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
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
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

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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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Daten bereitgestellt von Europe PubMed Central.

Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models.
Ferrão LFV, Ferrão RG, Ferrão MAG, Fonseca A, Carbonetto P, Stephens M, Garcia AAF., Heredity (Edinb) 122(3), 2019
PMID: 29941997
An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.
Dos Santos TB, Soares JDM, Lima JE, Silva JC, Ivamoto ST, Baba VY, Souza SGH, Lorenzetti APR, Paschoal AR, Meda AR, Nishiyama Júnior MY, de Oliveira ÚC, Mokochinski JB, Guyot R, Junqueira-de-Azevedo ILM, Figueira AVO, Mazzafera P, Júnior OR, Vieira LGE, Pereira LFP, Domingues DS., Funct Integr Genomics 19(1), 2019
PMID: 30196429
To flourish or perish: evolutionary TRiPs into the sensory biology of plant-herbivore interactions.
Startek JB, Voets T, Talavera K., Pflugers Arch 471(2), 2019
PMID: 30229297
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.
Xu CQ, Liu H, Zhou SS, Zhang DX, Zhao W, Wang S, Chen F, Sun YQ, Nie S, Jia KH, Jiao SQ, Zhang RG, Yun QZ, Guan W, Wang X, Gao Q, Bennetzen JL, Maghuly F, Porth I, Van de Peer Y, Wang XR, Ma Y, Mao JF., Gigascience 8(2), 2019
PMID: 30689848
Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.
Merot-L'anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M, Bellanger L, Tranchant-Dubreuil C, Coulée M, Pégard M, Metairon S, Fournier C, Stoffelen P, Janssens SB, Kiwuka C, Musoli P, Sumirat U, Legnaté H, Kambale JL, Ferreira da Costa Neto J, Revel C, de Kochko A, Descombes P, Crouzillat D, Poncet V., Plant Biotechnol J 17(7), 2019
PMID: 30582651
An Altered Circadian Clock Coupled with a Higher Photosynthesis Efficiency Could Explain the Better Agronomic Performance of a New Coffee Clone When Compared with a Standard Variety.
Toniutti L, Breitler JC, Guittin C, Doulbeau S, Etienne H, Campa C, Lambot C, Herrera Pinilla JC, Bertrand B., Int J Mol Sci 20(3), 2019
PMID: 30744144
Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.
Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH., Genome Biol 20(1), 2019
PMID: 30791939
The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development.
Li M, Yang S, Xu W, Pu Z, Feng J, Wang Z, Zhang C, Peng M, Du C, Lin F, Wei C, Qiao S, Zou H, Zhang L, Li Y, Yang H, Liao A, Song W, Zhang Z, Li J, Wang K, Zhang Y, Lin H, Zhang J, Tan W., BMC Plant Biol 19(1), 2019
PMID: 30935381
What Should We Do About Habitual Caffeine Use in Athletes?
Pickering C, Kiely J., Sports Med 49(6), 2019
PMID: 30173351
Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica.
Vieira NG, Ferrari IF, Rezende JC, Mayer JLS, Mondego JMC., Sci Rep 9(1), 2019
PMID: 31186437
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species.
Guyeux C, Charr JC, Tran HTM, Furtado A, Henry RJ, Crouzillat D, Guyot R, Hamon P., PLoS One 14(6), 2019
PMID: 31188829
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China.
Yang J, Wariss HM, Tao L, Zhang R, Yun Q, Hollingsworth P, Dao Z, Luo G, Guo H, Ma Y, Sun W., Gigascience 8(7), 2019
PMID: 31307060
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution.
Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, Andolfo G, Aprea G, Avanzato C, Bassolino L, Comino C, Molin AD, Ferrarini A, Maor LC, Portis E, Reyes-Chin-Wo S, Rinaldi R, Sala T, Scaglione D, Sonawane P, Tononi P, Almekias-Siegl E, Zago E, Ercolano MR, Aharoni A, Delledonne M, Giuliano G, Lanteri S, Rotino GL., Sci Rep 9(1), 2019
PMID: 31409808
Relationship between aluminum stress and caffeine biosynthesis in suspension cells of Coffea arabica L.
Pech-Kú R, Muñoz-Sánchez JA, Monforte-González M, Vázquez-Flota F, Rodas-Junco BA, González-Mendoza VM, Hernández-Sotomayor SMT., J Inorg Biochem 181(), 2018
PMID: 28867596
Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes.
Lyu H, He Z, Wu CI, Shi S., New Phytol 217(1), 2018
PMID: 28960318
Localization and transport of indole-3-acetic acid during somatic embryogenesis in Coffea canephora.
Márquez-López RE, Pérez-Hernández C, Ku-González Á, Galaz-Ávalos RM, Loyola-Vargas VM., Protoplasma 255(2), 2018
PMID: 29119309
Early Selection Enabled by the Implementation of Genomic Selection in Coffea arabica Breeding.
Sousa TV, Caixeta ET, Alkimim ER, Oliveira ACB, Pereira AA, Sakiyama NS, Zambolim L, Resende MDV., Front Plant Sci 9(), 2018
PMID: 30671077
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L.
Sant'Ana GC, Pereira LFP, Pot D, Ivamoto ST, Domingues DS, Ferreira RV, Pagiatto NF, da Silva BSR, Nogueira LM, Kitzberger CSG, Scholz MBS, de Oliveira FF, Sera GH, Padilha L, Labouisse JP, Guyot R, Charmetant P, Leroy T., Sci Rep 8(1), 2018
PMID: 29323254
Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.
Julca I, Marcet-Houben M, Vargas P, Gabaldón T., BMC Biol 16(1), 2018
PMID: 29370802
Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides.
Hoopes GM, Hamilton JP, Kim J, Zhao D, Wiegert-Rininger K, Crisovan E, Buell CR., G3 (Bethesda) 8(2), 2018
PMID: 29237703
Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions.
de Castro Nunes R, Orozco-Arias S, Crouzillat D, Mueller LA, Strickler SR, Descombes P, Fournier C, Moine D, de Kochko A, Yuyama PM, Vanzela ALL, Guyot R., Front Plant Sci 9(), 2018
PMID: 29497436
Natural product modulators of human sensations and mood: molecular mechanisms and therapeutic potential.
Pluskal T, Weng JK., Chem Soc Rev 47(5), 2018
PMID: 28933478
Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds.
Dussert S, Serret J, Bastos-Siqueira A, Morcillo F, Déchamp E, Rofidal V, Lashermes P, Etienne H, JOët T., J Exp Bot 69(7), 2018
PMID: 29361125
Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.
Tran HTM, Ramaraj T, Furtado A, Lee LS, Henry RJ., Plant Biotechnol J 16(10), 2018
PMID: 29509991
Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements.
Gui S, Peng J, Wang X, Wu Z, Cao R, Salse J, Zhang H, Zhu Z, Xia Q, Quan Z, Shu L, Ke W, Ding Y., Plant J 94(4), 2018
PMID: 29575237
Tools for Genetic Studies in Experimental Populations of Polyploids.
Bourke PM, Voorrips RE, Visser RGF, Maliepaard C., Front Plant Sci 9(), 2018
PMID: 29720992
Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality.
Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G, Sun J, Cao H, Tong W, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Li F, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Bennetzen JL, Zhao S, Wan X., Proc Natl Acad Sci U S A 115(18), 2018
PMID: 29678829
Ectopic expression of the Coffea canephora SERK1 homolog-induced differential transcription of genes involved in auxin metabolism and in the developmental control of embryogenesis.
Pérez-Pascual D, Jiménez-Guillen D, Villanueva-Alonzo H, Souza-Perera R, Godoy-Hernández G, Zúñiga-Aguilar JJ., Physiol Plant 163(4), 2018
PMID: 29607503
Pinning down ploidy in paleopolyploid plants.
Zhang Y, Zheng C, Sankoff D., BMC Genomics 19(suppl 5), 2018
PMID: 29745846
Resolution effects in reconstructing ancestral genomes.
Zheng C, Jeong Y, Turcotte MG, Sankoff D., BMC Genomics 19(suppl 2), 2018
PMID: 29764371
Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics.
Orozco-Arias S, Liu J, Tabares-Soto R, Ceballos D, Silva Domingues D, Garavito A, Ming R, Guyot R., Biology (Basel) 7(2), 2018
PMID: 29799487
Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus.
Deng X, Zhao L, Fang T, Xiong Y, Ogutu C, Yang D, Vimolmangkang S, Liu Y, Han Y., Hortic Res 5(), 2018
PMID: 29872534
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.
Dong AX, Xin HB, Li ZJ, Liu H, Sun YQ, Nie S, Zhao ZN, Cui RF, Zhang RG, Yun QZ, Wang XN, Maghuly F, Porth I, Cong RC, Mao JF., Gigascience 7(7), 2018
PMID: 29931210
Genetic diversity of promising 'conilon' coffee clones based on morpho-agronomic variables.
Giles JAD, Partelli FL, Ferreira A, Rodrigues JP, Oliosi G, Silva FHLE., An Acad Bras Cienc 90(2 suppl 1), 2018
PMID: 30133576
Intrinsic cooperativity potentiates parallel cis-regulatory evolution.
Sorrells TR, Johnson AN, Howard CJ, Britton CS, Fowler KR, Feigerle JT, Weil PA, Johnson AD., Elife 7(), 2018
PMID: 30198843
Caffeine Extraction, Enzymatic Activity and Gene Expression of Caffeine Synthase from Plant Cell Suspensions.
Pech-Kú R, Muñoz-Sánchez JA, Monforte-González M, Vázquez-Flota F, Rodas-Junco BA, Hernández-Sotomayor SMT., J Vis Exp (140), 2018
PMID: 30346406
Primer design and amplification efficiencies are crucial for reliability of quantitative PCR studies of caffeine biosynthetic N-methyltransferases in coffee.
Sreedharan SP, Kumar A, Giridhar P., 3 Biotech 8(11), 2018
PMID: 30402369
A simple and efficient agroinfiltration method in coffee leaves (Coffea arabica L.): assessment of factors affecting transgene expression.
Vargas-Guevara C, Vargas-Segura C, Villalta-Villalobos J, Pereira LFP, Gatica-Arias A., 3 Biotech 8(11), 2018
PMID: 30456005
Coffee Somatic Embryogenesis: How Did Research, Experience Gained and Innovations Promote the Commercial Propagation of Elite Clones From the Two Cultivated Species?
Etienne H, Breton D, Breitler JC, Bertrand B, Déchamp E, Awada R, Marraccini P, Léran S, Alpizar E, Campa C, Courtel P, Georget F, Ducos JP., Front Plant Sci 9(), 2018
PMID: 30483287
Diterpenes biochemical profile and transcriptional analysis of cytochrome P450s genes in leaves, roots, flowers, and during Coffea arabica L. fruit development.
Ivamoto ST, Sakuray LM, Ferreira LP, Kitzberger CSG, Scholz MBS, Pot D, Leroy T, Vieira LGE, Domingues DS, Pereira LFP., Plant Physiol Biochem 111(), 2017
PMID: 28002787
Genome sequence and genetic diversity of European ash trees.
Sollars ES, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, Swarbreck D, Kaithakottil G, Cooper ED, Uauy C, Havlickova L, Worswick G, Studholme DJ, Zohren J, Salmon DL, Clavijo BJ, Li Y, He Z, Fellgett A, McKinney LV, Nielsen LR, Douglas GC, Kjær ED, Downie JA, Boshier D, Lee S, Clark J, Grant M, Bancroft I, Caccamo M, Buggs RJ., Nature 541(7636), 2017
PMID: 28024298
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
Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis.
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
PMID: 28096377
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
PMID: 27994132
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
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
PMID: 28212875
Genomic innovation for crop improvement.
Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD., Nature 543(7645), 2017
PMID: 28300107
Evolutionary Analyses of GRAS Transcription Factors in Angiosperms.
Cenci A, Rouard M., Front Plant Sci 8(), 2017
PMID: 28303145
Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons.
Dupeyron M, de Souza RF, Hamon P, de Kochko A, Crouzillat D, Couturon E, Domingues DS, Guyot R., Mol Genet Genomics 292(4), 2017
PMID: 28314936
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
PMID: 28399192
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
PMID: 28448529
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
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
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
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
PMID: 28538728
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
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
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
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
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
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
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
PMID: 28961859
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
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
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
PMID: 29127298
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
PMID: 29281674
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
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
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
PMID: 26334613
Interaction of coffee compounds with serum albumins. Part II: Diterpenes.
Guercia E, Forzato C, Navarini L, Berti F., Food Chem 199(), 2016
PMID: 26776001
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
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
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
PMID: 26786968
Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture.
Thottathil GP, Jayasekaran K, Othman AS., Trop Life Sci Res 27(1), 2016
PMID: 27019684
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
PMID: 26849045
Evolution of plant genome architecture.
Wendel JF, Jackson SA, Meyers BC, Wing RA., Genome Biol 17(), 2016
PMID: 26926526
Caffeine as a Gelator.
Nonappa, Kolehmainen E., Gels 2(1), 2016
PMID: 30674141
Ancestors of modern plant crops.
Salse J., Curr Opin Plant Biol 30(), 2016
PMID: 26985732
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
PMID: 26978165
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
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
PMID: 27096083
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
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
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
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
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
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
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.
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
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
Towards integration of population and comparative genomics in forest trees.
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
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
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
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
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
PMID: 28185558
Application of Genomic Technologies to the Breeding of Trees.
Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ., Front Genet 7(), 2016
PMID: 27895664
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
PMID: 25392413
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
PMID: 25416290
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
PMID: 25428362
Regulation of specialized metabolism by WRKY transcription factors.
Schluttenhofer C, Yuan L., Plant Physiol 167(2), 2015
PMID: 25501946
A genome to unveil the mysteries of orchids.
Albert VA, Carretero-Paulet L., Nat Genet 47(1), 2015
PMID: 25547596
Coffee: grounds for concern?
Weisse AB., Proc (Bayl Univ Med Cent) 28(1), 2015
PMID: 25552819
Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements.
Chaparro C, Gayraud T, de Souza RF, Domingues DS, Akaffou S, Laforga Vanzela AL, Kochko Ad, Rigoreau M, Crouzillat D, Hamon S, Hamon P, Guyot R., Genome Biol Evol 7(2), 2015
PMID: 25573958
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
PMID: 25577200
High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba.
Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA., Mol Biol Evol 32(5), 2015
PMID: 25637935
Progress, challenges and the future of crop genomes.
Michael TP, VanBuren R., Curr Opin Plant Biol 24(), 2015
PMID: 25703261
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
Regulatory divergence between parental alleles determines gene expression patterns in hybrids.
Combes MC, Hueber Y, Dereeper A, Rialle S, Herrera JC, Lashermes P., Genome Biol Evol 7(4), 2015
PMID: 25819221
It's more than stamp collecting: how genome sequencing can unify biological research.
Richards S., Trends Genet 31(7), 2015
PMID: 26003218
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
Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review
van der Vossen H, Bertrand B, Charrier A., Euphytica 204(2), 2015
PMID: IND604395648
A Revolution in Plant Metabolism: Genome-Enabled Pathway Discovery.
Kim J, Buell CR., Plant Physiol 169(3), 2015
PMID: 26224805
Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.
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
PMID: 26245353
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
PMID: 26277190
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
PMID: 26355011
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
PMID: 26568680
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
PMID: 26449933
Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.
Hao DC, Xiao PG., Evol Bioinform Online 11(), 2015
PMID: 26461812
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
PMID: 26697127
Genome-wide analysis of LTR-retrotransposons in oil palm.
Beulé T, Agbessi MD, Dussert S, Jaligot E, Guyot R., BMC Genomics 16(), 2015
PMID: 26470789
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
PMID: 26712553
Botany. A wake-up call with coffee.
Zamir D., Science 345(6201), 2014
PMID: 25190782
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
PMID: 25477420

165 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, SYST GEOGR PLANTS 76(), 2006
Molecular characterisation and origin of the Coffea arabica L. genome.
Lashermes P, Combes MC, Robert J, Trouslot P, D'Hont A, Anthony F, Charrier A., Mol. Gen. Genet. 261(2), 1999
PMID: 10102360
Genome size variations in diploid African Coffea species.
Noirot M, Poncet V, Barre P, Hamon P, Hamon S, De Kochko A., Ann. Bot. 92(5), 2003
PMID: 14573524
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution.
Schaack S, Gilbert C, Feschotte C., Trends Ecol. Evol. (Amst.) 25(9), 2010
PMID: 20591532
Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae.
Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O., BMC Evol. Biol. 9(), 2009
PMID: 19291296
Widespread and frequent horizontal transfers of transposable elements in plants.
El Baidouri M, Carpentier MC, Cooke R, Gao D, Lasserre E, Llauro C, Mirouze M, Picault N, Jackson SA, Panaud O., Genome Res. 24(5), 2014
PMID: 24518071
The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years.
Moisy C, Schulman AH, Kalendar R, Buchmann JP, Pelsy F., Theor. Appl. Genet. 127(5), 2014
PMID: 24590356
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization., Nature 449(7161), 2007
PMID: 17721507
The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium, Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, Xu X, Pan S, Cheng S, Liu X, Ren Y, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels RM, Bombarely A, Gosselin JR, Huang M, Leto JA, Menda N, Strickler S, Mao L, Gao S, Tecle IY, York T, Zheng Y, Vrebalov JT, Lee J, Zhong S, Mueller LA, Stiekema WJ, Ribeca P, Alioto T, Yang W, Huang S, Du Y, Zhang Z, Gao J, Guo Y, Wang X, Li Y, He J, Li C, Cheng Z, Zuo J, Ren J, Zhao J, Yan L, Jiang H, Wang B, Li H, Li Z, Fu F, Chen B, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, McCombie WR, Lippman ZB, Chia JM, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson LK, Chang SB, Royer SM, Shearer LA, Stack SM, Rose JK, Xu Y, Eannetta N, Matas AJ, McQuinn R, Tanksley SD, Camara F, Guigo R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang C, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia Z, Zhang J, Ye Z, Bishop GJ, Butcher S, Lopez-Cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal JK, Pandit A, Singh PK, Mahato AK, Gaikwad VD, Sharma RR, Mohapatra T, Singh NK, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latche A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Pericard P, Osorio S, Fernandez del Carmen A, Monforte A, Granell A, Fernandez-Munoz R, Conte M, Lichtenstein G, Carrari F, De Bellis G, Fuligni F, Peano C, Grandillo S, Termolino P, Pietrella M, Fantini E, Falcone G, Fiore A, Giuliano G, Lopez L, Facella P, Perotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek MG, Feron RM, van Oeveren J, de Heer P, daPonte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk MJ, Janssen A, van Haaren MJ, Jungeun Kim SH, Kwon SY, Kim S, Koo DH, Lee S, Hur CG, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jocker A, Warfsmann J, Gobel U, Kawamura S, Yano K, Sherman JD, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen EG, van de Belt J, van Haarst JC, Peters SA, van Staveren MA, Henkens MH, Mooyman PJ, Hesselink T, van Ham RC, Jiang G, Droege M, Choi D, Kang BC, Kim BD, Park M, Kim S, Yeom SI, Lee YH, Choi YD, Li G, Gao J, Liu Y, Huang S, Fernandez-Pedrosa V, Collado C, Zuniga S, Wang G, Cade R, Dietrich RA, Rogers J, Knapp S, Fei Z, White RA, Thannhauser TW, Giovannoni JJ, Botella MA, Gilbert L, Gonzalez R, Goicoechea JL, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Meyers BC, Gurazada AB, Green PJ, Vyas SM, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi AK, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk WB, Li J, Guo H, Lee TH, Wang Y, Zhang D, Paterson AH, Wang X, Tang H, Barone A, Chiusano ML, Ercolano MR, D'Agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour GB, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe BA, Vezzi A, D'Angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson DR, De Paoli E, Szinay D, de Jong HH, Bai Y, Visser RG, Klein R, Beasley H, McLaren K, Nicholson C, Riddle C, Gianese G., Nature 485(7400), 2012
PMID: 22660326
BadiRate: estimating family turnover rates by likelihood-based methods.
Librado P, Vieira FG, Rozas J., Bioinformatics 28(2), 2011
PMID: 22080468
Resistance gene complexes: evolution and utilization.
Hulbert SH, Webb CA, Smith SM, Sun Q., Annu Rev Phytopathol 39(), 2001
PMID: 11701867
Plant NBS-LRR proteins: adaptable guards.
McHale L, Tan X, Koehl P, Michelmore RW., Genome Biol. 7(4), 2006
PMID: 16677430
Caffeine and related methylxanthines: possible naturally occurring pesticides.
Nathanson JA., Science 226(4671), 1984
PMID: 6207592

AUTHOR UNKNOWN, ALLELOPATHY J 21(), 2008
Caffeine and related purine alkaloids: biosynthesis, catabolism, function and genetic engineering.
Ashihara H, Sano H, Crozier A., Phytochemistry 69(4), 2007
PMID: 18068204
The structure of two N-methyltransferases from the caffeine biosynthetic pathway.
McCarthy AA, McCarthy JG., Plant Physiol. 144(2), 2007
PMID: 17434991
7-Methylxanthine methyltransferase of coffee plants. Gene isolation and enzymatic properties.
Ogawa M, Herai Y, Koizumi N, Kusano T, Sano H., J. Biol. Chem. 276(11), 2000
PMID: 11108716
Convergent evolution in plant specialized metabolism.
Pichersky E, Lewinsohn E., Annu Rev Plant Biol 62(), 2011
PMID: 21275647
Metabolic diversification--independent assembly of operon-like gene clusters in different plants.
Field B, Osbourn AE., Science 320(5875), 2008
PMID: 18356490
Evolution of a novel phenolic pathway for pollen development.
Matsuno M, Compagnon V, Schoch GA, Schmitt M, Debayle D, Bassard JE, Pollet B, Hehn A, Heintz D, Ullmann P, Lapierre C, Bernier F, Ehlting J, Werck-Reichhart D., Science 325(5948), 2009
PMID: 19779199
Formation of plant metabolic gene clusters within dynamic chromosomal regions.
Field B, Fiston-Lavier AS, Kemen A, Geisler K, Quesneville H, Osbourn AE., Proc. Natl. Acad. Sci. U.S.A. 108(38), 2011
PMID: 21876149
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.
Zhang J, Nielsen R, Yang Z., Mol. Biol. Evol. 22(12), 2005
PMID: 16107592
Genotypic and environmental effects on coffee (Coffea arabica L.) bean fatty acid profile: impact on variety and origin chemometric determination.
Villarreal D, Laffargue A, Posada H, Bertrand B, Lashermes P, Dussert S., J. Agric. Food Chem. 57(23), 2009
PMID: 19908899
Effectiveness of the fatty acid and sterol composition of seeds for the chemotaxonomy of Coffea subgenus Coffea.
Dussert S, Laffargue A, de Kochko A, Joet T., Phytochemistry 69(17), 2008
PMID: 18995872
Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study.
Joet T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S., New Phytol. 182(1), 2009
PMID: 19207685
Towards a Phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences.
Maurin O, Davis AP, Chester M, Mvungi EF, Jaufeerally-Fakim Y, Fay MF., Ann. Bot. 100(7), 2007
PMID: 17956855
Doubled haploids of Coffea canephora: development, fertility and agronomic characteristics.
Lashermes P, Couturon E, Charrier A., Euphytica 74(1/2), 1994
PMID: IND21970636
Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee.
Agwanda CO, Lashermes P, Trouslot P, Combes MC, Charrier A., Euphytica 97(2), 1997
PMID: IND20906166
An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods.
Carrier G, Santoni S, Rodier-Goud M, Canaguier A, Kochko Ad, Dubreuil-Tranchant C, This P, Boursiquot JM, Cunff LL., Am. J. Bot. 98(1), 2011
PMID: IND44481127
BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.
Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes MC, Gavory F, de Kochko A, Kudrna D, Leroy T, Poulain J, Rondeau M, Song X, Wing R, Lashermes P., Plant Mol. Biol. 83(3), 2013
PMID: 23708951
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168
Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621
BLAT--the BLAST-like alignment tool.
Kent WJ., Genome Res. 12(4), 2002
PMID: 11932250
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.
Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P., BMC Genomics 9(), 2008
PMID: 19087275
De novo assembly of human genomes with massively parallel short read sequencing.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J., Genome Res. 20(2), 2009
PMID: 20019144
Differences in evolution rates among eudicotyledon species observed by analysis of protein divergence.
Cenci A, Combes MC, Lashermes P., J. Hered. 104(4), 2013
PMID: 23596284
Organization and molecular evolution of a disease-resistance gene cluster in coffee trees.
Ribas AF, Cenci A, Combes MC, Etienne H, Lashermes P., BMC Genomics 12(), 2011
PMID: 21575174
Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades.
Guyot R, Lefebvre-Pautigny F, Tranchant-Dubreuil C, Rigoreau M, Hamon P, Leroy T, Hamon S, Poncet V, Crouzillat D, de Kochko A., BMC Genomics 13(), 2012
PMID: 22433423
Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.
Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A., BMC Plant Biol. 9(), 2009
PMID: 19243618

AUTHOR UNKNOWN, Curr Protoc Bioinformatics 10(), 2003

AUTHOR UNKNOWN, TREE GENETICS AND GENOMES 6(), 2010
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts.
Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD., Theor. Appl. Genet. 112(1), 2005
PMID: 16273343
Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade.
Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD., Genetics 174(3), 2006
PMID: 16951058

AUTHOR UNKNOWN, ANN EUGENICS 12(), 1944

AUTHOR UNKNOWN, Curr Protoc Bioinformatics 4(), 2004
Repbase Update, a database of eukaryotic repetitive elements.
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J., Cytogenet. Genome Res. 110(1-4), 2005
PMID: 16093699
Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982
De novo identification of repeat families in large genomes.
Price AL, Jones NC, Pevzner PA., Bioinformatics 21 Suppl 1(), 2005
PMID: 15961478
GeneWise and Genomewise.
Birney E, Clamp M, Durbin R., Genome Res. 14(5), 2004
PMID: 15123596
Gene finding in novel genomes.
Korf I., BMC Bioinformatics 5(), 2004
PMID: 15144565

AUTHOR UNKNOWN, Genome biology 7(), 2006

Mott, Bioinformatics 13(4), 1997
A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica.
Vidal RO, Mondego JM, Pot D, Ambrosio AB, Andrade AC, Pereira LF, Colombo CA, Vieira LG, Carazzolle MF, Pereira GA., Plant Physiol. 154(3), 2010
PMID: 20864545
SOAP2: an improved ultrafast tool for short read alignment.
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J., Bioinformatics 25(15), 2009
PMID: 19497933
Annotating genomes with massive-scale RNA sequencing.
Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli C, Jaillon O, Artiguenave F., Genome Biol. 9(12), 2008
PMID: 19087247
GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
Howe KL, Chothia T, Durbin R., Genome Res. 12(9), 2002
PMID: 12213779
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M., Bioinformatics 21(18), 2005
PMID: 16081474
Additional gene ontology structure for improved biological reasoning.
Myhre S, Tveit H, Mollestad T, Laegreid A., Bioinformatics 22(16), 2006
PMID: 16787968

AUTHOR UNKNOWN, J R STAT SOC B 57(), 1995
CD-HIT: accelerated for clustering the next-generation sequencing data.
Fu L, Niu B, Zhu Z, Wu S, Li W., Bioinformatics 28(23), 2012
PMID: 23060610
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li L, Stoeckert CJ Jr, Roos DS., Genome Res. 13(9), 2003
PMID: 12952885
PMRD: plant microRNA database.
Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19808935
LeARN: a platform for detecting, clustering and annotating non-coding RNAs.
Noirot C, Gaspin C, Schiex T, Gouzy J., BMC Bioinformatics 9(), 2008
PMID: 18194551
Evolution and functional diversification of MIRNA genes.
Cuperus JT, Fahlgren N, Carrington JC., Plant Cell 23(2), 2011
PMID: 21317375
Mitochondrial DNA repairs double-strand breaks in yeast chromosomes.
Ricchetti M, Fairhead C, Dujon B., Nature 402(6757), 1999
PMID: 10573425
The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus.
Mourier T, Hansen AJ, Willerslev E, Arctander P., Mol. Biol. Evol. 18(9), 2001
PMID: 11504863
NUMTs in sequenced eukaryotic genomes.
Richly E, Leister D., Mol. Biol. Evol. 21(6), 2004
PMID: 15014143
Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.
Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC., Nature 402(6763), 1999
PMID: 10617197
Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats.
Stupar RM, Lilly JW, Town CD, Cheng Z, Kaul S, Buell CR, Jiang J., Proc. Natl. Acad. Sci. U.S.A. 98(9), 2001
PMID: 11309509
In-depth view of structure, activity, and evolution of rice chromosome 10.
Rice Chromosome 10 Sequencing Consortium., Science 300(5625), 2003
PMID: 12791992
The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux.
Matsuo M, Ito Y, Yamauchi R, Obokata J., Plant Cell 17(3), 2005
PMID: 15705954
Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization.
Michalovova M, Vyskot B, Kejnovsky E., Heredity (Edinb) 111(4), 2013
PMID: 23715017
Considering transposable element diversification in de novo annotation approaches.
Flutre T, Duprat E, Feuillet C, Quesneville H., PLoS ONE 6(1), 2011
PMID: 21304975
A unified classification system for eukaryotic transposable elements.
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH., Nat. Rev. Genet. 8(12), 2007
PMID: 17984973
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.
D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbeguie-A-Mbeguie D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P., Nature 488(7410), 2012
PMID: 22801500
Genomic duplication, fractionation and the origin of regulatory novelty.
Langham RJ, Walsh J, Dunn M, Ko C, Goff SA, Freeling M., Genetics 166(2), 2004
PMID: 15020478
Fractionation, rearrangement and subgenome dominance.
Sankoff D, Zheng C., Bioinformatics 28(18), 2012
PMID: 22962459

AUTHOR UNKNOWN, BMC Bioinformatics 13(), 2012

AUTHOR UNKNOWN, TROP PLANT BIOL 1(), 2008
How to usefully compare homologous plant genes and chromosomes as DNA sequences.
Lyons E, Freeling M., Plant J. 53(4), 2008
PMID: 18269575
Insights from the comparison of plant genome sequences.
Paterson AH, Freeling M, Tang H, Wang X., Annu Rev Plant Biol 61(), 2010
PMID: 20441528
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J., Genome Biol. 14(5), 2013
PMID: 23663246
Selectionism and neutralism in molecular evolution.
Nei M., Mol. Biol. Evol. 22(12), 2005
PMID: 16120807
CAFE: a computational tool for the study of gene family evolution.
De Bie T, Cristianini N, Demuth JP, Hahn MW., Bioinformatics 22(10), 2006
PMID: 16543274

Spencer, Evol. Bioinform. Online 2(), 2006
The Pfam protein families database.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18039703
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
Katoh K, Kuma K, Toh H, Miyata T., Nucleic Acids Res. 33(2), 2005
PMID: 15661851
The map-based sequence of the rice genome.
International Rice Genome Sequencing Project., Nature 436(7052), 2005
PMID: 16100779
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D., Science 313(5793), 2006
PMID: 16973872
The genome of Theobroma cacao.
Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C., Nat. Genet. 43(2), 2010
PMID: 21186351
Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family.
Porter BW, Paidi M, Ming R, Alam M, Nishijima WT, Zhu YJ., Mol. Genet. Genomics 281(6), 2009
PMID: 19263082
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis.
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW., Plant Cell 15(4), 2003
PMID: 12671079
Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme.
Yoneyama N, Morimoto H, Ye CX, Ashihara H, Mizuno K, Kato M., Mol. Genet. Genomics 275(2), 2005
PMID: 16333668
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res. 32(5), 2004
PMID: 15034147
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S., Mol. Biol. Evol. 24(8), 2007
PMID: 17488738
Architecture and evolution of a minute plant genome.
Ibarra-Laclette E, Lyons E, Hernandez-Guzman G, Perez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juarez MJ, Simpson J, Fernandez-Cortes A, Arteaga-Vazquez M, Gongora-Castillo E, Acevedo-Hernandez G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Perez SA, de Jesus Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L., Nature 498(7452), 2013
PMID: 23665961
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
Yang Z., Mol. Biol. Evol. 15(5), 1998
PMID: 9580986
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.
Yang Z, Nielsen R., Mol. Biol. Evol. 19(6), 2002
PMID: 12032247
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution.
Bielawski JP, Yang Z., J. Mol. Evol. 59(1), 2004
PMID: 15383915
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Goldman N, Yang Z., Mol. Biol. Evol. 11(5), 1994
PMID: 7968486
Bayes empirical bayes inference of amino acid sites under positive selection.
Yang Z, Wong WS, Nielsen R., Mol. Biol. Evol. 22(4), 2005
PMID: 15689528
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization.
Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, Zhou H, Lin H, Gonzalez-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao M, Huang Z, Zhou A, Yao X, Cui J, Li W, Chen Z, Feng Y, Niu Y, Bi S, Yang X, Li W, Cai H, Luo X, Montes-Hernandez S, Leyva-Gonzalez MA, Xiong Z, He X, Bai L, Tan S, Tang X, Liu D, Liu J, Zhang S, Chen M, Zhang L, Zhang L, Zhang Y, Liao W, Zhang Y, Wang M, Lv X, Wen B, Liu H, Luan H, Zhang Y, Yang S, Wang X, Xu J, Li X, Li S, Wang J, Palloix A, Bosland PW, Li Y, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu J, Hu K, Zhang Z., Proc. Natl. Acad. Sci. U.S.A. 111(14), 2014
PMID: 24591624
Understanding the functions of plant disease resistance proteins.
Martin GB, Bogdanove AJ, Sessa G., Annu Rev Plant Biol 54(), 2003
PMID: 14502984
Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily.
Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND., Plant J. 20(3), 1999
PMID: 10571892
The tomato R gene products I-2 and MI-1 are functional ATP binding proteins with ATPase activity.
Tameling WI, Elzinga SD, Darmin PS, Vossen JH, Takken FL, Haring MA, Cornelissen BJ., Plant Cell 14(11), 2002
PMID: 12417711
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation.
Tameling WI, Vossen JH, Albrecht M, Lengauer T, Berden JA, Haring MA, Cornelissen BJ, Takken FL., Plant Physiol. 140(4), 2006
PMID: 16489136
Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity.
Ellis JG, Lawrence GJ, Luck JE, Dodds PN., Plant Cell 11(3), 1999
PMID: 10072407
Regions outside of the leucine-rich repeats of flax rust resistance proteins play a role in specificity determination.
Luck JE, Lawrence GJ, Dodds PN, Shepherd KW, Ellis JG., Plant Cell 12(8), 2000
PMID: 10948256
NB-LRRs work a "bait and switch" on pathogens.
Collier SM, Moffett P., Trends Plant Sci. 14(10), 2009
PMID: 19720556
The evolution of resistance genes in multi-protein plant resistance systems.
Friedman AR, Baker BJ., Curr. Opin. Genet. Dev. 17(6), 2007
PMID: 17942300
Recent duplications dominate NBS-encoding gene expansion in two woody species.
Yang S, Zhang X, Yue JX, Tian D, Chen JQ., Mol. Genet. Genomics 280(3), 2008
PMID: 18563445
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions.
Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z, Min J, Guo X, Murat F, Ham BK, Zhang Z, Gao S, Huang M, Xu Y, Zhong S, Bombarely A, Mueller LA, Zhao H, He H, Zhang Y, Zhang Z, Huang S, Tan T, Pang E, Lin K, Hu Q, Kuang H, Ni P, Wang B, Liu J, Kou Q, Hou W, Zou X, Jiang J, Gong G, Klee K, Schoof H, Huang Y, Hu X, Dong S, Liang D, Wang J, Wu K, Xia Y, Zhao X, Zheng Z, Xing M, Liang X, Huang B, Lv T, Wang J, Yin Y, Yi H, Li R, Wu M, Levi A, Zhang X, Giovannoni JJ, Wang J, Li Y, Fei Z, Xu Y., Nat. Genet. 45(1), 2012
PMID: 23179023
The arms race is ancient history in Arabidopsis, the wildflower.
Holub EB., Nat. Rev. Genet. 2(7), 2001
PMID: 11433358
The draft genome of sweet orange (Citrus sinensis).
Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y., Nat. Genet. 45(1), 2012
PMID: 23179022
Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops.
Wan H, Yuan W, Bo K, Shen J, Pang X, Chen J., BMC Genomics 14(), 2013
PMID: 23418910
From beans to berries and beyond: teamwork between plant chemicals for protection of optimal human health.
Lila MA., Ann. N. Y. Acad. Sci. 1114(), 2007
PMID: 17986598
Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part II: Reconstruction of multienzyme pathways in plants and microbes.
Ververidis F, Trantas E, Douglas C, Vollmer G, Kretzschmar G, Panopoulos N., Biotechnol J 2(10), 2007
PMID: 17935118

AUTHOR UNKNOWN, INT J FOOD SCI TECHNOL 43(), 2008
Inhibition of pro-inflammatory responses and antioxidant capacity of Mexican blackberry (Rubus spp.) extracts.
Cuevas-Rodriguez EO, Dia VP, Yousef GG, Garcia-Saucedo PA, Lopez-Medina J, Paredes-Lopez O, Gonzalez de Mejia E, Lila MA., J. Agric. Food Chem. 58(17), 2010
PMID: 20715775
Chlorogenic acids and other cinnamates--nature, occurrence, dietary burden, absorption and metabolism.
Clifford MN., J. Sci. Food Agric. 80(7), 2000
PMID: IND22079353
Relations between and inheritance of chlorogenic acid contents in an interspecific cross between Coffea pseudozanguebariae and Coffea liberica var 'dewevrei'.
Ky CL, Louarn J, Guyot B, Charrier A, Hamon S, Noirot M., Theor. Appl. Genet. 98(3/4), 1999
PMID: IND22010145

AUTHOR UNKNOWN, Food Chem 75(), 2001

AUTHOR UNKNOWN, Plant Sci. 165(), 2003

AUTHOR UNKNOWN, Plant Sci. 172(), 2007
Biosynthesis of chlorogenic acids in growing and ripening fruits of Coffea arabica and Coffea canephora plants.
Koshiro Y, Jackson MC, Katahira R, Wang ML, Nagai C, Ashihara H., Z. Naturforsch., C, J. Biosci. 62(9-10), 2007
PMID: 18069248
Antioxidant activity of polyphenolics in diets. Rate constants of reactions of chlorogenic acid and caffeic acid with reactive species of oxygen and nitrogen.
Kono Y, Kobayashi K, Tagawa S, Adachi K, Ueda A, Sawa Y, Shibata H., Biochim. Biophys. Acta 1335(3), 1997
PMID: 9202196
Effect of roasting on the antioxidant activity of coffee brews.
del Castillo MD, Ames JM, Gordon MH., J. Agric. Food Chem. 50(13), 2002
PMID: 12059145
Dicaffeoylquinic and dicaffeoyltartaric acids are selective inhibitors of human immunodeficiency virus type 1 integrase.
McDougall B, King PJ, Wu BW, Hostomsky Z, Reinecke MG, Robinson WE Jr., Antimicrob. Agents Chemother. 42(1), 1998
PMID: 9449274
Dicaffeoylquinic acid inhibitors of human immunodeficiency virus integrase: inhibition of the core catalytic domain of human immunodeficiency virus integrase.
Robinson WE Jr, Cordeiro M, Abdel-Malek S, Jia Q, Chow SA, Reinecke MG, Mitchell WM., Mol. Pharmacol. 50(4), 1996
PMID: 8863829
Inhibitors of HIV-1 replication [corrected; erratum to be published] that inhibit HIV integrase.
Robinson WE Jr, Reinecke MG, Abdel-Malek S, Jia Q, Chow SA., Proc. Natl. Acad. Sci. U.S.A. 93(13), 1996
PMID: 8692814
Effect of roasting on the formation of chlorogenic acid lactones in coffee.
Farah A, de Paulis T, Trugo LC, Martin PR., J. Agric. Food Chem. 53(5), 2005
PMID: 15740032
Chlorogenic acids and lactones in regular and water-decaffeinated arabica coffees.
Farah A, de Paulis T, Moreira DP, Trugo LC, Martin PR., J. Agric. Food Chem. 54(2), 2006
PMID: 16417293
Real-time monitoring of 4-vinylguaiacol, guaiacol, and phenol during coffee roasting by resonant laser ionization time-of-flight mass spectrometry.
Dorfner R, Ferge T, Kettrup A, Zimmermann R, Yeretzian C., J. Agric. Food Chem. 51(19), 2003
PMID: 12952431
Genetic mapping of a caffeoyl-coenzyme A 3-O-methyltransferase gene in coffee trees. Impact on chlorogenic acid content.
Campa C, Noirot M, Bourgeois M, Pervent M, Ky CL, Chrestin H, Hamon S, de Kochko A., Theor. Appl. Genet. 107(4), 2003
PMID: 12861362
Isolation and genetic mapping of a Coffea canephora phenylalanine ammonia-lyase gene (CcPAL1) and its involvement in the accumulation of caffeoyl quinic acids.
Mahesh V, Rakotomalala JJ, Le Gal L, Vigne H, de Kochko A, Hamon S, Noirot M, Campa C., Plant Cell Rep. 25(9), 2006
PMID: 16586075
Functional characterization of two p-coumaroyl ester 3'-hydroxylase genes from coffee tree: evidence of a candidate for chlorogenic acid biosynthesis.
Mahesh V, Million-Rousseau R, Ullmann P, Chabrillange N, Bustamante J, Mondolot L, Morant M, Noirot M, Hamon S, de Kochko A, Werck-Reichhart D, Campa C., Plant Mol. Biol. 64(1-2), 2007
PMID: 17333503
Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae).
Lepelley M, Mahesh V, McCarthy J, Rigoreau M, Crouzillat D, Chabrillange N, de Kochko A, Campa C., Planta 236(1), 2012
PMID: 22349733
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
CD-Search: protein domain annotations on the fly.
Marchler-Bauer A, Bryant SH., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215404
CDD: specific functional annotation with the Conserved Domain Database.
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18984618
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
PMID: 21109532
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
PMID: 18513762
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
PMID: 19996151
Engineering plants with increased levels of the antioxidant chlorogenic acid.
Niggeweg R, Michael AJ, Martin C., Nat. Biotechnol. 22(6), 2004
PMID: 15107863
Purification, cloning, and properties of an acyltransferase controlling shikimate and quinate ester intermediates in phenylpropanoid metabolism.
Hoffmann L, Maury S, Martz F, Geoffroy P, Legrand M., J. Biol. Chem. 278(1), 2002
PMID: 12381722
Silencing of hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyltransferase affects phenylpropanoid biosynthesis.
Hoffmann L, Besseau S, Geoffroy P, Ritzenthaler C, Meyer D, Lapierre C, Pollet B, Legrand M., Plant Cell 16(6), 2004
PMID: 15161961

AUTHOR UNKNOWN, Food Chem 106(), 2008
Novel hydroxycinnamoyl-coenzyme A quinate transferase genes from artichoke are involved in the synthesis of chlorogenic acid.
Sonnante G, D'Amore R, Blanco E, Pierri CL, De Palma M, Luo J, Tucci M, Martin C., Plant Physiol. 153(3), 2010
PMID: 20431089
Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus.
Tsai CJ, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y., New Phytol. 172(1), 2006
PMID: 16945088
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
Insecticidal activity of caffeine aqueous solutions and caffeine oleate emulsions against Drosophila melanogaster and Hypothenemus hampei.
Araque P, Casanova H, Ortiz C, Henao B, Pelaez C., J. Agric. Food Chem. 55(17), 2007
PMID: 17658827
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
Tolerance of coffee (Coffea spp.) seeds to ultra-low temperature exposure in relation to calorimetric properties of tissue water, lipid composition, and cooling procedure.
Dussert S, Chabrillange N, Rocquelin G, Engelmann F, Lopez M, Hamon S., Physiol Plant 112(4), 2001
PMID: 11473709
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
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