsley; David Sankoff; Giovanni Giuliano; Victor A. Albert; Patrick Wincker; Philippe Lashermes

doi:10.1126/science.1255274

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, Priyono, 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, Jayarama, Ray Ming, Chifumi Nagai, Steve Rounsley, David Sankoff, Giovanni Giuliano, Victor A. Albert, Patrick Wincker, Philippe Lashermes

Biological Sciences

Genoscope - Centre National de Séquençage
CNRS
University of Evry
SUNY Buffalo
Institut de recherche pour le développement
CIRAD, UMR Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales (AGAP)
EVODYN
Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo economico sostenibile
University of Ottawa
Bioversity International
Nestlé Research and Development Centre
ENEA Trisaia Research Center
Bielefeld University
Institut National de la Recherche Agronomique (INRA), Unité de Recherches en Génomique-Info (UR INRA 1164), Centre de Recherche de Versailles
Chongqing University of Science and Technology
University of Illinois at Urbana-Champaign
University of Barcelona
University of Maryland, College Park
University of Trieste
Indonesian Coffee and Cocoa Institute
Empresa Brasileira de Pesquisa Agropecuária
Centre de coopération internationale en recherche agronomique pour le développement
DNA Analytica Srl
University of Queensland
Coffee Board
State of Hawaii, Department of Agriculture
University of Arizona

Research output: Contribution to journal › Article › peer-review

545 Scopus citations

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.

Original language	English
Pages (from-to)	1181-1184
Number of pages	4
Journal	Science
Volume	345
Issue number	6201
DOIs	https://doi.org/10.1126/science.1255274
State	Published - Sep 5 2014

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Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., Aury, J. M., Bento, P., Bernard, M., Bocs, S., Campa, C., Cenci, A., Combes, M. C., Crouzillat, D., Da Silva, C., ... Lashermes, P. (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345(6201), 1181-1184. https://doi.org/10.1126/science.1255274

@article{b5753b23845640d4946d72d6e0b5e9dc,

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.",

author = "France Denoeud and Lorenzo Carretero-Paulet and Alexis Dereeper and Ga{\"e}tan Droc and Romain Guyot and Marco Pietrella and Chunfang Zheng and Adriana Alberti and Fran{\c c}ois Anthony and Giuseppe Aprea and Aury, \{Jean Marc\} and Pascal Bento and Maria Bernard and St{\'e}phanie Bocs and Claudine Campa and Alberto Cenci and Combes, \{Marie Christine\} and Dominique Crouzillat and \{Da Silva\}, Corinne and Loretta Daddiego and \{De Bellis\}, Fabien and St{\'e}phane Dussert and Olivier Garsmeur and Thomas Gayraud and Valentin Guignon and Katharina Jahn and V{\'e}ronique Jamilloux and Thierry Jo{\"e}t and Karine Labadie and Tianying Lan and Julie Leclercq and Maud Lepelley and Thierry Leroy and Li, \{Lei Ting\} and Pablo Librado and Loredana Lopez and Adriana Mu{\~n}oz and Benjamin Noel and Alberto Pallavicini and Gaetano Perrotta and Val{\'e}rie Poncet and David Pot and Priyono and Michel Rigoreau and Mathieu Rouard and Julio Rozas and Christine Tranchant-Dubreuil and Robert VanBuren and Qiong Zhang and Andrade, \{Alan C.\} and Xavier Argout and Beno{\^i}t Bertrand and \{De Kochko\}, Alexandre and Giorgio Graziosi and Henry, \{Robert J.\} and Jayarama and Ray Ming and Chifumi Nagai and Steve Rounsley and David Sankoff and Giovanni Giuliano and Albert, \{Victor A.\} and Patrick Wincker and Philippe Lashermes",

year = "2014",

month = sep,

day = "5",

doi = "10.1126/science.1255274",

language = "English",

volume = "345",

pages = "1181--1184",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6201",

}

Denoeud, F, Carretero-Paulet, L, Dereeper, A, Droc, G, Guyot, R, Pietrella, M, Zheng, C, Alberti, A, Anthony, F, Aprea, G, Aury, JM, Bento, P, Bernard, M, Bocs, S, Campa, C, Cenci, A, Combes, MC, Crouzillat, D, Da Silva, C, Daddiego, L, De Bellis, F, Dussert, S, Garsmeur, O, Gayraud, T, Guignon, V, Jahn, K, Jamilloux, V, Joët, T, Labadie, K, Lan, T, Leclercq, J, Lepelley, M, Leroy, T, Li, LT, Librado, P, Lopez, L, Muñoz, A, Noel, B, Pallavicini, A, Perrotta, G, Poncet, V, Pot, D, Priyono, Rigoreau, M, Rouard, M, Rozas, J, Tranchant-Dubreuil, C, VanBuren, R, Zhang, Q, Andrade, AC, Argout, X, Bertrand, B, De Kochko, A, Graziosi, G, Henry, RJ, Jayarama, Ming, R, Nagai, C, Rounsley, S, Sankoff, D, Giuliano, G, Albert, VA, Wincker, P & Lashermes, P 2014, 'The coffee genome provides insight into the convergent evolution of caffeine biosynthesis', Science, vol. 345, no. 6201, pp. 1181-1184. https://doi.org/10.1126/science.1255274

TY - JOUR

T1 - The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

AU - Denoeud, France

AU - Carretero-Paulet, Lorenzo

AU - Dereeper, Alexis

AU - Droc, Gaëtan

AU - Guyot, Romain

AU - Pietrella, Marco

AU - Zheng, Chunfang

AU - Alberti, Adriana

AU - Anthony, François

AU - Aprea, Giuseppe

AU - Aury, Jean Marc

AU - Bento, Pascal

AU - Bernard, Maria

AU - Bocs, Stéphanie

AU - Campa, Claudine

AU - Cenci, Alberto

AU - Combes, Marie Christine

AU - Crouzillat, Dominique

AU - Da Silva, Corinne

AU - Daddiego, Loretta

AU - De Bellis, Fabien

AU - Dussert, Stéphane

AU - Garsmeur, Olivier

AU - Gayraud, Thomas

AU - Guignon, Valentin

AU - Jahn, Katharina

AU - Jamilloux, Véronique

AU - Joët, Thierry

AU - Labadie, Karine

AU - Lan, Tianying

AU - Leclercq, Julie

AU - Lepelley, Maud

AU - Leroy, Thierry

AU - Li, Lei Ting

AU - Librado, Pablo

AU - Lopez, Loredana

AU - Muñoz, Adriana

AU - Noel, Benjamin

AU - Pallavicini, Alberto

AU - Perrotta, Gaetano

AU - Poncet, Valérie

AU - Pot, David

AU - Priyono,

AU - Rigoreau, Michel

AU - Rouard, Mathieu

AU - Rozas, Julio

AU - Tranchant-Dubreuil, Christine

AU - VanBuren, Robert

AU - Zhang, Qiong

AU - Andrade, Alan C.

AU - Argout, Xavier

AU - Bertrand, Benoît

AU - De Kochko, Alexandre

AU - Graziosi, Giorgio

AU - Henry, Robert J.

AU - Jayarama,

AU - Ming, Ray

AU - Nagai, Chifumi

AU - Rounsley, Steve

AU - Sankoff, David

AU - Giuliano, Giovanni

AU - Albert, Victor A.

AU - Wincker, Patrick

AU - Lashermes, Philippe

PY - 2014/9/5

Y1 - 2014/9/5

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/84907200661

U2 - 10.1126/science.1255274

DO - 10.1126/science.1255274

M3 - Article

C2 - 25190796

AN - SCOPUS:84907200661

SN - 0036-8075

VL - 345

SP - 1181

EP - 1184

JO - Science

JF - Science

IS - 6201

ER -

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

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