An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

BMC Plant Biology

Volumn 11, Issue , 2011, Pages

  Mondego, Jorge M C ^a   Vidal, Ramon O ^b,c   Carazzolle, Marcelo F ^b   Tokuda, Eric K ^b   Parizzi, Lucas P ^b   Costa, Gustavo G L ^b   Pereira, Luiz F P ^d   Andrade, Alan C ^e   Colombo, Carlos A ^a   Vieira, Luiz G E ^d   Pereira, Gonçalo A G ^b  

^a INSTITUTO AGRONÔMICO   (Brazil)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c BRAZILIAN CENTER FOR RESEARCH IN ENERGY AND MATERIALS CNPEM   (Brazil)

^d INSTITUTO AGRONÔMICO DO PARANÁ   (Brazil)

^e EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

COFFEA; COFFEA ARABICA; COFFEA CANEPHORA; COFFEA EUGENIOIDES; VITACEAE; VITIS VINIFERA;

PLANT DNA;

ARTICLE; CLUSTER ANALYSIS; COFFEE; DNA BASE COMPOSITION; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; MOLECULAR GENETICS; MULTIGENE FAMILY; PLANT GENE; PLANT GENOME; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE COMPOSITION; CLUSTER ANALYSIS; COFFEA; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 79551689279     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-11-30     Document Type: Article

References (136)

1. Pay E. The market for organic and fair-trade coffee. FAO Rome 2009,
2. Charrier A, Berthaud J. Botanical classification of coffee. Coffee: botany, biochemistry, and production of beans and beverage. New York 1985, 13-47. Clifforf MN, Wilsson KC.
3. Lashermes P, Combes MC, Robert J, Trouslot P, D'Hont A, Anthony F, Charrier A. Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 1999, 261(2):259-266. 10.1007/s004380050965, 10102360.
4. Anthony F, Combes C, Astorga C, Bertrand B, Graziosi G, Lashermes P. The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theor Appl Genet 2002, 104(5):894-900. 10.1007/s00122-001-0798-8, 12582651.
5. Geromel C, Ferreira LP, Guerreiro SM, Cavalari AA, Pot D, Pereira LF, Leroy T, Vieira LG, Mazzafera P, Marraccini P. Biochemical and genomic analysis of sucrose metabolism during coffee (Coffea arabica) fruit development. J Exp Bot 2006, 57(12):3243-3258. 10.1093/jxb/erl084, 16926239.
6. Privat I, Foucrier S, Prins A, Epalle T, Eychenne M, Kandalaft L, Caillet V, Lin C, Tanksley S, Foyer C, et al. Differential regulation of grain sucrose accumulation and metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta) revealed through gene expression and enzyme activity analysis. New Phytol 2008, 178(4):781-797. 10.1111/j.1469-8137.2008.02425.x, 18384509.
7. Joet T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S. Metabolic pathways in tropical dicotyledonous albuminous seeds Coffea arabica as a case study. New Phytol 2009, 182(1):146-162. 10.1111/j.1469-8137.2008.02742.x, 2713855, 19207685.
8. Leroy T, Marraccini P, Dufour M, Montagnon C, Lashermes P, Sabau X, Ferreira LP, Jourdan I, Pot D, Andrade AC, et al. Construction and characterization of a Coffea canephora BAC library to study the organization of sucrose biosynthesis genes. Theor Appl Genet 2005, 111(6):1032-1041. 10.1007/s00122-005-0018-z, 16133319.
9. Wintgens JN. Coffee: growing, processing, sustainable production. Weinheim 2004,
10. Maluf MP, Silvestrini M, Ruggiero LMD, Guerreiro O, Colombo CA. Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems. Scientia Agricola 2005, 62(4):366-373.
11. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL, et al. Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 2003, 13(12):2725-2735. 10.1101/gr.1532103, 403815, 14613979.
12. da Silva FG, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman MA, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, et al. Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol 2005, 139(2):574-597. 10.1104/pp.105.065748, 1255978, 16219919.
13. Verza NC, TR ES, Neto GC, Nogueira FT, Fisch PH, de Rosa VE, Rebello MM, Vettore AL, da Silva FR, Arruda P. Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags. Plant Mol Biol 2005, 59(2):363-374. 10.1007/s11103-005-8924-7, 16247562.
14. Ramirez M, Graham MA, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair MW, Hernandez G, Vance CP, Lara M. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 2005, 137(4):1211-1227. 10.1104/pp.104.054999, 1088315, 15824284.
15. Sakurai T, Plata G, Rodriguez-Zapata F, Seki M, Salcedo A, Toyoda A, Ishiwata A, Tohme J, Sakaki Y, Shinozaki K, et al. Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response. BMC Plant Biol 2007, 7:66. 10.1186/1471-2229-7-66, 2245942, 18096061.
16. Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci AM, Da Silva C, Cascardo J, Allegre M, et al. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genomics 2008, 9:512. 10.1186/1471-2164-9-512, 2642826, 18973681.
17. Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB, et al. Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 2009, 69(1-2):179-194. 10.1007/s11103-008-9415-4, 2709227, 18937034.
18. Marques MC, Alonso-Cantabrana H, Forment J, Arribas R, Alamar S, Conejero V, Perez-Amador MA. A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus. BMC Genomics 2009, 10:428. 10.1186/1471-2164-10-428, 2754500, 19747386.
19. Leroy T, Henry AM, Royer M, Altosaar I, Frutos R, Duris D, Philippe R. Genetically modified coffee plants expressing the Bacillus thuringiensis cry1Ac gene for resistance to leaf miner. Plant Cell Rep 2000, 19(4):382-389.
20. Ogita S, Uefuji H, Yamaguchi Y, Koizumi N, Sano H. Producing decaffeinated coffee plants. Nature 2003, 423(6942):823. 10.1038/423823a, 12815419.
21. Vieira LGE, Andrade AC, Colombo CA, Moraes AHA, Metha A, Oliveira AC, Labate CA, Marino CL, Monteiro-Vitorello CB, Monte DC, et al. Brazilian coffee genome project: an EST-based genomic resource. Brazil J Plant Physiol 2006, 18:95-108.
22. Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD. Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 2005, 112(1):114-130. 10.1007/s00122-005-0112-2, 1544375, 16273343.
23. Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, et al. The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 2005, 138(3):1310-1317. 10.1104/pp.105.060707, 1176404, 16010005.
24. Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 2006, 7:438. 10.1186/1471-2105-7-438, 1618865, 17029635.
25. Carels N, Bernardi G. Two classes of genes in plants. Genetics 2000, 154(4):1819-1825. 1461008, 10747072.
26. Glemin S, Bazin E, Charlesworth D. Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc Biol Sci 2006, 273(1604):3011-3019. 10.1098/rspb.2006.3657, 1639510, 17015349.
27. Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. Milling SNPs from EST databases. Genome Res 1999, 9(2):167-174. 310719, 10022981.
28. Batley J, Hayes PK. Development of high throughput single nucleotide polymorphism genotyping for the analysis of Nodularia (Cyanobacteria) population genetics. J Phycol 2003, 39(1):248-252.
29. Dantec LL, Chagne D, Pot D, Cantin O, Garnier-Gere P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V, et al. Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol Biol 2004, 54(3):461-470. 10.1023/B:PLAN.0000036376.11710.6f, 15284499.
30. Vidal RO, Mondego JM, Pot D, Ambrosio AB, Andrade AC, Pereira LF, Colombo CA, Vieira LG, Carazzolle MF, Pereira GA. A high-throughput data mining of SNPs in Coffea spp ESTs suggests differential homeologous gene expression in the allotetraploid Coffea arabica. Plant Physiol 2010, 154(3):1053-1066. 10.1104/pp.110.162438, 20864545.
31. Koski LB, Gray MW, Lang BF, Burger G. AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 2005, 6:151. 10.1186/1471-2105-6-151, 1182349, 15960857.
32. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007, 449(7161):463-467. 10.1038/nature06148, 17721507.
33. Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, et al. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 2008, 148(4):1772-1781. 10.1104/pp.108.124867, 2593677, 18952863.
34. Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A. 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. BMC Plant Biol 2009, 9:22. 10.1186/1471-2229-9-22, 2656508, 19243618.
35. Cenci A, Combes MC, Lashermes P. Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome. Mol Genet Genomics 2010, 283(5):493-501. 10.1007/s00438-010-0534-7, 20361338.
36. Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol 2000, 15(12):496-503. 10.1016/S0169-5347(00)01994-7, 11114436.
37. Roth C, Liberles DA. A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol 2006, 6:12. 10.1186/1471-2229-6-12, 1540423, 16784532.
38. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. 10.1186/1471-2164-9-312, 2483731, 18590545.
39. Stukenbrock EH, McDonald BA. Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions. Mol Plant Microbe Interact 2009, 22(4):371-380. 10.1094/MPMI-22-4-0371, 19271952.
40. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005, 33(19):6083-6089. 10.1093/nar/gki892, 1266070, 16246909.
41. Vitte C, Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 2005, 110(1-4):91-107. 10.1159/000084941, 16093661.
42. Lopes FR, Carazzolle MF, Pereira GA, Colombo CA, Carareto CM. Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants. Mol Genet Genomics 2008, 279(4):385-401. 10.1007/s00438-008-0319-4, 18231813.
43. Conesa A, Gotz S. Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. Int J Plant Genomics 2008, 2008:619832. 2375974, 18483572.
44. Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004, 5(12):R101. 10.1186/gb-2004-5-12-r101, 545796, 15575967.
45. Frenal K, Callebaut I, Wecker K, Prochnicka-Chalufour A, Dendouga N, Zinn-Justin S, Delepierre M, Tomavo S, Wolff N. Structural and functional characterization of the TgDRE multidomain protein, a DNA repair enzyme from Toxoplasma gondii. Biochemistry 2006, 45(15):4867-4874. 10.1021/bi051948e, 16605254.
46. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13(9):2178-2189. 10.1101/gr.1224503, 403725, 12952885.
47. Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, (34 Database):D363-368. 10.1093/nar/gkj123, 1347485, 16381887.
48. Gouzy J, Carrere S, Schiex T. FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics 2009, 25(5):670-671. 10.1093/bioinformatics/btp024, 2647831, 19153134.
49. Luo ZY, Lu QH, Liu SP, Chen XH, Luo JQ, Tan LJ, Hu WX. Screening and identification of novel genes involved in biosynthesis of ginsenoside in Panax ginseng plant. Acta biochim biophys Sinica 2003, 35(6):554-560.
50. Salmona J, Dussert S, Descroix F, de Kochko A, Bertrand B, Joet T. Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches. Plant Mol Biol 2008, 66(1-2):105-124. 10.1007/s11103-007-9256-6, 18026845.
51. Barsalobres-Cavallari CF, Severino FE, Maluf MP, Maia IG. Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol Biol 2009, 10:1. 10.1186/1471-2199-10-1, 2629470, 19126214.
52. Cruz F, Kalaoun S, Nobile P, Colombo C, Almeida J, Barros LMG, Romano E, Grossi-de-Sa MF, Vaslin M, Alves-Ferreira M. Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR. Mol Breed 2009, 23(4):607-616.
53. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3(7):RESEARCH0034. 10.1186/gb-2002-3-7-research0034, 126239, 12184808.
54. Linster CL, Gomez TA, Christensen KC, Adler LN, Young BD, Brenner C, Clarke SG. Arabidopsis VTC2 encodes a GDP-L-galactose phosphorylase, the last unknown enzyme in the Smirnoff-Wheeler pathway to ascorbic acid in plants. J Biol Chem 2007, 282(26):18879-18885. 10.1074/jbc.M702094200, 2556065, 17462988.
55. Stekel DJ, Git Y, Falciani F. The comparison of gene expression from multiple cDNA libraries. Genome Res 2000, 10(12):2055-2061. 10.1101/gr.GR-1325RR, 313085, 11116099.
56. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997, 7(10):986-995.
57. Romualdi C, Bortoluzzi S, D'Alessi F, Danieli GA. IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics 2003, 12(2):159-162.
58. Brandalise M, Severino FE, Maluf MP, Maia IG. The promoter of a gene encoding an isoflavone reductase-like protein in coffee (Coffea arabica) drives a stress-responsive expression in leaves. Plant Cell Rep 2009, 28(11):1699-1708. 10.1007/s00299-009-0769-0, 19756631.
59. van Loon LC, Rep M, Pieterse CM. Significance of inducible defense-related proteins in infected plants. Annu Rev Phytopathol 2006, 44:135-162. 10.1146/annurev.phyto.44.070505.143425, 16602946.
60. Sels J, Mathys J, De Coninck BM, Cammue BP, De Bolle MF. Plant pathogenesis-related (PR) proteins: a focus on PR peptides. Plant Physiol Biochem 2008, 46(11):941-950. 10.1016/j.plaphy.2008.06.011, 18674922.
61. Carvalho Ade O, Gomes VM. Plant defensins-prospects for the biological functions and biotechnological properties. Peptides 2009, 30(5):1007-1020. 10.1016/j.peptides.2009.01.018, 19428780.
62. Zubini P, Zambelli B, Musiani F, Ciurli S, Bertolini P, Baraldi E. The RNA hydrolysis and the cytokinin binding activities of PR-10 proteins are differently performed by two isoforms of the Pru p 1 peach major allergen and are possibly functionally related. Plant Physiol 2009, 150(3):1235-1247. 10.1104/pp.109.139543, 2705045, 19474212.
63. Ramiro DA, Escoute J, Petitot AS, Nicole M, Maluf MP, Fernandez D. Biphasic haustorial differentiation of coffee rust (Hemileia vastatrix race II) associated with defence responses in resistant and susceptible coffee cultivars. Plant Pathology 2009, 58(5):944-955.
64. Koshino LL, Gomes CP, Silva LP, Eira MT, Bloch C, Franco OL, Mehta A. Comparative proteomical analysis of zygotic embryo and endosperm from Coffea arabica seeds. J Agric Food Chem 2008, 56(22):10922-10926. 10.1021/jf801734m, 18959416.
65. Botton A, Andreotti C, Costa G, Ramina A. Peach (Prunus persica L. Batsch) allergen-encoding genes are developmentally regulated and affected by fruit load and light radiation. J Agric Food Chem 2009, 57(2):724-734. 10.1021/jf802709k, 19090764.
66. Helleboid S, Hendriks T, Bauw G, Inze D, Vasseur J, Hilbert JL. Three major somatic embryogenesis related proteins in Cichorium identified as PR proteins. J Exp Bot 2000, 51(348):1189-1200. 10.1093/jexbot/51.348.1189, 10937694.
67. Yasuda H, Nakajima M, Ito T, Ohwada T, Masuda H. Partial characterization of genes whose transcripts accumulate preferentially in cell clusters at the earliest stage of carrot somatic embryogenesis. Plant Mol Biol 2001, 45(6):705-712. 10.1023/A:1010624803295, 11430432.
68. Rojas-Herrera R, Loyola-Vargas VM. Induction of a class III acidic chitinase in foliar explants of Coffea arabica L. during somatic embryogenesis and wounding. Plant Sci 2002, 163(4):705-711.
69. Borderies G, le Bechec M, Rossignol M, Lafitte C, Le Deunff E, Beckert M, Dumas C, Elisabeth MR. Characterization of proteins secreted during maize microspore culture: arabinogalactan proteins (AGPs) stimulate embryo development. Eur J Cell Biol 2004, 83(5):205-212. 10.1078/0171-9335-00378, 15346810.
70. Kragh KM, Hendriks T, de Jong AJ, Lo Schiavo F, Bucherna N, Hojrup P, Mikkelsen JD, de Vries SC. Characterization of chitinases able to rescue somatic embryos of the temperature-sensitive carrot variant ts 11. Plant Mol Biol 1996, 31(3):631-645. 10.1007/BF00042235, 8790295.
71. van Hengel AJ, Guzzo F, van Kammen A, de Vries SC. Expression pattern of the carrot EP3 endochitinase genes in suspension cultures and in developing seeds. Plant Physiol 1998, 117(1):43-53. 10.1104/pp.117.1.43, 35020, 9576773.
72. Belkhadir Y, Subramaniam R, Dangl JL. Plant disease resistance protein signaling: NBS-LRR proteins and their partners. Curr Opin Plant Biol 2004, 7(4):391-399. 10.1016/j.pbi.2004.05.009, 15231261.
73. McHale L, Tan X, Koehl P, Michelmore RW. Plant NBS-LRR proteins: adaptable guards. Genome Biol 2006, 7(4):212. 10.1186/gb-2006-7-4-212, 1557992, 16677430.
74. Noir S, Combes MC, Anthony F, Lashermes P. Origin, diversity and evolution of NBS-type disease-resistance gene homologues in coffee trees (Coffea L.). Mol Genet Genomics 2001, 265(4):654-662. 10.1007/s004380100459, 11459185.
75. Paal J, Henselewski H, Muth J, Meksem K, Menendez CM, Salamini F, Ballvora A, Gebhardt C. Molecular cloning of the potato Gro1-4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach. Plant J 2004, 38(2):285-297. 10.1111/j.1365-313X.2004.02047.x, 15078331.
76. Eitas TK, Nimchuk ZL, Dangl JL. Arabidopsis TAO1 is a TIR-NB-LRR protein that contributes to disease resistance induced by the Pseudomonas syringae effector AvrB. Proc Natl Acad Sci USA 2008, 105(17):6475-6480. 10.1073/pnas.0802157105, 2327211, 18424557.
77. Pan Q, Wendel J, Fluhr R. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J Mol Evol 2000, 50(3):203-213.
78. Tian Y, Fan L, Thurau T, Jung C, Cai D. The absence of TIR-type resistance gene analogues in the sugar beet (Beta vulgaris L.) genome. J Mol Evol 2004, 58(1):40-53. 10.1007/s00239-003-2524-4, 14743313.
79. DaMatta FM, Ramalho JDC. Impacts of drought and temperature stress on coffee physiology and production: a review. Brazil J Plant Physiol 2006, 18:55-81.
80. Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, et al. Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 2007, 7(2):111-134. 10.1007/s10142-006-0039-y, 17136344.
81. Lu CM, Zhang JH. Effects of water stress on photosystem II photochemistry and its thermostability in wheat plants. J Exp Bot 1999, 50(336):1199-1206.
82. Montavon P, Bortlik K. Evolution of robusta green coffee redox enzymatic activities with maturation. J Agric Food Chem 2004, 52(11):3590-3594. 10.1021/jf0308004, 15161235.
83. Du YY, Wang PC, Chen J, Song CP. Comprehensive functional analysis of the catalase gene family in Arabidopsis thaliana. J Integr Plant Biol 2008, 50(10):1318-1326. 10.1111/j.1744-7909.2008.00741.x, 19017119.
84. Montane MH, Petzold B, Kloppstech K. Formation of early-light-inducible-protein complexes and status of xanthophyll levels under high light and cold stress in barley (Hordeum vulgare L.). Planta 1999, 208(4):519-527.
85. Bruno AK, Wetzel CM. The early light-inducible protein (ELIP) gene is expressed during the chloroplast-to-chromoplast transition in ripening tomato fruit. J Exp Bot 2004, 55(408):2541-2548. 10.1093/jxb/erh273, 15475376.
86. Canel C, Bailey-Serres JN, Roose ML. Pummelo fruit transcript homologous to ripening-induced genes. Plant Physiol 1995, 108(3):1323-1324. 10.1104/pp.108.3.1323, 157501, 7630961.
87. Padmanabhan V, Dias DM, Newton RJ. Expression analysis of a gene family in loblolly pine (Pinus taeda L.) induced by water deficit stress. Plant Mol Biol 1997, 35(6):801-807. 10.1023/A:1005897921567, 9426600.
88. Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol 2006, 7(11):847-859. 10.1038/nrm2020, 16990790.
89. Staswick PE, Serban B, Rowe M, Tiryaki I, Maldonado MT, Maldonado MC, Suza W. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell 2005, 17(2):616-627. 10.1105/tpc.104.026690, 548830, 15659623.
90. Dahlke RI, Luethen H, Steffens B. ABP1: An auxin receptor for fast responses at the plasma membrane. Plant Signal Behav 2010, 5(1).
91. Matsubayashi Y, Sakagami Y. Peptide hormones in plants. Annu Rev Plant Biol 2006, 57:649-674. 10.1146/annurev.arplant.56.032604.144204, 16669777.
92. Pearce G, Moura DS, Stratmann J, Ryan CA. RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development. Proc Natl Acad Sci USA 2001, 98(22):12843-12847. 10.1073/pnas.201416998, 60141, 11675511.
93. Matos JL, Fiori CS, Silva-Filho MC, Moura DS. A conserved dibasic site is essential for correct processing of the peptide hormone AtRALF1 in Arabidopsis thaliana. FEBS Lett 2008, 582(23-24):3343-3347. 10.1016/j.febslet.2008.08.025, 18775699.
94. Srivastava R, Liu JX, Guo H, Yin Y, Howell SH. Regulation and processing of a plant peptide hormone, AtRALF23, in Arabidopsis. Plant J 2009, 59(6):930-939. 10.1111/j.1365-313X.2009.03926.x, 19473327.
95. Fusaro AF, Sachetto-Martins G. Blooming time for plant glycine-rich proteins. Plant Signal Behav 2007, 2(5):386-387. 2634221, 19704608.
96. Mangeon A, Junqueira RM, Sachetto-Martins G. Functional diversity of the plant glycine-rich proteins superfamily. Plant Signal Behav 2010, 5(2):99-104. 10.4161/psb.5.2.10336, 2884108, 20009520.
97. Park AR, Cho SK, Yun UJ, Jin MY, Lee SH, Sachetto-Martins G, Park OK. Interaction of the Arabidopsis receptor protein kinase Wak1 with a glycine-rich protein, AtGRP-3. J Biol Chem 2001, 276(28):26688-26693. 10.1074/jbc.M101283200, 11335717.
98. Domingo C, Sauri A, Mansilla E, Conejero V, Vera P. Identification of a novel peptide motif that mediates cross-linking of proteins to cell walls. Plant J 1999, 20(5):563-570. 10.1046/j.1365-313X.1999.00631.x, 10652128.
99. Margis R, Reis EM, Villeret V. Structural and phylogenetic relationships among plant and animal cystatins. Arch Biochem Biophys 1998, 359(1):24-30. 10.1006/abbi.1998.0875, 9799556.
100. Martinez M, Diaz I. The origin and evolution of plant cystatins and their target cysteine proteinases indicate a complex functional relationship. BMC Evol Biol 2008, 8:198. 10.1186/1471-2148-8-198, 2474614, 18616807.
101. Rivard D, Girard C, Anguenot R, Vezina LP, Trepanier S, Michaud D. MsCYS1, a developmentally-regulated cystatin from alfalfa. Plant Physiol Biochem 2007, 45(6-7):508-514. 10.1016/j.plaphy.2007.03.028, 17507234.
102. Martinez M, Cambra I, Carrillo L, Diaz-Mendoza M, Diaz I. Characterization of the entire cystatin gene family in barley and their target cathepsin L-like cysteine-proteases, partners in the hordein mobilization during seed germination. Plant Physiol 2009, 151(3):1531-1545. 10.1104/pp.109.146019, 2773090, 19759340.
103. Kordis D, Turk V. Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes. BMC Evol Biol 2009, 9:266. 10.1186/1471-2148-9-266, 2784779, 19919722.
104. Rawlings ND, Barrett AJ, Bateman A. MEROPS: the peptidase database. Nucleic Acids Res 2010, (38 Database):D227-233. 10.1093/nar/gkp971, 2808883, 19892822.
105. Srinivasan T, Kumar KR, Kirti PB. Constitutive expression of a trypsin protease inhibitor confers multiple stress tolerance in transgenic tobacco. Plant Cell Physiol 2009, 50(3):541-553. 10.1093/pcp/pcp014, 19179349.
106. De Maria CAB, Trugo LC, Aquino Neto FR, Moreira RFA, Alviano CS. Composition of green coffee water-soluble fractions and identification of volatiles formed during roasting. Food Chem 1996, 55:203-207.
107. Leloup V, Louvrier A, Liardon R. Degradation mechanisms of chlorogenic acids during roasting. Proc Internat Congr ASIC 1995, 16:192-198.
108. Fischer M, Reimann S, Trovato V, Redgwell RJ. Polysaccharides of green Arabica and Robusta coffee beans. Carbohydr Res 2001, 330(1):93-101. 10.1016/S0008-6215(00)00272-X, 11217967.
109. Marraccini P, Rogers WJ, Allard C, Andre ML, Caillet V, Lacoste N, Lausanne F, Michaux S. Molecular and biochemical characterization of endo-beta-mannanases from germinating coffee (Coffea arabica) grains. Planta 2001, 213(2):296-308. 10.1007/s004250100541, 11469596.
110. Redgwell RJ, Trovato V, Curti D, Fischer M. Effect of roasting on degradation and structural features of polysaccharides in Arabica coffee beans. Carbohydr Res 2002, 337(5):421-431. 10.1016/S0008-6215(02)00010-1, 11861016.
111. Kasai N, Konishi A, Iwai K, Maeda G. Efficient digestion and structural characteristics of cell walls of coffee beans. J Agric Food Chem 2006, 54(17):6336-6342. 10.1021/jf0609072, 16910728.
112. Pre M, Caillet V, Sobilo J, McCarthy J. Characterization and expression analysis of genes directing galactomannan synthesis in coffee. Ann Bot 2008, 102(2):207-220. 10.1093/aob/mcn076, 2712370, 18562467.
113. Somerville C. Cellulose synthesis in higher plants. Annu Rev Cell Dev Biol 2006, 22:53-78. 10.1146/annurev.cellbio.22.022206.160206, 16824006.
114. Richmond TA, Somerville CR. The cellulose synthase superfamily. Plant Physiol 2000, 124(2):495-498. 10.1104/pp.124.2.495, 1539280, 11027699.
115. Liepman AH, Nairn CJ, Willats WG, Sorensen I, Roberts AW, Keegstra K. Functional genomic analysis supports conservation of function among cellulose synthase-like a gene family members and suggests diverse roles of mannans in plants. Plant Physiol 2007, 143(4):1881-1893. 10.1104/pp.106.093989, 1851810, 17307900.
116. Cocuron JC, Lerouxel O, Drakakaki G, Alonso AP, Liepman AH, Keegstra K, Raikhel N, Wilkerson CG. A gene from the cellulose synthase-like C family encodes a beta-1,4 glucan synthase. Proc Natl Acad Sci USA 2007, 104(20):8550-8555. 10.1073/pnas.0703133104, 1895987, 17488821.
117. Arya M, Rao LJ. An impression of coffee carbohydrates. Crit Rev Food Sci Nutr 2007, 47(1):51-67. 10.1080/10408390600550315, 17364695.
118. Chahan Y, Jordon A, Badoud R, Lindinger W. From the green bean to the cup of coffee:investing coffee roasting by on-line monitoring of volatiles. Eur Food Res Technol 2002, 214:92-104.
119. Helentjaris T, Bate NJ, Allen SM. Novel invertase inhibitors and methods of use. Patent WO/2001/058939. USA 2001,
120. Bate NJ, Niu X, Wang Y, Reimann KS, Helentjaris TG. An invertase inhibitor from maize localizes to the embryo surrounding region during early kernel development. Plant Physiol 2004, 134(1):246-254. 10.1104/pp.103.027466, 316304, 14657403.
121. Lehle L, Tanner W. The function of myo-inositol in the biosynthesis of raffinose. Purification and characterization of galactinol:sucrose 6-galactosyltransferase from Vicia faba seeds. Eur J Biochem 1973, 38(1):103-110. 10.1111/j.1432-1033.1973.tb03039.x, 4774118.
122. Rogers WJ, Michaux S, Bastin M, Bucheli P. Changes to the content of sugars, sugar alcohols, myo-inositol, carboxylic acids and inorganic anions in developing grains from different varieties of Robusta (Coffea canephora) and Arabica (C. arabica) coffees. Plant Sci 1999, 149(2):115-123.
123. Chabrillange N, Dussert S, Engelmann F, Doulbeau S, Hamon S. Desiccation tolerance in relation to soluble sugar contents in seeds of ten coffee (Coffea L.) species. Seed Sci Res 2000, 10(3):393-396.
124. Peters S, Mundree SG, Thomson JA, Farrant JM, Keller F. Protection mechanisms in the resurrection plant Xerophyta viscosa (Baker): both sucrose and raffinose family oligosaccharides (RFOs) accumulate in leaves in response to water deficit. J Exp Bot 2007, 58(8):1947-1956. 10.1093/jxb/erm056, 17452754.
125. Nishizawa A, Yabuta Y, Shigeoka S. Galactinol and raffinose constitute a novel function to protect plants from oxidative damage. Plant Physiol 2008, 147(3):1251-1263. 10.1104/pp.108.122465, 2442551, 18502973.
126. Marraccini P, Rogers WJ, Caillet V, Deshayes A, Granato D, Lausanne F, Lechat S, Pridmore D, Petiard V. Biochemical and molecular characterization of alpha-D-galactosidase from coffee beans. Plant Physiol Biochem 2005, 43(10-11):909-920. 10.1016/j.plaphy.2005.08.010, 16310367.
127. Gruber CW, Cemazar M, Heras B, Martin JL, Craik DJ. Protein disulfide isomerase: the structure of oxidative folding. Trends Biochem Sci 2006, 31(8):455-464. 10.1016/j.tibs.2006.06.001, 16815710.
128. Alvarez C, Calo L, Romero LC, Garcia I, Gotor C. An O-acetylserine(thiol)lyase homolog with L-cysteine desulfhydrase activity regulates cysteine homeostasis in Arabidopsis. Plant Physiol 2010, 152(2):656-669. 10.1104/pp.109.147975, 2815857, 19955263.
129. Marraccini P, Deshayes A, Petiard V, Rogers WJ. Molecular cloning of the complete 11 S seed storage protein gene of Coffea arabica and promoter analysis in transgenic tobacco plants. Plant Physiol Biochem 1999, 37(4):273-282.
130. Aerts RJ, Baumann TW. Distribution and Utilization of Chlorogenic Acid in Coffea Seedlings. J Exp Bot 1994, 45(273):497-503.
131. Ky CL, Louarn J, Dussert S, Guyot B, Hamon S, Noirot M. Caffeine, trigonelline, chlorogenic acids and sucrose diversity in wild Coffea arabica L. and C. canephora. Food Chem 2001, 75:223-230.
132. Stadler RH, Varga N, Milo C, Schilter B, Vera FA, Welti DH. Alkylpyridiniums. 2. Isolation and quantification in roasted and ground coffees. J Agric Food Chem 2002, 50(5):1200-1206. 10.1021/jf011235c, 11853504.
133. Mazzafera P. Catabolism of caffeine in plants and microorganisms. Front Biosci 2004, 9:1348-1359. 10.2741/1339, 14977550.
134. Baudet C, Dias Z. New EST Trimming Procedure Applied to SUCEST Sequences. Advances in Bioinformatics and Computational Biology, Proceedings 2007, 57-68.
135. Nei M, Gojobori T. Simple Methods for Estimating the Numbers of Synonymous and Nonsynonymous Nucleotide Substitutions. Mol Biol Evol 1986, 3(5):418-426.
136. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.