In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

Genetics and Molecular Biology

Volumn 33, Issue 4, 2010, Pages 795-806

  Alvarenga, Samuel Mazzinghy ^a   Caixeta, Eveline Teixeira ^a,b   Hufnagel, Bárbara ^a   Thiebaut, Flávia ^a   Maciel Zambolim, Eunize ^a   Zambolim, Laércio ^a   Sakiyama, Ney Sussumu ^a  

^a FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^b Vila Gianetti   (Brazil)

Author keywords

Bioinformatics; Coffea; Data mining; ESTs; Genomics; In silico

Indexed keywords

CATALASE; CATECHOL OXIDASE; CHALCONE SYNTHASE; CHITINASE; COMPLEMENTARY DNA; CYTOCHROME P450; GLUCAN GLUCOSIDASE; GLUCOSYLTRANSFERASE; HEAT SHOCK PROTEIN; KARYOPHERIN; PHYTOALEXIN; THAUMATIN;

ARTICLE; BIOTIC STRESS; BRAZIL; COFFEE; COMPUTER ANALYSIS; COMPUTER MODEL; CONTIG MAPPING; DATA ANALYSIS SOFTWARE; DATA MINING; DISEASE RESISTANCE; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENOME ANALYSIS; HYPERSENSITIVITY REACTION; NUCLEOTIDE BINDING SITE; PATHOGENESIS; PLANT DEFENSE; PLANT DISEASE; PLANT GENOME; PLANT PATHOGEN INTERACTION; PREDICTION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS;

COFFEA;

EID: 79251561198     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572010000400031     Document Type: Article

References (87)

1. Aarts N, Metz M, Holub E, Staskawicz BJ, Daniels MJ and Parker JE (1998) Different requirements for EDS1 and NDR1 by disease resistance genes define at least two R gene-mediated signaling pathways in Arabidopsis. Proc Natl Acad Sci USA 95:10306-10311.
2. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymero- poulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, et al. (1991) Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 252:1651-1656.
3. Allan AC and Fluhr R (1997) Two distinct sources of elicited re- active oxygen species in tobacco epidermal cells. Plant Cell 9:1559-1572.
4. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410.
5. Baker B, Zambryski P, Staskawicz B and Dinesh-Kumar SP (1997) Signaling in plant-microbe interactions. Science 276:726-733.
6. Belkhadir Y, Subramaniam R and Dangl J (2004) Plant disease re- sistance protein signaling: NBS-LRR proteins and their part-ners. Curr Opin Plant Biol 7:391-399.
7. Bendahmane A, Kanyuka K and Baulcombe DC (1999) The Rx gene from potato controls separate virus resistance and cell death responses. Plant Cell 11:781-791
8. Boller T, Métraux JP (1988) Extracellular localization of chiti-nases in cucumber. Physiol Mol Plant Pathol 33:11-16.
9. Botella MA, Parker JE, Frost LN, Bittner-Eddy PD, Beynon JL, Daniels MJ, Holub EB and Jones JDG (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10:1847-1860.
10. Cannon SB, Zhu H, Baumgarten AM, Spangler R, May G, Cook DR and Young ND (2002) Diversity, distribution, and an-cient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. J Mol Evol 54:548-562.
11. Caplan J and Dinesh-Kumar SP (2006) Recognition and signal transduction associated with R gene-mediated resistance. In: Loebenstein G and Carr JP (eds) Natural Resistance Mechanisms of Plants to Viruses. Springer, Amsterdam, pp 73-98.
12. Carazzolle MF, Formighieri EF, Digiampietri LA, Araujo MRR, Costa GGL and Pereira GAG (2007) Gene projects: A genome Web tool for ongoing mining and annotation applied to CitEST. Genet Mol Biol 30:1030-1036.
13. Chong J, Balyz R, Schitt C, Beffa R, Fritig B and Saindrenan P (2002) Downregulation of a pathogen-responsive tobacco UDP-Glc: Phenylpropanoid glucosyltransferase reduces scopoletin glucoside accumulation, enhances oxidative stress, and weakens virus resistance. Plant Cell 14:1093-1107.
14. Conesa A, Götz S, García-Gomez JM, Terol J, Talón M and Robles M (2005) Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676.
15. Dangl JL and Jones JD (2001) Plant pathogens and integrated defense responses to infection. Nature 411:826-833.
16. Dat J, Vandenabeele S, Vranová E, Montagu MV, Inzé D and Breusegem FV (2000) Dual action of the active oxygen species during plant stress responses. Cell Mol Life Sci 57:779-795.
17. Deslandes L, Olivier J, Peeters N, Feng DX, Khounlotham M, Boucher C, Somssich I, Genin S and Marco Y (2003) Physi-cal interaction between RRS1-R, a protein conferring resis- tance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proc Natl Acad Sci USA 13:8024-8029.
18. Dinesh-Kumar SP, Tham W and Baker BJ (2000) Structure- function analysis of the tobacco mosaic virus resistance gene N. Proc Natl Acad Sci USA 97:14789-14794.
19. Dixon RA, Harrison MJ and Lamb CJ (1994) Early events in the activation of plant defense responses. Annu Rev Phyto- pathol 32:479-501.
20. Dreher K and Callis J (2007) Ubiquitin, hormones and biotic stress in plants. Ann Bot 99:787-822.
21. Ellis J and Jones D (1998) Structure and function of proteins controlling strain-specific pathogen resistance in plants. Curr Opin Plant Biol 1:288-293.
22. Ellis J, Dodds P and Pryor T (2000) Structure, function and evolution of plant disease resistance genes. Curr Opin Plant Biol 3:278-284.
23. Ellis JG, Lawrence GJ, Luck JE and Dodds PN (1999) Identifica- tion of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell 11:495-506.
24. Fernandez D, Santos P, Agostini C, Bon MC, Petitot AS, Silva MC, Guerra-Guimarães L, Ribeiro A, Argout X and Nicole M (2004) Coffee (Coffea arabica L.) genes early expressed during infection by the rust fungus (Hemileia vastatrix). Mol Plant Pathol 5:527-536.
25. Feys BJ and Parker JE (2000) Interplay of signaling pathways in plant disease resistance. Trends Genet 16:449-455.
26. 2 from contingency ta-bles, and the calculation of P. J Royal Stat Soc 85:87-94.
27. Flor HH (1942) Inheritance of pathogenicity in Melampsora lini. Phytopathology 32:653-669.
28. Gai XW, Lal S, Xing LQ, Brendel V and Walbot V (2000) Gene discovery using the maize genome database ZmDB. Nucleic Acids Res 28:94-96.
29. Gassmann W, Hinsch ME and Staskawicz BJ (1999) The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes. Plant J 20:265-277.
30. Grenier J, Potvin C and Asselin A (1993) Barley pathogenesis- related proteins with fungal cell wall lytic activity inhibit the growth of yeasts. Plant Physiol 103:1277-1283.
31. Guyot R, Mare M, Viader V, Hamon P, Coriton O, Bustamante- Porras J, Poncet V, Campa C, Hamon S and Kochko A (2009) Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyle-donous sequenced genomes. BMC Plant Biol 9:22-36.
32. Guzzo SD (2004) Aspectos Bioquímicos e Moleculares da Resis- tência Sistêmica Adquirida em Cafeeiro contra Hemileia vastatrix. Centro de Energia Nuclear na Agricultura, São Paulo, 236 pp.
33. Hamel F, Boivin R, Tremblay C and Bellemare G (1997) Structural and evolutionary relationships among chitinases of flowering plants. J Mol Evol 44:614-624.
34. Hattori J, Boutilier KA, van Lookeren Campagne MM and Miki BL (1998) A conserved BURP domain defines a novel group of plant proteins with unusual primary structures. Mol Gen Genet 259:424-428.
35. Hermsmeier D, Schittko U and Baldwin IT (2001) Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. I. Large-scale changes in the accumulation of growth- and defense-related plant mRNAs. Plant Physiol 125:683-700.
36. Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moi- san A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D, et al. (1993) An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 4:1051-1061.
37. Huang X and Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868-877.
38. Jach G, Gornhardt B, Mundy J, Logemann J, Pinsdorf E, Leah R, Schell J and Maas C (1995) Enhanced quantitative resis-tance against fungal disease by combinatorial expression of different barley antifungal proteins in transgenic tobacco. Plant J 8:97-109.
39. Jackson AO and Taylor CB (1996) Plant-microbe interactions: Life and death at the interface. Plant Cell 8:1651-1668.
40. Jekel PA, Hartmann BH and Beintema JJ (1991) The primary structure of hevamine, an enzyme with lysozyme/chitinase activity from Hevea brasiliensis latex. Eur J Biochem 200:123-130.
41. Jia Y, McAdams SA, Bryan GT, Hershey HP and Valent B (2000) Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J 19:4004-4014.
42. Jones DA, Thomas CM, Hammond-Kosack KE, Balint-Kurti PJ and Jones JDG (1994) Isolation of the tomato Cf-9 gene for resistance to Cladosporiom fulvum by transposon tagging. Science 266:789-793.
43. Lamb C and Dixon RA (1997) The oxidative burst in plant disease resistance. Annu Rev Plant Physiol Plant Mol Biol 48:251-275.
44. Lazo GR, Chao S, Hummel DD, Edwards H, Crossman CC, Lui N, Matthews DE, Carollo VL, Hane DL, You FM, et al. (2004) Development of an expressed sequence tag (EST) re- source for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics 168:585-593.
45. Lin C, Mueller LA, Carthy JM, Crouzillat D, Pétiard V and 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.
46. Lupas A (1996) Coiled coils: New structures and new functions. Trends Biochem Sci 21:375-382.
47. Margis-Pinheiro M, Martin C, Didierjan L and Burkard G (1993) Differential expression of bean chitinase genes by virus in- fection, chemical treatment and UV irradiation. Plant Mol Biol 22:659-668.
48. Martin G, Brommonschenkel S, Chunwongse J, Frary A, Ganal M, Spivey R, Wu T, Earle E and Tanksley S (1993) Map- based cloning of a protein kinase gene conferring disease re- sistance in tomato. Science 262:1432-1436.
49. Melo GA, Shimizu MM and Mazzafera P (2006) Polypheno- loxidase activity in coffee leaves and its role in resistance against the coffee leaf miner and coffee leaf rust. Phyto- chemistry 67:277-285.
50. Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW and Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:317-332.
51. Noir S, Combes MC, Anthony F and Lashermes P (2001) Origin, diversity and evolution of NBS-type disease-resistance gene homologues in coffee trees (Coffea L.). Mol Genet Ge- nomics 265:654-662.
52. Pan Q, Wendel J and Fluhr R (2000) Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J Mol Evol 50:203-213.
53. Park SM, Kim DH, Truong NH and Itoh Y (2002) Heterologous expression and characterization of class III chitinases from rice (Oryza sativa L.). Enzym Microb Tech 30:697-702.
54. Parniske M, Hammondkosack KE, Golstein C, Thomas CM, Jones DA, Harrison K, Wulff BBH and Jones JDG (1997) Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 lo- cus of tomato. Cell 91:821-832.
55. Pascholati SF and Leite B (1994) Mecanismos bioquímicos de resistência às doenças. Revis Anu Patol Plantas 2:1-51.
56. Punja ZK and Zhang YY (1993) Plant chitinases and their roles in resistance to fungal diseases. J Nematol 25:526-540.
57. Qi X, Bakht S, Qin B, Leggett M, Hemmings A, Mellon F, Eagles J, Werck-Reichhart D, Schaller H, Lesot A, et al. (2006) A Coffee ESTs associated with disease resistance different function for a member of an ancient and highly conserved cytochrome P450 family: From essential sterols to plant defense. Proc Natl Acad Sci USA 103:18848-18853.
58. Resende MLV, Salgado SML and Chaves ZM (2003) Reactive oxygen species on plant defense responses to pathogens. Fitopatol Bras 28:123-130.
59. Richly E, Kurth J and Leister D (2002) Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol Biol Evol 19:76-84.
60. Richter TE and Ronald PC (2000) The evolution of disease resis- tance genes. Plant Mol Biol 42:195-204.
61. Riedle-Bauer M (2000) Role of reactive oxygen species and anti- oxidant enzymes in systemic virus infections of plants. J Phytopathol 148:297-302.
62. Roberts W and Selitrennikoff CP (1990) Zeamatin, an antifungal protein from maize with membrane-permeabilizing activity. J Genet Microbiol 136:1771-1778.
63. Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, et al. (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 131:419-429.
64. Ryder TB, Cramer CL, Bell JN, Robbins MP, Dixon RA and Lamb CJ (1984) Elicitor rapidly induces chalcone synthase mRNA in Phaseolus vulgaris cells at the onset of the phytoalexin defense response. Proc Natl Acad Sci USA 81:5724-5728.
65. Sahai AS and Manocha MS (1993) Chitinases of plants and fungi: Their involvement in morphogenesis and host-parasite interaction. FEMS Microbiol Rev 11:317-338.
66. Selitrennikoff CP (2001) Antifungal proteins. Appl Environ Microbiol 67:2883-2894.
67. Shoemaker R, Keim P, Vodkin L, Retzel E, Clifton SW, Waterston R, Smoller D, Coryell V, Khanna A, Erpelding J, et al. (2002) A compilation of soybean ESTs: Generation and analysis. Genome 45:329-338.
68. Silva MC, Várzea V, Guerra-Guimarães L, Azinheira HG, Fernandez D, Petitot A, Bertrand B, Lashermes P and Nicole M (2006) Coffee resistance to the main diseases: Leaf rust and coffee berry disease. Braz J Plant Physiol 18:119-147.
69. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai W, Zhu LH, et al. (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804-1806.
70. Staskawicz BJ, Ausubel FM, Baker BJ, Ellis JG and Jones JD (1995) Molecular genetics of plant disease resistance. Science 268:661-667.
71. Stintzi A, Heitz T, Prasad V, Wiedemann-Merdinoglu S, Kauffmann S, Geoffroy P, Legrand M and Fritig B (1993) Plant 'pathogenesis-related' proteins and their role in defense against pathogens. Biochimie 75:687-706.
72. Stoessl A (1986) Secondary plant metabolites in plant disease re- sistance. Part II: Phytoalexins. Fitopatol Bras 11:25-53.
73. Tai TH, Dahlbeck D, Clark ET, Gajiwala P, Pasion R, Whalen MC, Stall RE and Staskawicz BJ (1999) Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. Proc Natl Acad Sci USA 96:14153-14158.
74. Takemoto D, Hayashi M, Doke N, Nishimura M and Kawakita K (1999) Molecular cloning of a defense-response-related cytochrome p450 gene from tobacco. Plant Cell Physiol 40:1232-1242.
75. Thomas CM, Jones DA, Parniske M, Harrison K, Balint-Kurti PJ, Hatzixanthis K and Jones JDG (1997) Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9. Plant Cell 9:2209-2224.
76. Trudel J, Grenier J, Potvin C and Asselin A (1998) Several thaumatin-like proteins bind to -1,3-glucans. Plant Physiol 118:1431-1438.
77. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, et al. (2006) A global assembly of cotton ESTs. Genome Res 16:441-450.
78. Van Der Biezen EA, Sun J, Coleman MJ, Bibb MJ and Jones JDG (2000) Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signaling. Proc Natl Acad Sci USA 97:3747-3752.
79. Vieira LGE, Andrade AC, Colombo CA, Moraes AHA, Metha A, Oliveira AC, Labate CA, Marino CL, Monteiro-Vitorello CB, Monte DC, et al. (2006) Brazilian coffee genome project: An EST-based genomic resource. Braz J Plant Physiol 18:95-108.
80. Wang G, Ruan D, Song W, Sideris S, Chen L, Pi L, Zhang S, Zhang Z, Fauquet C, Gaut BS, et al. (1998) Xa21D encodes a receptor-like molecule with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution. Plant Cell 10:765-779.
81. 2 and is indispensable for stress defense in C3 plants. EMBO J 16:4806-4816.
82. Wolfsberg TG and Landsman DA (1997) Comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res 25:1626-1632.
83. Yamamoto K and Sasaki TL (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135-144.
84. Young ND (2000) The genetic architecture of resistance. Curr Opin Plant Biol 3:285-290.
85. Yun D, Zhao Y, Pardo JM, Narasimhan ML, Damsz B, Lee H, Abad LR, D'urzo MP, Hasegawa PM and Bressan RA (1997) Stress proteins on the yeast cell surface determine re- sistance to osmotin, a plant antifungal protein. Proc Natl Acad Sci USA 94:7082-7087.
86. Yun DJ, Ibeas JI, Lee H, Coca MA, Narasimhan ML, Uesono Y, Hasegawa PM, Pardo JM and Bressan RA (1998) Osmotin, a plant antifungal protein, subverts signal transduction to en- hance fungal cell susceptibility. Mol Cell 1:807-817.
87. Zhou N, Tootle TL and Glazebrook J (1999) Arabidopsis PAD3, a gene required for camalexin biosynthesis, encodes a puta- tive cytochrome P450 monooxygenase. Plant Cell 11:2419- 2428.