Brazilian coffee genome project: An EST-based genomic resource

Brazilian Journal of Plant Physiology

Volumn 18, Issue 1, 2006, Pages 95-108

  Esteves Vieira, Luiz Gonzaga ^a   Andrade, Alan Carvalho ^b   Colombo, Carlos Augusto ^c   De Araújo Moraes, Ana Heloneida ^b   Metha, Ângela ^b   De Oliveira, Angélica Carvalho ^b   Labate, Carlos Alberto ^d   Marino, Celso Luis ^e   Monteiro Vitorello, Claúdia De Barros ^l   Monte, Damares De Castro ^b   Giglioti, Éder ^f   Kimura, Edna Teruko ^d   Romano, Eduardo ^b   Kuramae, Eiko Eurya ^e   Macedo Lemos, Eliana Gertrudes ^e   Pereira De Almeida, Elionor Rita ^b   Jorge, Érika C ^d   Albuquerque, Érika V S ^b   Da Silva, Felipe Rodrigues Da ^b   Vinecky, Felipe ^b   Sawazaki, Haiko Enok ^c   Dorry, Hamza Fahmi A ^d   Carrer, Helaine ^d   Abreu, Ilka Nacif ^g   Batista, João A N ^b   Teixeira, João Batista ^b   Kitajima, João Paulo ^g   Xavier, Karem Guimarães ^d   De Lima, Liziane Maria ^b   Aranha De Camargo, Luis Eduardo ^d   Protasio Pereira, Luiz Filipe ^a   Coutinho, Luiz Lehmann ^d   Franco Lemos, Manoel Victor ^e   Romano, Marcelo Ribeiro ^k   Machado, Marcos Antonio ^c   Do Carmo Costa, Marcos Mota ^b   Grossi De Sá, Maria Fátima ^b   Goldman, Maria Helena S ^d   Ferro, Maria Inês T ^e   Penha Tinoco, Maria Laine ^b   Oliveira, Mariana C ^d   Van Sluys, Marie Anne ^d   Shimizu, Milton Massao ^g   Maluf, Mirian Perez ^c   Souza Da Eira, Mirian Therezinha ^h   Guerreiro Filho, Oliveiro ^c   Arruda, Paulo ^g   Mazzafera, Paulo ^g   Correa Mariani, Pilar Drummond Sampaio ^g   De Oliveira, Regina L B C ⁱ   Harakava, Ricardo ^j   Balbao, Silvia Filippi ^g   Siu, Mui Tsai ^d   Zingaretti Di Mauro, Sonia Marli ^e   Santos, Suzana Neiva ^b   Siqueira, Walter José ^c   Lacerda Costa, Gustavo Gilson ^g   Formighieri, Eduardo Fernandes ^g   Carazzolle, Marcelo Falsarella ^g   Guimarães Pereira, Gonçalo Amarante ^g   more..

^a INSTITUTO AGRONÔMICO DO PARANÁ   (Brazil)

^b EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^c INSTITUTO AGRONÔMICO   (Brazil)

^d UNIVERSITY OF SÃO PAULO   (Brazil)

^e SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^f FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

^g UNIVERSITY OF CAMPINAS   (Brazil)

^h IAC ^*  (Brazil)

ⁱ UNIVERSIDADE DE MOGI DAS CRUZES   (Brazil)

^j INSTITUTO BIOLÓGICO   (Brazil)

^k STATE UNIVERSITY OF PONTA GROSSA   (Brazil)

^l LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

more..

Author keywords

cDNA; Coffea; EST; Transcriptome

Indexed keywords

COFFEA; COFFEA ARABICA; COFFEA CANEPHORA; COFFEA RACEMOSA; RUBIACEAE;

EID: 33745381574     PISSN: 16770420     EISSN: 16770420     Source Type: Journal    
DOI: 10.1590/S1677-04202006000100008     Document Type: Short Survey

References (58)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651-1656.
2. Aldwinckle SH, Gaitan AL (2002) Constitutive and inducible promoters from coffee plants. [US Patent N° 6,441,273].
3. Aldwinckle SH, Gaitan AL, (2005) Constitutive α-tubulin promoter from coffee plants and uses thereof. [US Patent N° 6903247].
4. Aga E, Bekele E, Bryngelsson T (2005) Inter-simple sequence repeat (ISSR) variation in forest coffee trees (Coffea arabica L.) populations from Ethiopia. Genetica 124:213-221.
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman, DJ (1990) Basic local alignment search tool. J. Mol. Biol. 215:403-10.
6. Andrade AE, Albuquerque EVS, Grossi de Sá MF, Carneiro RMDG, Metha, A (2005) Expressão diferencial de proteínas em raízes de Coffea canephora infectadas com o nematóide endoparasita Meloidogyne paranaensis. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil. Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café, CD-ROM.
7. Anthony F, Combes MC, Astorga C, Bertrand B, Graziosi G, Lashermes, P (2002) The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theor. Appl. Genet. 104:894-900.
8. Arruda P (2001) Sugarcane transcriptome: a landmark in plant genomics in the tropics. In: Arruda P (ed), Special volume on Sugarcane Transcriptome. Genet. Mol. Biol. 24:1-296.
9. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9:208-218.
10. Bertrand B, Anthony F, Lashermes P (2001) Breeding for resistance to Meloidogyne exigua in Coffea arabica by introgression of resistance genes of Coffea canephora. Plant Pathol. 50:637-643.
11. Brandalise M, Maluf M.P, Guerreiro Filho O,Gonçalves W, Maia IG (2005) Caracterização de genes com expressão tecido específica em raízes e folhas de Coffea arabica. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil,Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café, CD-ROM.
12. Bridson DM, Verdcourt B (1988) Flora of tropical East Africa: Rubiaceae. (Part 2). Cape Town: Iziko Museums of Cape Town, pp.415-747.
13. Charrier A, Berthaud J (1985) Botanical classification of coffee. In: Clifford MN, Wilson KC (eds), Coffee: botany, biochemistry and production of beans and beverage, pp.13-47. Croom Helm, London, Sydney.
14. Chenwei, L, Mueller, LA, Mc Carthy, J, Crouzillat, D, Pétiard, V, Tanksley, SD (2005). Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts, Theor. Appl. Genet. 112:114-130.
15. Chevalier A, Dagron M (1928) Recherches historiques sur les débuts de la culture du caféier en Amérique. Communications et Actes de Ácadémie des Sciences Coloniales, Paris.
16. Carvalho A, Fazuoli LC (1993) O melhoramento de plantas no Instituto Agronômico. In: Furlani AMC, Viégas GP (eds), Café. pp.29-76. Campinas, Brasil
17. Carvalho A (1945) Distribuição geográfica e classificação botânica do gênero Coffea com referência especial à espécie Arabica. Bol. Superint. Serv. Café. 21:174-180.
18. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194.
19. Ewing B, Hillier L, Wend MC, Green P (1998) Basecalling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185.
20. Gaspari-Pezzopane C, Maluf MP, Pinto FO (2005) Expressão gênica diferencial em frutos de Coffea arabica L. em diferentes estádios de desenvolvimento e maturação. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil, Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café, CD-ROM.
21. Geromel C, Ferreira LP, Cavalari AA, Pereira LFP, Vieira LGE, Leroy T, Mazzafera P, Marraccini, P (2005) Metabolismo de açúcares durante o desenvolvimento de frutos de café. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil, Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café, CD-ROM.
22. Guerreiro Filho O, Medina Filho HP, Carvalho A (1991) Fontes de resistência ao bicho-mineiro. Perileucoptera coffeella em Coffea sp. Bragantia 50:45-55.
23. Hajduch M, Ganapathy A, Stein JW, Thelen JJ (2005) A Systematic Proteomic Study of Seed Filling in Soybean. Establishment of High-Resolution Two-Dimensional Reference Maps, Expression Profiles, and an Interactive Proteome Database Plant Physiol. 137:1397-1419.
24. Hatanaka T, Choi YE, Kusano T, Sano H (1999) Transgenic plants of Coffea canephora from embryogenic callus via Agrobacterium tumefaciens-mediated transformation. Plant Cell Rep. 19:106-110.
25. Herrera JC, Combes MC, Cortina H, Lashermes P (2004) Factors influencing gene introgression into the allotetraploid Coffea arabica L. from its diploid relatives. Genome 47:1053-1060.
26. Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D, Giraudat J, Quigley F, Thomas F, Yu DY, Mache R, Raynal M, Cooke R, Grellet F, Delseny M, Parmentier Y, Marcillac G, Gigot C, Fleck J, Philipps G, Axelos M, Bardet C, Tremousaygue D, Lescure B (1993) An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J. 4:1051-1061.
27. Huang X, Madan A (1999) CAP3: A DNA assembly program. Genome Res. 9:868-877.
28. Khun E (2001) From library screening to microarray technology: Strategies to determine gene expression profiles and to identify differentially regulated genes in plants. Ann. Bot. 87:139-155.
29. Krug CA, Mendes JET, Carvalho A (1938) Taxonomia de Coffea arabica L. Descrição das variedades e formas encontradas no Estado de São Paulo. Boletim Técnico do Instituto Agronômico. Campinas, Brasil, 62:1-57.
30. Lashermes P, Cros J, Marmey P, Charrier A (1993) Use of random amplified DNA markers to analyze genetic variability and relationships of Coffea species. Genet. Res. Crop Evol. 40:91-99.
31. Lashermes P, Cros J, Combes MC, Trouslot P, Anthony F, Hamon S, Charrier A (1996) Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. Theor. Appl. Genet. 93:626-632.
32. Lashermes P, Combes MC, Trouslot P, Charrier A (1997) Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor. Appl. Genet. 94:947-955.
33. Lashermes P, Combes MC, Robert J, Trouslot P, D'Hont A, Anthony F, Charrier A (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol. Gen. Genet. 261:259-266.
34. Leroy T, Henry AM, Royer M, Altosar I, Frutos R, Duris D, Philippe R (2000) Genetically modified coffee plants expressing the Bacillus thuringiensis cry1Ac gene for resistance to leaf miner. Plant Cell Rep. 19:382-389.
35. Leroy T, Marraccini, P, Dufour, M, Montagnon, C, Lashermes, P., Sabau, X., Ferreira L.P., Jourdan, I., Pot, D., Andrade A. C., Glaszmann, J.C., Vieira, L.G. E. and Piffanelli P. (2005). Construction and characterization of a Coffea canephora BAC library to study the organization of sucrose biosynthesis genes. Theor. Appl. Genet. 111:1032-1041.
36. Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature, 405:827-836.
37. Maluf MP, Silvestrini M, Ruggiero LCM, Guerreiro Filho O, Colombo CA (2005) Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems. Sci. Agric. 62:366-373.
38. Marraccini P, Deshayes A, Petiard V, Rogers WJ (1999) Molecular cloning of the complete 11S seed storage protein gene of Coffea arabica and promoter analysis in transgenic tobacco plants. Plant Physiol. Biochem. 37:273-282.
39. Marraccini P, Courjault C, Caillet V, Lausanne F, Lepage B, Rogers WJ, Tessereau S, Deshayes A (2003) Rubisco small subunit of Coffea arabica: cDNA sequence, gene cloning and promoter analysis in transgenic tobacco plants. Plant Physiol. Biochem. 41:17-25.
40. Noir S, Patheyron S, Combes MC, Lashermes P, Chalhoub B (2004) Construction and characterization of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.). Theor. Appl. Genet. 109:225-230.
41. Ogita S, Uejuji H, Yamaguchi Y, Koizumi N, Sano H (2003) RNA interference: Producing decaffeinated coffee plants. Nature 423:823.
42. Pereira A (2000) A transgenic perspective on plant functional genomics. Transgenic Res. 9:245-260.
43. Pearl HM, Nagai C, Moore PH, Steiger DL, Osgood RV, Ming R (2004) Construction of a genetic map for arabica coffee. Theor. Appl. Genet. 108:829-835.
44. Prakash NS, Combes MC, Somanna N, Lashermes P (2002) AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid. Euphytica 124:265-271.
45. Prakash NS, Marques DV, Varzea VMP, Silva MC, Combes MC, Lashermes P (2004) Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into C. arabica L. Theor. Appl. Genet. 109:1311-1317.
46. Prakash N, Combes MC, Dussert S, Naveen S, Lashermes P (2005) Analysis of genetic diversity in Indian robusta coffee genepool (Coffea canephora) in comparison with a representative core collection using SSRs and AFLPs. Genet. Resour. Crop Evol. 52:333-343.
47. Ribas AF, Kobayashi AK, Pereira LFP, Vieira, LGE (2005) Genetic transformation of Coffea canephora P. by particle bombardment. Biol. Plant. 49:493-497.
48. Ribas, A.F., Kobayashi, A.K., Pereira, L.F.P. and Vieira, L.G.E. (2006). Production of herbicide-resistant coffee plants (Coffea canephora P.) via Agrobacterium tumefaciens-mediated transformation. Brazil. Arch. Biol. Technol. (accepted for publication).
49. Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JG, Kerlavage AR (1996) The construction of Arabidopsis expressed sequence tag assemblies. Plant Physiol. 112:1177-1183.
50. Rufino RJN, Caixeta ET, Zambolim EM, Pena GF, Almeida RF, Alavarenga SM, Zambolim L, Sakaiyama NS (2005) Microsatellite markers for coffee tree. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil.Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café. CD-ROM.
51. Sales RMOB, Andrade AC, da Silva FR (2005) Determinação do Unigene do Projeto Genoma Café. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café. CD-ROM.
52. Satyanarayana KV, Kumar V, Chandrashekar A, Ravishankar GA (2005) Isolation of promoter for N-methyltransferase gene associated with caffeine biosynthesis in Coffea canephora. J. Biotech. 119:20-25.
53. Sera T, Ruas PM, Ruas CD, Diniz LEC, Carvalho VD, Rampim L, Ruas EA, Silveira SR (2003) Genetic polymorphism among 14 elite Coffea arabica L. cultivars using RAPD markers associated with restriction digestion. Genet. Mol. Biol. 1:59-64.
54. Telles GP, da Silva FR (2001) Trimming and clustering sugarcane ESTs. Gen. Mol. Biol. 24:17-23.
55. Vincent D, Lapierre C, Pollet B, Cornic G, Negroni L, Zivy M (2005) Water deficits affect caffeate O-methyltransferase, lignification, and related enzymes in maize leaves. A proteomic investigation. Plant Physiol. 137: 949-960.
56. Vinecky F, Brito KM, da Silva FR, Andrade AC (2005) Análise in silico de genes potencialmente envolvidos na resposta aos estresses abióticos presentes na base de dados do Genoma Café. In: Anais do IV Simpósio de Pesquisa dos Cafés do Brasil. Londrina, Brasil. Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café. CD-ROM.
57. Yamamoto K, Sasaki TL (1997). Large-scale EST sequencing in rice. Plant Mol. Biol. 35:135-144.
58. Wolfsberg TG, Landsman D (1997) A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res. 25:1626-1632.