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.
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Autor*in
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
Alle
Alle
Abstract / Bemerkung
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.
Erscheinungsjahr
2014
Zeitschriftentitel
Science
Band
345
Ausgabe
6201
Seite(n)
1181-1184
ISSN
0036-8075
eISSN
1095-9203
Page URI
https://pub.uni-bielefeld.de/record/2697280
Zitieren
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. https://doi.org/10.1126/science.1255274
Denoeud, France, Carretero-Paulet, Lorenzo, Dereeper, Alexis, Droc, Gaetan, Guyot, Romain, Pietrella, Marco, Zheng, Chunfang, et al. 2014. “The coffee genome provides insight into the convergent evolution of caffeine biosynthesis”. Science 345 (6201): 1181-1184.
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, n.a., 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, n.a., 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, n.a., 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, n.a., 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.
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MicroRNA annotation of plant genomes - Do it right or not at all.
Taylor RS, Tarver JE, Foroozani A, Donoghue PC., Bioessays 39(2), 2017
PMID: 28054378
Taylor RS, Tarver JE, Foroozani A, Donoghue PC., Bioessays 39(2), 2017
PMID: 28054378
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Ivamoto ST, Reis O, Domingues DS, Dos Santos TB, de Oliveira FF, Pot D, Leroy T, Vieira LG, Carazzolle MF, Pereira GA, Pereira LF., PLoS One 12(1), 2017
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Ivamoto ST, Reis O, Domingues DS, Dos Santos TB, de Oliveira FF, Pot D, Leroy T, Vieira LG, Carazzolle MF, Pereira GA, Pereira LF., PLoS One 12(1), 2017
PMID: 28068432
Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas.
Hu Y, Wu Q, Ma S, Ma T, Shan L, Wang X, Nie Y, Ning Z, Yan L, Xiu Y, Wei F., Proc Natl Acad Sci U S A 114(5), 2017
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Hu Y, Wu Q, Ma S, Ma T, Shan L, Wang X, Nie Y, Ning Z, Yan L, Xiu Y, Wei F., Proc Natl Acad Sci U S A 114(5), 2017
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Evolution of floral diversity: genomics, genes and gamma.
Chanderbali AS, Berger BA, Howarth DG, Soltis DE, Soltis PS., Philos Trans R Soc Lond B Biol Sci 372(1713), 2017
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Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics.
Neale DB, Martínez-García PJ, De La Torre AR, Montanari S, Wei XX., Annu Rev Plant Biol 68(), 2017
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PMID: 28226237
Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.
Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R., Mol Phylogenet Evol 109(), 2017
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Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R., Mol Phylogenet Evol 109(), 2017
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Genomic innovation for crop improvement.
Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD., Nature 543(7645), 2017
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Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD., Nature 543(7645), 2017
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Evolutionary Analyses of GRAS Transcription Factors in Angiosperms.
Cenci A, Rouard M., Front Plant Sci 8(), 2017
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Dupeyron M, de Souza RF, Hamon P, de Kochko A, Crouzillat D, Couturon E, Domingues DS, Guyot R., Mol Genet Genomics 292(4), 2017
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Genome-wide identification, classification and transcriptional analysis of nitrate and ammonium transporters in Coffea.
Santos TB, Lima JE, Felicio MS, Soares JDM, Domingues DS., Genet Mol Biol 40(1 suppl 1), 2017
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Santos TB, Lima JE, Felicio MS, Soares JDM, Domingues DS., Genet Mol Biol 40(1 suppl 1), 2017
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A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms.
Noronha Fernandes-Brum C, Marinho Rezende P, Cherubino Ribeiro TH, Ricon de Oliveira R, Cunha de Sousa Cardoso T, Rodrigues do Amaral L, de Souza Gomes M, Chalfun-Junior A., PLoS One 12(4), 2017
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Noronha Fernandes-Brum C, Marinho Rezende P, Cherubino Ribeiro TH, Ricon de Oliveira R, Cunha de Sousa Cardoso T, Rodrigues do Amaral L, de Souza Gomes M, Chalfun-Junior A., PLoS One 12(4), 2017
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Differential fine-tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water deficit.
Alves GSC, Torres LF, Déchamp E, Breitler JC, Joët T, Gatineau F, Andrade AC, Bertrand B, Marraccini P, Etienne H., J Exp Bot 68(11), 2017
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Alves GSC, Torres LF, Déchamp E, Breitler JC, Joët T, Gatineau F, Andrade AC, Bertrand B, Marraccini P, Etienne H., J Exp Bot 68(11), 2017
PMID: 28830103
The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis.
Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y, Liu Y, Zhu T, Li W, Huang H, Tong Y, Nan H, Shi C, Shi C, Jiang JJ, Mao SY, Jiao JY, Zhang D, Zhao Y, Zhao YJ, Zhang LP, Liu YL, Liu BY, Yu Y, Shao SF, Ni DJ, Eichler EE, Gao LZ., Mol Plant 10(6), 2017
PMID: 28473262
Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y, Liu Y, Zhu T, Li W, Huang H, Tong Y, Nan H, Shi C, Shi C, Jiang JJ, Mao SY, Jiao JY, Zhang D, Zhao Y, Zhao YJ, Zhang LP, Liu YL, Liu BY, Yu Y, Shao SF, Ni DJ, Eichler EE, Gao LZ., Mol Plant 10(6), 2017
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A Novel N-Methyltransferase in Arabidopsis Appears to Feed a Conserved Pathway for Nicotinate Detoxification among Land Plants and Is Associated with Lignin Biosynthesis.
Li W, Zhang F, Wu R, Jia L, Li G, Guo Y, Liu C, Wang G., Plant Physiol 174(3), 2017
PMID: 28533213
Li W, Zhang F, Wu R, Jia L, Li G, Guo Y, Liu C, Wang G., Plant Physiol 174(3), 2017
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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.
Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brière C, Owens GL, Carrère S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Bérard A, Bergès H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR, Marage G, Marchand G, Marquand E, Bret-Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Varès D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Muños S, Vincourt P, Rieseberg LH, Langlade NB., Nature 546(7656), 2017
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Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brière C, Owens GL, Carrère S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Bérard A, Bergès H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR, Marage G, Marchand G, Marquand E, Bret-Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Varès D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Muños S, Vincourt P, Rieseberg LH, Langlade NB., Nature 546(7656), 2017
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Transcriptome analysis explores genes related to shikonin biosynthesis in Lithospermeae plants and provides insights into Boraginales' evolutionary history.
Wu FY, Tang CY, Guo YM, Bian ZW, Fu JY, Lu GH, Qi JL, Pang YJ, Yang YH., Sci Rep 7(1), 2017
PMID: 28667265
Wu FY, Tang CY, Guo YM, Bian ZW, Fu JY, Lu GH, Qi JL, Pang YJ, Yang YH., Sci Rep 7(1), 2017
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Identification and Analysis of Jasmonate Pathway Genes in Coffea canephora (Robusta Coffee) by In Silico Approach.
Bharathi K, Sreenath HL., Pharmacogn Mag 13(suppl 2), 2017
PMID: 28808380
Bharathi K, Sreenath HL., Pharmacogn Mag 13(suppl 2), 2017
PMID: 28808380
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation.
Acquadro A, Barchi L, Portis E, Mangino G, Valentino D, Mauromicale G, Lanteri S., Sci Rep 7(1), 2017
PMID: 28717205
Acquadro A, Barchi L, Portis E, Mangino G, Valentino D, Mauromicale G, Lanteri S., Sci Rep 7(1), 2017
PMID: 28717205
The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis.
Qin G, Xu C, Ming R, Tang H, Guyot R, Kramer EM, Hu Y, Yi X, Qi Y, Xu X, Gao Z, Pan H, Jian J, Tian Y, Yue Z, Xu Y., Plant J 91(6), 2017
PMID: 28654223
Qin G, Xu C, Ming R, Tang H, Guyot R, Kramer EM, Hu Y, Yi X, Qi Y, Xu X, Gao Z, Pan H, Jian J, Tian Y, Yue Z, Xu Y., Plant J 91(6), 2017
PMID: 28654223
Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities.
Campos NA, Panis B, Carpentier SC., Front Plant Sci 8(), 2017
PMID: 28871271
Campos NA, Panis B, Carpentier SC., Front Plant Sci 8(), 2017
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Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway.
Moghe GD, Leong BJ, Hurney SM, Daniel Jones A, Last RL., Elife 6(), 2017
PMID: 28853706
Moghe GD, Leong BJ, Hurney SM, Daniel Jones A, Last RL., Elife 6(), 2017
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Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation.
Cheng J, Guo X, Cai P, Cheng X, Piškur J, Ma Y, Jiang H, Gu Z., Mol Biol Evol 34(11), 2017
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Cheng J, Guo X, Cai P, Cheng X, Piškur J, Ma Y, Jiang H, Gu Z., Mol Biol Evol 34(11), 2017
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Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts.
Cheng B, Furtado A, Henry RJ., Gigascience 6(11), 2017
PMID: 29048540
Cheng B, Furtado A, Henry RJ., Gigascience 6(11), 2017
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High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.
Florez JC, Mofatto LS, do Livramento Freitas-Lopes R, Ferreira SS, Zambolim EM, Carazzolle MF, Zambolim L, Caixeta ET., Plant Mol Biol 95(6), 2017
PMID: 29094279
Florez JC, Mofatto LS, do Livramento Freitas-Lopes R, Ferreira SS, Zambolim EM, Carazzolle MF, Zambolim L, Caixeta ET., Plant Mol Biol 95(6), 2017
PMID: 29094279
Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.
Saski CA, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J, Chen ZJ., Sci Rep 7(1), 2017
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Saski CA, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J, Chen ZJ., Sci Rep 7(1), 2017
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Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.
Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C., PLoS One 12(12), 2017
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Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C., PLoS One 12(12), 2017
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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
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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
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Genomics of crop wild relatives: expanding the gene pool for crop improvement.
Brozynska M, Furtado A, Henry RJ., Plant Biotechnol J 14(4), 2016
PMID: 26311018
Brozynska M, Furtado A, Henry RJ., Plant Biotechnol J 14(4), 2016
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Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits.
Yuyama PM, Reis Júnior O, Ivamoto ST, Domingues DS, Carazzolle MF, Pereira GA, Charmetant P, Leroy T, Pereira LF., Mol Genet Genomics 291(1), 2016
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Yuyama PM, Reis Júnior O, Ivamoto ST, Domingues DS, Carazzolle MF, Pereira GA, Charmetant P, Leroy T, Pereira LF., Mol Genet Genomics 291(1), 2016
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Interaction of coffee compounds with serum albumins. Part II: Diterpenes.
Guercia E, Forzato C, Navarini L, Berti F., Food Chem 199(), 2016
PMID: 26776001
Guercia E, Forzato C, Navarini L, Berti F., Food Chem 199(), 2016
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Transcriptome Analysis of Hamelia patens (Rubiaceae) Anthers Reveals Candidate Genes for Tapetum and Pollen Wall Development.
Yue L, Twell D, Kuang Y, Liao J, Zhou X., Front Plant Sci 7(), 2016
PMID: 28119704
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Caffeine: Friend or Foe?
Doepker C, Lieberman HR, Smith AP, Peck JD, El-Sohemy A, Welsh BT., Annu Rev Food Sci Technol 7(), 2016
PMID: 26735800
Doepker C, Lieberman HR, Smith AP, Peck JD, El-Sohemy A, Welsh BT., Annu Rev Food Sci Technol 7(), 2016
PMID: 26735800
The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny.
Scaglione D, Reyes-Chin-Wo S, Acquadro A, Froenicke L, Portis E, Beitel C, Tirone M, Mauro R, Lo Monaco A, Mauromicale G, Faccioli P, Cattivelli L, Rieseberg L, Michelmore R, Lanteri S., Sci Rep 6(), 2016
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Scaglione D, Reyes-Chin-Wo S, Acquadro A, Froenicke L, Portis E, Beitel C, Tirone M, Mauro R, Lo Monaco A, Mauromicale G, Faccioli P, Cattivelli L, Rieseberg L, Michelmore R, Lanteri S., Sci Rep 6(), 2016
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Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture.
Thottathil GP, Jayasekaran K, Othman AS., Trop Life Sci Res 27(1), 2016
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Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies.
Wei C, Chen J, Kuang H., PLoS One 11(2), 2016
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Evolution of plant genome architecture.
Wendel JF, Jackson SA, Meyers BC, Wing RA., Genome Biol 17(), 2016
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Evidence of horizontal gene transfer between obligate leaf nodule symbionts.
Pinto-Carbó M, Sieber S, Dessein S, Wicker T, Verstraete B, Gademann K, Eberl L, Carlier A., ISME J 10(9), 2016
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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
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Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species.
Gomez C, Despinoy M, Hamon S, Hamon P, Salmon D, Akaffou DS, Legnate H, de Kochko A, Mangeas M, Poncet V., Ecol Evol 6(10), 2016
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Gomez C, Despinoy M, Hamon S, Hamon P, Salmon D, Akaffou DS, Legnate H, de Kochko A, Mangeas M, Poncet V., Ecol Evol 6(10), 2016
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The effect of bean origin and temperature on grinding roasted coffee.
Uman E, Colonna-Dashwood M, Colonna-Dashwood L, Perger M, Klatt C, Leighton S, Miller B, Butler KT, Melot BC, Speirs RW, Hendon CH., Sci Rep 6(), 2016
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Uman E, Colonna-Dashwood M, Colonna-Dashwood L, Perger M, Klatt C, Leighton S, Miller B, Butler KT, Melot BC, Speirs RW, Hendon CH., Sci Rep 6(), 2016
PMID: 27086837
Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.
Mofatto LS, Carneiro Fde A, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GA, Andrade AC, Marraccini P., BMC Plant Biol 16(), 2016
PMID: 27095276
Mofatto LS, Carneiro Fde A, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GA, Andrade AC, Marraccini P., BMC Plant Biol 16(), 2016
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Resistance to root-knot nematodes Meloidogyne spp. in woody plants.
Saucet SB, Van Ghelder C, Abad P, Duval H, Esmenjaud D., New Phytol 211(1), 2016
PMID: 27128375
Saucet SB, Van Ghelder C, Abad P, Duval H, Esmenjaud D., New Phytol 211(1), 2016
PMID: 27128375
Next-generation biology: Sequencing and data analysis approaches for non-model organisms.
da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, Zepeda-Mendoza ML, Campos PF, Heller R, Pereira RJ., Mar Genomics 30(), 2016
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da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, Zepeda-Mendoza ML, Campos PF, Heller R, Pereira RJ., Mar Genomics 30(), 2016
PMID: 27184710
Evolutionary origin of the NCSI gene subfamily encoding norcoclaurine synthase is associated with the biosynthesis of benzylisoquinoline alkaloids in plants.
Vimolmangkang S, Deng X, Owiti A, Meelaph T, Ogutu C, Han Y., Sci Rep 6(), 2016
PMID: 27189519
Vimolmangkang S, Deng X, Owiti A, Meelaph T, Ogutu C, Han Y., Sci Rep 6(), 2016
PMID: 27189519
Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.
Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Deutsch J, Salazar W, Hernandez-Ochoa M, Grygleski E, Steffan S, Iorizzo M, Polashock J, Vorsa N, Zalapa J., BMC Genomics 17(), 2016
PMID: 27295982
Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Deutsch J, Salazar W, Hernandez-Ochoa M, Grygleski E, Steffan S, Iorizzo M, Polashock J, Vorsa N, Zalapa J., BMC Genomics 17(), 2016
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Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.
Medema MH, Osbourn A., Nat Prod Rep 33(8), 2016
PMID: 27321668
Medema MH, Osbourn A., Nat Prod Rep 33(8), 2016
PMID: 27321668
Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.
Guyot R, Darré T, Dupeyron M, de Kochko A, Hamon S, Couturon E, Crouzillat D, Rigoreau M, Rakotomalala JJ, Raharimalala NE, Akaffou SD, Hamon P., Mol Genet Genomics 291(5), 2016
PMID: 27469896
Guyot R, Darré T, Dupeyron M, de Kochko A, Hamon S, Couturon E, Crouzillat D, Rigoreau M, Rakotomalala JJ, Raharimalala NE, Akaffou SD, Hamon P., Mol Genet Genomics 291(5), 2016
PMID: 27469896
Advances in genomics for the improvement of quality in coffee
Tran HT, Agnelo Furtado, Heather Smyth, L Slade Lee, Robert J Henry., J Sci Food Agric 96(10), 2016
PMID: IND605232892
Tran HT, Agnelo Furtado, Heather Smyth, L Slade Lee, Robert J Henry., J Sci Food Agric 96(10), 2016
PMID: IND605232892
Towards integration of population and comparative genomics in forest trees.
Ingvarsson PK, Hvidsten TR, Street NR., New Phytol 212(2), 2016
PMID: 27575589
Ingvarsson PK, Hvidsten TR, Street NR., New Phytol 212(2), 2016
PMID: 27575589
Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.
Huang R, O'Donnell AJ, Barboline JJ, Barkman TJ., Proc Natl Acad Sci U S A 113(38), 2016
PMID: 27638206
Huang R, O'Donnell AJ, Barboline JJ, Barkman TJ., Proc Natl Acad Sci U S A 113(38), 2016
PMID: 27638206
Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.).
Lashermes P, Hueber Y, Combes MC, Severac D, Dereeper A., G3 (Bethesda) 6(9), 2016
PMID: 27440920
Lashermes P, Hueber Y, Combes MC, Severac D, Dereeper A., G3 (Bethesda) 6(9), 2016
PMID: 27440920
The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae.
Sabir JS, Jansen RK, Arasappan D, Calderon V, Noutahi E, Zheng C, Park S, Sabir MJ, Baeshen MN, Hajrah NH, Khiyami MA, Baeshen NA, Obaid AY, Al-Malki AL, Sankoff D, El-Mabrouk N, Ruhlman TA., Sci Rep 6(), 2016
PMID: 27653669
Sabir JS, Jansen RK, Arasappan D, Calderon V, Noutahi E, Zheng C, Park S, Sabir MJ, Baeshen MN, Hajrah NH, Khiyami MA, Baeshen NA, Obaid AY, Al-Malki AL, Sankoff D, El-Mabrouk N, Ruhlman TA., Sci Rep 6(), 2016
PMID: 27653669
Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico.
Garavito A, Montagnon C, Guyot R, Bertrand B., BMC Plant Biol 16(1), 2016
PMID: 27814672
Garavito A, Montagnon C, Guyot R, Bertrand B., BMC Plant Biol 16(1), 2016
PMID: 27814672
Economic importance, taxonomic representation and scientific priority as drivers of genome sequencing projects.
Vallée GC, Muñoz DS, Sankoff D., BMC Genomics 17(suppl 10), 2016
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Application of Genomic Technologies to the Breeding of Trees.
Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ., Front Genet 7(), 2016
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The coffee genome hub: a resource for coffee genomes.
Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G., Nucleic Acids Res 43(database issue), 2015
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The Draft Genome of Hop (Humulus lupulus), an Essence for Brewing.
Natsume S, Takagi H, Shiraishi A, Murata J, Toyonaga H, Patzak J, Takagi M, Yaegashi H, Uemura A, Mitsuoka C, Yoshida K, Krofta K, Satake H, Terauchi R, Ono E., Plant Cell Physiol 56(3), 2015
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Natsume S, Takagi H, Shiraishi A, Murata J, Toyonaga H, Patzak J, Takagi M, Yaegashi H, Uemura A, Mitsuoka C, Yoshida K, Krofta K, Satake H, Terauchi R, Ono E., Plant Cell Physiol 56(3), 2015
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The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.
Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA., Nucleic Acids Res 43(database issue), 2015
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Schluttenhofer C, Yuan L., Plant Physiol 167(2), 2015
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A genome to unveil the mysteries of orchids.
Albert VA, Carretero-Paulet L., Nat Genet 47(1), 2015
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Albert VA, Carretero-Paulet L., Nat Genet 47(1), 2015
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Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements.
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Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.
Carretero-Paulet L, Chang TH, Librado P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA., Genome Biol Evol 7(2), 2015
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Progress, challenges and the future of crop genomes.
Michael TP, VanBuren R., Curr Opin Plant Biol 24(), 2015
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Achar D, Awati MG, Udayakumar M, Prasad TG., Mol Biol Int 2015(), 2015
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Combes MC, Hueber Y, Dereeper A, Rialle S, Herrera JC, Lashermes P., Genome Biol Evol 7(4), 2015
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Richards S., Trends Genet 31(7), 2015
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Xie Z, Si W, Gao R, Zhang X, Yang S., Mol Genet Genomics 290(6), 2015
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Kim J, Buell CR., Plant Physiol 169(3), 2015
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Dias ES, Hatt C, Hamon S, Hamon P, Rigoreau M, Crouzillat D, Carareto CM, de Kochko A, Guyot R., Plant Mol Biol 89(1-2), 2015
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New Insights on Coffea miRNAs: Features and Evolutionary Conservation.
Chaves SS, Fernandes-Brum CN, Silva GF, Ferrara-Barbosa BC, Paiva LV, Nogueira FT, Cardoso TC, Amaral LR, de Souza Gomes M, Chalfun-Junior A., Appl Biochem Biotechnol 177(4), 2015
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The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents.
Bertrand B, Bardil A, Baraille H, Dussert S, Doulbeau S, Dubois E, Severac D, Dereeper A, Etienne H., Plant Cell Physiol 56(10), 2015
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The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology.
Feltus FA, Breen JR, Deng J, Izard RS, Konger CA, Ligon WB, Preuss D, Wang KC., Bioinform Biol Insights 9(suppl 1), 2015
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Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events.
Zheng C, Santos Muñoz D, Albert VA, Sankoff D., BMC Genomics 16 Suppl 10(), 2015
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Zheng C, Santos Muñoz D, Albert VA, Sankoff D., BMC Genomics 16 Suppl 10(), 2015
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Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.
Hao DC, Xiao PG., Evol Bioinform Online 11(), 2015
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Hao DC, Xiao PG., Evol Bioinform Online 11(), 2015
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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 ÉV, Bezerra CA, Romero JV, Valencia JW, Valencia-Jiménez A, Pimenta LM, Barbosa AE, Silva MC, Meneguim AM, Sá ME, Engler G, de Almeida-Engler J, Fernandez D, Grossi-de-Sá MF., Trop Plant Biol 8(), 2015
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Albuquerque ÉV, Bezerra CA, Romero JV, Valencia JW, Valencia-Jiménez A, Pimenta LM, Barbosa AE, Silva MC, Meneguim AM, Sá ME, Engler G, de Almeida-Engler J, Fernandez D, Grossi-de-Sá MF., Trop Plant Biol 8(), 2015
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Genome-wide analysis of LTR-retrotransposons in oil palm.
Beulé T, Agbessi MD, Dussert S, Jaligot E, Guyot R., BMC Genomics 16(), 2015
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Beulé T, Agbessi MD, Dussert S, Jaligot E, Guyot R., BMC Genomics 16(), 2015
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New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination.
Jacques MA, Denancé N, Legendre B, Morel E, Briand M, Mississipi S, Durand K, Olivier V, Portier P, Poliakoff F, Crouzillat D., Appl Environ Microbiol 82(5), 2015
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Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps.
Tennessen JA, Govindarajulu R, Ashman TL, Liston A., Genome Biol Evol 6(12), 2014
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The tomato genome sequence provides insights into fleshy fruit evolution.
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CDD: a Conserved Domain Database for the functional annotation of proteins.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH., Nucleic Acids Res. 39(Database issue), 2010
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Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH., Nucleic Acids Res. 39(Database issue), 2010
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Modulation of chlorogenic acid biosynthesis in Solanum lycopersicum; consequences for phenolic accumulation and UV-tolerance.
Cle C, Hill LM, Niggeweg R, Martin CR, Guisez Y, Prinsen E, Jansen MA., Phytochemistry 69(11), 2008
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Cle C, Hill LM, Niggeweg R, Martin CR, Guisez Y, Prinsen E, Jansen MA., Phytochemistry 69(11), 2008
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Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes.
Shi R, Sun YH, Li Q, Heber S, Sederoff R, Chiang VL., Plant Cell Physiol. 51(1), 2009
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Niggeweg R, Michael AJ, Martin C., Nat. Biotechnol. 22(6), 2004
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Hoffmann L, Besseau S, Geoffroy P, Ritzenthaler C, Meyer D, Lapierre C, Pollet B, Legrand M., Plant Cell 16(6), 2004
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Novel hydroxycinnamoyl-coenzyme A quinate transferase genes from artichoke are involved in the synthesis of chlorogenic acid.
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D'Auria JC., Curr. Opin. Plant Biol. 9(3), 2006
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Ashihara H, Zheng XQ, Katahira R, Morimoto M, Ogita S, Sano H., Phytochemistry 67(9), 2006
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Kato M, Mizuno K, Crozier A, Fujimura T, Ashihara H., Nature 406(6799), 2000
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Tolerance of coffee (Coffea spp.) seeds to ultra-low temperature exposure in relation to calorimetric properties of tissue water, lipid composition, and cooling procedure.
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Kreuml MT, Majchrzak D, Ploederl B, Koenig J., Food Sci Nutr 1(4), 2013
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Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.
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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
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Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Duchaussoy F, Meyers BC, Boerjan W, Martin F., Plant Mol. Biol. 66(6), 2008
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Protein database searches using compositionally adjusted substitution matrices.
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