In silico of resistance (R) genes in Eucalyptus transcriptome

Genetics and Molecular Biology

Volumn 28, Issue 3 SUPPL., 2005, Pages 562-574

  Barbosa da Silva, Adriano ^a   Wanderley Nogueira, Ana C ^a   Silva, Raphaela R M ^a   Berlarmino, Luiz C ^a   Soares Cavalcanti, Nina M ^a   Benko Iseppon, Ana M ^a  

^a DEPARTAMENTO DE MICOLOGIA   (Brazil)

Author keywords

Gene for gene interaction; Leucine rich repeats; Nucleotide binding site; Serine threonine kinase

Indexed keywords

PROTEIN SERINE THREONINE KINASE; TRANSCRIPTOME;

ARABIDOPSIS; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; CROP; EUCALYPTUS; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC TRAIT; GENOME; GYMNOSPERM; HIGHER PLANT; IMMUNE RESPONSE; NONHUMAN; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PLANT BREEDING; PLANT DEFENSE; PLANT GENETICS; RICE; SCOTS PINE; SEQUENCE ALIGNMENT;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRASSICACEAE; DICOTYLEDONEAE; EMBRYOPHYTA; EUCALYPTUS; GYMNOSPERMAE; LILIOPSIDA; ORYZA SATIVA; PINUS SYLVESTRIS;

EID: 30844439646     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/s1415-47572005000400011     Document Type: Article

References (83)

1. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Mille W and Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
3. Ballvora A, Ercolano MR, Weiss J, Meksem K, Bormann CA, Oberhagemann P, Salamini F and Gebhardt C (2002) The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/ LRR class of plant resistance genes. Plant J 30:361-371.
4. Barber PA, Smith IW and Keane PJ (2003) Foliar diseases of Eucalyptus spp. grown for ornamental cut foliage. Austral Plant Pathol 32:109-111.
5. Bendahmane A, Kohn BA, Dedi C and Baulcombe DC (1995) The coat protein of potato virus X is a strain-specific elicitor of Rx1-mediated virus resistance in potato. Plant J 8:933-941.
6. Bendahmane A, Querci M, Kanyuka K and Baulcombe DC (2000) Agrobacterium transient expression system as a tool for the isolation of disease resistance genes: Application to the Rx2 locus in potato. Plant J 21:73-81.
7. Benko-Iseppon AM, Winter P, Huettel B, Staginnus C, Muehlbauer FJ and Kahl G (2003) Molecular markers closely linked to fusarium resistance genes in chickpea show significant alignments to pathogenesis-related genes located on Arabidopsis chromosomes 1 and 5. Theor Appl Genet 107:379-386.
8. Bennett MD (1972) Nuclear DNA content and minimum generation time in herbaceous plants. Proc R Soc Lond Bot 181:109-135.
9. Bennet MD and Leitch IJ (1995) Nuclear DNA Amounts in Angiosperms. Ann Bot 76:113-176.
10. Bennet MD and Leitch, IJ (2000) Variation in nuclear DNA amount (C-value) in monocots and its significance. In: Wilson KL and Morrison DA (eds) Monocots: Systematics and Evolution. 1st edition. CSIRO Publishers, Sydney, pp 137-146.
11. Bittner-Eddy PD, Crute IR, Holub EB and Beynon JL (2000) RPP 13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica. Plant J 21:177-88.
12. Bonas U and Lahaye T (2002) Plant disease resistance triggered by pathogen-derived molecules: Refined models of specific recognition. Curr Opin Microbiol 5:44-50.
13. Botella MA, Parker JE, Frost LN, Bittner-Eddy PD, Beynon JL, Daniels MJ, Holub EB and Jones JD (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10:1847-1860.
14. Boyes DC, Nam J and Dangl JL (1998) The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proc Natl Acad Sci USA 95:15849-15854.
15. BRACELPA (2004), Associação Brasileira de Celulose e Papel. Brazil. Available from World Wide Web: http://www.bracelpa.org.br, release date 20/March/2004, cited 25/April/ 2004.
16. Brommonschenkel SH, Frary A and Tanksley SD (2000) The broad-spectrum tospovirus resistance gene Sw-5 of tomato is a homolog of the root-knot nematode resistance gene Mi. Mol Plant-Microbe Interact 13:1130-38.
17. Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, Faulk KN, Donaldson GK, Tarchini R and Valent B (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033-2046.
18. Buschges R, Holtricher K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, Diergaarde P, Groenendijk J, Topsch S, Vos P, Salamini F and Schulze-Lefert P (1997) The barley Mlo gene: A novel control element of plant pathogen resistance. Cell 88:695-705.
19. Chinnaiyan AM, Chaudhary D, O'Rourke K, Koonin E and Dixit M (1997) Role of CED-4 in the activation of CED-3. Nature 388:728-729.
20. Collins N, Drake J, Ayliffe M, Sun Q, Ellis J, Hulbert S and Pryor T (1999) Molecular characterization of the maize Rp1-D rust resistance haplotype and its mutants. Plant Cell 11:1365-1376.
21. Dixon MS, Jones JGD, Keddie JS, Thomas CM, Harisson K and Jones JGD (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell 84:451-459.
22. Dixon MS, Hatzixanthis K, Jones DA, Harisson K and Jones JGD (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number. Plant Cell 10: 1915-1925.
23. Dodds P, Lawrence G and Ellis J (2001) Six amino acid changes confined to the leucine-rich repeat beta-strand/beta-turn motif determine the difference between the P and P2 rust resistance specificities in flax. Plant Cell 13:163-78.
24. Ehrendorfer F (1982) Speciation patterns in woody angiosperms of tropical origin. In: Barigozzi C (ed) Mechanisms of Speciation. Alan R. Liss. Inc., New York, pp 479-509.
25. 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.
26. Ellis JG, Lawrence GJ, Luck JE and Dodds N (1999) Identification of regions in alleles of the flax rust resistance gene L that determines differences in gene-for-gene specificity. Plant Cell 11:495-506.
27. Ellis J, Dodds P and Pryor T (2000a) The generation of plant disease resistance genes specificities. Trends Plant Sci 5:373-379.
28. Ellis J, Dodds P and Pryor T (2000b) Structure, function and evolution of plant disease resistance genes. Curr Opin Plant Biol 3:278-284.
29. Emanuelsson O, Nielsen H, Brunak B and von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005-1016.
30. Ernst K, Kumar A, Kriseleit D, Kloos DU, Phillips MS and Ganal MW (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J 31:127-136.
31. Flor HH (1956) The complementary genetic systems in flax and flax rust. Adv Genet 8:29-54.
32. Flor HH (1971) Current status of the gene-for-gene concept. Annu Rev Plant Pathol 9:275-296.
33. Gassmann W, Hinsch ME and Staskawicz BJ (1999) The Arabidopsis PPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes. Plant J 20:265-277.
34. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N. Robinson R, Feldhaus J, Macalma T, Oliphant A and Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100.
35. Grant MR, Godiard L, Straube E, Ashfield T, Lewald J, Sattler A, Innes RW and Dangl JL (1995) Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science 269:843-846.
36. Halterman D, Zhou F, Wei F, Wise RP and Schulze-Lefert P (2001) The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria graminis f. sp. hordei in barley and wheat. Plant J 3:335-348.
37. James WC, Teng PS and Nutter FW (1990) Estimated losses of crops from plant pathogens. In: Pimentel D (ed) CRC Handbook of Pest Management, CRC Press, Boca-Raton, pp 15-50.
38. Johal GS and Briggs SP (1992) Reductase activity encoded by the HM1 disease resistance gene in maize. Science 158:958-987.
39. Jones DA, Thomas CM, Hammond-Kosac KE, Balint-Kurti J and Jones JGD (1994) Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266:789-793.
40. Jones DG (2001) Putting the knowledge of plant disease resistance genes to work. Curr Opin Plant Biol 4:281-287.
41. Jones JB, Stall RE and Bouzar H (1998) Diversity among xanthomonads pathogenic on pepper and tomato. Ann Rev Phytopathol 36:41-58.
42. Joosten MH, Cozijnsen TJ and De Wit PJ (1994) Host resistance to a fungal tomato pathogen lost by a single base-pair change in an avirulence gene. Nature 367:384-386.
43. Koczyk G and Chelkowski J (2003) An assessment of the resistance gene analogues of Oryza sativa ssp. japonica, their presence and structure. Cell Mol Biol Lett 8:963-972.
44. Koonin EV and Aravind L (2000) The NACHT family - A new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem Sci 25:223-224.
45. Lawrence GJ, Finnegan EJ, Ayliffe MA and Ellis JG (1995) The L6 gene for flax rust resistance is related to Arabidopsis bacterial resistance gene RPP2 and tobacco viral gene N. Plant Cell 7:1195-1206.
46. Mafia RG and Alfenas AC (2003) Diferenciação sintornatológica de manchas foliares em Eucalyptus spp. causadas por patógenos fúngicos c bacterianos. Fitopatol Bras 28:688-688.
47. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY and Bryant SH (2002) CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucl Acids Res 30:281-283.
48. Martin GB (1999) Functional analysis of plant disease resistance genes and their downstream effectors. Curr Opin Plant Biol 2:273-279.
49. Martin GB, de Vicente MC and Tanksley SD (1993) Hight resolution linkage analysis and physical characterization of the Pto bacterial locus in tomato. Mol Plant-Microbe Interact 6:26-34.
50. Martin GB, Bogdanove AJ and Sessa G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Physiol Plant Mol Biol 54:23-61.
51. McDowell JM, Dhandaydham M, Long TA, Aarts MG, Goff S, Holub EB and Dangl JL (1998) Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10: 1861-1874.
52. McNabb K (2002) Clonal propagation of Eucalyptus in Brazilian nurseries. In: Dumroese RK, Riley LE and Landis TD (eds) National Proceedings: Forest and Conservation Nursery Associations. USDA Forest Service, Rocky Mountain Research Station, Ogden, pp 165-168.
53. Meyers BC, Chin DB, Shen KA, Sivaramakrishnan S, Lavelle DO, Zhang Z and Michelmore RW (1998) The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell 10: 1817-32.
54. Meyers BC, Dickcman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW and Young ND (1999) Plant disease resistance genes encodes members of an ancient and diverse protein family within the nucleotide-biding superfamily. Plant J 20:317-332.
55. Meyers BC, Kozik A, Griego A, Kuang H and Michelmore RW (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15:809-834.
56. Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P and Williamson VM (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 10:1307-19.
57. Mindrinos M, Katagiri F, Yu GL and Ausubel FM (1994) The A. thaliana disease resistance gene RPS2 encodes a protein containing a nucleotide-biding site and leucine-rich repeats. Cell 78:1089-1099.
58. Morais DAL (2003) Análise bioinformática de genes de resistência a patógenos no genoma da cana-de-açúcar. Master Dissertation, Universidade Federal de Pernambuco, Recife.
59. Morawetz W (1984) How stable are genomes of tropical woody plants? Heterozygosity in C-banded Karyotypes of Porcelia as compared with Annona (Annonaceae) and Drymys (Winteraceae). Pl Syst Evol 145:29-39.
60. Morawetz W (1986) Remarks on karyological differentiation patterns in tropical woody plants. Pl Syst Evol 152:49-100.
61. Myburg AA, Griffin AR, Sederoff RR and Whetten RW (2003) Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach. Theor Appl Genet 107:1028-1042.
62. Noel L, Moores TL, van Der Biezen EA, Parniske M, Daniels MJ, Parker JE and Jones JD (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11:2099-2112.
63. Ori N, Eshed Y, Paran I, Presting G, Aviv D, Tanksley S, Zamir D and Fluhr R (1997) The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat superfamily of plant resistance genes. Plant Cell 9:521-532.
64. Pan Q, Liu YS, Budai-Hadrian O, Sela M, Carmel-Goren L, Zamir D and Fluhr R (2000) Comparative genetics of nucleotide binding site leucine-rich repeat resistance gene homologues in the genomes of two dycotyledons: Tomato and Arabidopsis. Genetics 155:309-322.
65. Parker JE, Coleman MJ, Dean C and Jones JGD (1997) The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the Toll and interleukin-1 receptors with N and L6. Plant Cell 9:879-894.
66. Piffanelli P, Zhou F, Casais C, Orme J, Jarosch B, Schaffrath U, Collins NC, Panstruga R and Schulze-Lefert P (2002) The barley MLO modulator of defense and cell death is responsive to biotic and abiotic stress stimuli. Plant Physiol 129:1076-1085.
67. 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.
68. Richter TE and Ronald PC (2000) The evolution of disease resistance genes. Plant Mol Biol 42:195-204.
69. Romeis T (2001) Protein kinases in the plant defense response. Curr Opin Plant Biol 4:407-414.
70. Rommens CM and Kishore GM (2000) Exploiting the full potential of disease resistance genes for agricultural use. Curr Opin Biotechnol 11:120-125.
71. Ronald PC (1997) The molecular basis of disease resistance in rice. Plant Mol Biol 35:179-186.
72. Simmons G, Groenendijik J, Wijbrandi J, Reijans M, Groenen J, Diergaarde van der Lee T, Bleeker M, Onstenk J, De Both M, Haring M, Mes J, Cornelissen B, Zabue M and V os P (1998) Dissection of the fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. Plant Cell 10:1055-1068.
73. Song WY, Pi LY, Wang GL, Gardner J, Holsten T and Ronald PC (1997) Evolution of the rice Xa21 disease resistance genes family. Plant Cell 9:1279-1287.
74. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C and Ronald PC (1995) A receptor kinase-like protein encoded by the rice disease resistance gene Xa21. Science 270:1804-1806.
75. The Arabidopsis Genome Iniciative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
76. Thomas CM, Jones DA, Parniske M, Harrison K, Balint-Kurti PJ, Hatzixanthis K and Jones JD (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.
77. van der Biezen EA and Jones JGD (1998) The NB-ARC domais: A novel signaling motif shared by plant resistance gene products and regulators of cell death in animals. Curr Biol 8:R226-R227.
78. van der Biezen EA, Freddie CT, Kahn K, Parker JE and Jones JD (2002) Arabidopsis RPP4 is a member of the RPP5 multigene family of TIR-NB-LRR genes and confers downy mildew resistance through multiple signaling components. Plant J 29:439-51.
79. van der Vossen EA, van der Voort JN, Kanyuka K, Bendahmane A, Sandbrink H, Baulcombe DC, Bakker J, Stiekema WJ and Klein-Lankhorst RM (2000) Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogens: A virus and a nematode. Plant J 23:567-576.
80. Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L, Hayasaka H, Katayose Y and Sasaki T (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19:55-64.
81. Whithan S, McCormick S and Baker B (1996) The N gene of tobacco confers resistance to tobacco mosaic virus in transgenic tomato. Proc Natl Acad Sci USA 93:8776-81.
82. Xiao S, Ellwood S, Calis O, Patrick E, Li T, Coleman M and Turner JG (2001) Broad-spectrum mildew resistance in Arabidopsis thaliana mediated by RPW8. Science 291:118-20.
83. Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, Kono I, Kurata N, Iwata N and Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663-1668.