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

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury J-M, et al. (2014)
Science 345(6201): 1181-1184.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ; ; ; ; ; ; ;
All
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.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Denoeud F, Carretero-Paulet L, Dereeper A, et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014;345(6201):1181-1184.
Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., et al. (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345(6201), 1181-1184. doi:10.1126/science.1255274
Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., et al. (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345, 1181-1184.
Denoeud, F., et al., 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345(6201), p 1181-1184.
F. Denoeud, et al., “The coffee genome provides insight into the convergent evolution of caffeine biosynthesis”, Science, vol. 345, 2014, pp. 1181-1184.
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., Daddiego, L., De Bellis, F., Dussert, S., Garsmeur, O., Gayraud, T., Guignon, V., Jahn, K., Jamilloux, V., Joet, T., Labadie, K., Lan, T., Leclercq, J., Lepelley, M., Leroy, T., Li, L.-T., Librado, P., Lopez, L., Munoz, 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, A.C., Argout, X., Bertrand, B., de Kochko, A., Graziosi, G., Henry, R.J., Jayarama,, Ming, R., Nagai, C., Rounsley, S., Sankoff, D., Giuliano, G., Albert, V.A., Wincker, P., Lashermes, P.: The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 345, 1181-1184 (2014).
Denoeud, France, Carretero-Paulet, Lorenzo, Dereeper, Alexis, Droc, Gaetan, Guyot, Romain, Pietrella, Marco, Zheng, Chunfang, Alberti, Adriana, Anthony, Francois, Aprea, Giuseppe, Aury, Jean-Marc, Bento, Pascal, Bernard, Maria, Bocs, Stephanie, Campa, Claudine, Cenci, Alberto, Combes, Marie-Christine, Crouzillat, Dominique, Da Silva, Corinne, Daddiego, Loretta, De Bellis, Fabien, Dussert, Stephane, Garsmeur, Olivier, Gayraud, Thomas, Guignon, Valentin, Jahn, Katharina, Jamilloux, Veronique, Joet, Thierry, Labadie, Karine, Lan, Tianying, Leclercq, Julie, Lepelley, Maud, Leroy, Thierry, Li, Lei-Ting, Librado, Pablo, Lopez, Loredana, Munoz, Adriana, Noel, Benjamin, Pallavicini, Alberto, Perrotta, Gaetano, Poncet, Valerie, Pot, David, Priyono,, Rigoreau, Michel, Rouard, Mathieu, Rozas, Julio, Tranchant-Dubreuil, Christine, VanBuren, Robert, Zhang, Qiong, Andrade, Alan C., Argout, Xavier, Bertrand, Benoit, de Kochko, Alexandre, Graziosi, Giorgio, Henry, Robert J., Jayarama,, Ming, Ray, Nagai, Chifumi, Rounsley, Steve, Sankoff, David, Giuliano, Giovanni, Albert, Victor A., Wincker, Patrick, and Lashermes, Philippe. “The coffee genome provides insight into the convergent evolution of caffeine biosynthesis”. Science 345.6201 (2014): 1181-1184.
This data publication is cited in the following publications:
This publication cites the following data publications:

82 Citations in Europe PMC

Data provided by Europe PubMed Central.

Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture.
Thottathil GP, Jayasekaran K, Othman AS., Trop Life Sci Res 27(1), 2016
PMID: 27019684
Advances in genomics for the improvement of quality in coffee.
Tran HT, Lee LS, Furtado A, Smyth H, Henry RJ., J. Sci. Food Agric. 96(10), 2016
PMID: 26919810
Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.
Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A., Mol. Genet. Genomics 291(1), 2016
PMID: 26231981
Seed-Specific Stable Expression of the α-AI1 Inhibitor in Coffee Grains and the In Vivo Implications for the Development of the Coffee Berry Borer.
Albuquerque EV, Bezerra CA, Romero JV, Valencia JW, Valencia-Jimenez A, Pimenta LM, Barbosa AE, Silva MC, Meneguim AM, Sa ME, Engler G, de Almeida-Engler J, Fernandez D, Grossi-de-Sa MF., Trop Plant Biol 8(), 2015
PMID: 26697127
Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events.
Zheng C, Santos Munoz D, Albert VA, Sankoff D., BMC Genomics 16 Suppl 10(), 2015
PMID: 26449933
Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family.
Xie Z, Si W, Gao R, Zhang X, Yang S., Mol. Genet. Genomics 290(6), 2015
PMID: 26008792
Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner.
Achar D, Awati MG, Udayakumar M, Prasad TG., Mol Biol Int 2015(), 2015
PMID: 25821599

165 References

Data provided by Europe PubMed Central.

Acyltransferases in plants: a good time to be BAHD.
D'Auria JC., Curr. Opin. Plant Biol. 9(3), 2006
PMID: 16616872
Caffeine biosynthesis and adenine metabolism in transgenic Coffea canephora plants with reduced expression of N-methyltransferase genes.
Ashihara H, Zheng XQ, Katahira R, Morimoto M, Ogita S, Sano H., Phytochemistry 67(9), 2006
PMID: 16624354

AUTHOR UNKNOWN, Z. Naturforsch., C, Biosci. 65(), 2010
Caffeine synthase gene from tea leaves.
Kato M, Mizuno K, Crozier A, Fujimura T, Ashihara H., Nature 406(6799), 2000
PMID: 10984041
Phytochrome functions in Arabidopsis development.
Franklin KA, Quail PH., J. Exp. Bot. 61(1), 2010
PMID: 19815685

Yang, Bioinformatics 13(5), 1997

AUTHOR UNKNOWN, THE ARABIDOPSIS BOOK 11(), 2013
Changes in sensory quality characteristics of coffee during storage.
Kreuml MT, Majchrzak D, Ploederl B, Koenig J., Food Sci Nutr 1(4), 2013
PMID: 24804030

AUTHOR UNKNOWN, LWT FOOD SCI TECHNOL 50(), 2013
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.
Lang D, Weiche B, Timmerhaus G, Richardt S, Riano-Pachon DM, Correa LG, Reski R, Mueller-Roeber B, Rensing SA., Genome Biol Evol 2(), 2010
PMID: 20644220
Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja.
Lozano R, Ponce O, Ramirez M, Mostajo N, Orjeda G., PLoS ONE 7(4), 2012
PMID: 22493716
Genome-wide identification of NBS resistance genes in Populus trichocarpa.
Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Duchaussoy F, Meyers BC, Boerjan W, Martin F., Plant Mol. Biol. 66(6), 2008
PMID: 18247136
Protein database searches using compositionally adjusted substitution matrices.
Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schaffer AA, Yu YK., FEBS J. 272(20), 2005
PMID: 16218944

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 25190796
PubMed | Europe PMC

Search this title in

Google Scholar