Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis

Genetics and Molecular Research

Volumn 6, Issue 4, 2007, Pages 866-889

  Wanderley Nogueira, A C ^a   Soares Cavalcanti, N M ^a   Morais, D A L ^a   Belarmino, L C ^a   Barbosa Silva, A ^a   Benko Iseppon, A M ^a  

^a FEDERAL UNIVERSITY OF PERNAMBUCO   (Brazil)

Author keywords

Defense; Expression profile; Kinase; NBS LRR; Pathogens; Saccharum

Indexed keywords

INTERLEUKIN 1 RECEPTOR; LEUCINE; TOLL LIKE RECEPTOR 1; TRANSCRIPTOME;

BREEDING; CLUSTER ANALYSIS; COMPUTER MODEL; CONFERENCE PAPER; FLOWER; GENE EXPRESSION; GENE INTERACTION; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GRASS; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PLANT; PLANT ROOT; PREVALENCE; SCREENING; SUGARCANE; TRANSCRIPTOMICS;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; IMMUNITY, NATURAL; PHYLOGENY; PLANT DISEASES; REGULATORY SEQUENCES, NUCLEIC ACID; SACCHARUM; VARIATION (GENETICS);

DICOTYLEDONEAE; ORYZA SATIVA; POACEAE; SACCHARUM; ZEA MAYS;

EID: 37349047099     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (88)

1. Altschul SF, Gish W, Miller W, Myers EW, et al. (1990). Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Anderson JC, Pascuzzi PE, Xiao F, Sessa G, et al. (2006). Host-mediated phosphorylation of type III effector AvrPto promotes Pseudomonas virulence and avirulence in tomato. Plant Cell 18: 502-514.
3. Bai J, Pennill LA, Ning J, Lee SW, et al. (2002). Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res. 12: 1871-1884.
4. Barbosa da Silva A, Wanderley-Nogueira AC, Silva RRM, Belarmino LC, et al. (2005). In silico survey of resistance (R) genes in Eucalyptus transcriptome. Genet. Mol. Biol. 28: 562-574.
5. Bastian F, Cohen A, Piccoli P, Luna V, et al. (1998). Production of indole-3-acetic acid and gibberellins A(1) and A(3) by Gluconacetobacter diazotrophicus and Herbaspirillum seropedicae in chemically-defined culture media. Plant Growth Regul. 24: 7-11.
6. Benko-Iseppon AM, Winter P, Huettel B, Staginnus C, et al. (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.
7. Bent AF (1996). Plant disease resistance genes: function meets structure. Plant Cell 8: 1757-1771.
8. Bittner-Eddy PD, Crute IR, Holub EB and Beynon JL (2000). RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica. Plant J. 21: 177-188.
9. Bonas U and Van den Anckerveken G (1999). Gene-for-gene interactions: bacterial avirulence proteins specify plant disease resistance. Curr. Opin. Microbiol. 2: 94-98.
10. Borevitz JO and Ecker JR (2004). Plant genomics: the third wave. Annu. Rev. Genomics Hum. Genet. 5: 443-477.
11. Botella MA, Parker JE, Frost LN, Bittner-Eddy PD, et al. (1998). Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10: 1847-1860.
12. Brommonschenkel SH, Frary A, 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: 1130-1138.
13. Bryan GT, Wu KS, Farrall L, Jia Y, et al. (2000). A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12: 2033-2046.
14. Chinnaiyan AM, Chaudhary D, O'Rourke K, Koonin EV, et al. (1997). Role of CED-4 in the activation of CED-3. Nature 388: 728-729.
15. Dixon MS, Jones DA, Keddie JS, Thomas CM, et al. (1996). The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell 84: 451-459.
16. Dodds PN, Lawrence GJ and Ellis JG (2001). Six amino acid changes confined to the leucine-rich repeat betastrand/beta-turn motif determine the difference between the P and P2 rust resistance specificities in flax. Plant Cell 13: 163-178.
17. Eisen MB, Spellman PT, Brown PO and Botstein D (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868.
18. Ellis J and Jones D (2000). Structure and function of proteins controlling strain-specific pathogen resistance in plants. Curr. Opin. Plant Biol. 1: 288-293.
19. Ellis JG, Lawrence GJ, Luck JE and Dodds PN (1999). Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell 11: 495-506.
20. Ernst K, Kumar A, Kriseleit D, Kloos DU, et al. (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.
21. Expert Protein Analysis System (ExPASy). http://expasy.org. Accessed May 25, 2006.
22. Ewing RM, Ben KA, Poirot O, Lopez F, et al. (1999). Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9: 950-959.
23. Flor HH (1956). The complementary genetic systems in flax and flax rust. Adv. Genet. 8: 29-54.
24. Flor HH (1971). Current status of the gene-for-gene concept. Annu. Rev. Plant Pathol. 9: 275-296.
25. Fuentes-Ramirez LE, Jimenez-Salgado T, Abarca-Ocampo IR and Caballero-Mellado J (1993). Gluconacetobacter diazotrophicus, an indole acetic acid-producing bacterium isolated from sugarcane cultivars in Mexico. Plant Soil 154: 145-150.
26. 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.
27. Grant MR, Godiard L, Straube E, Ashfield T, et al. (1995). Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science 269: 843-846.
28. Grivet L and Arruda P (2001). Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr. Opin. Plant Biol. 5: 122-127.
29. Hammond-Kosack KE and Jones JD (1996). Resistance gene-dependent plant defense responses. Plant Cell 8: 1773-1791.
30. Johal GS and Briggs SP (1992). Reductase activity encoded by the HM1 disease resistance gene in maize. Science 258: 985-987.
31. Jones DG (2001). Putting the knowledge of plant disease resistance genes to work. Curr. Opin. Plant Biol. 4: 281-287.
32. Jones DA, Thomas CM, Hammond-Kosack KE, Balint-Kurti PJ, et al. (1994). Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266: 789-793.
33. 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.
34. Kruijt M, Kip DJ, Joosten MH, Brandwagt BF, et al. (2005). The Cf-4 and Cf-9 resistance genes against Cladosporium fulvum are conserved in wild tomato species. Mol. Plant Microbe Interact. 18: 1011-1021.
35. Ku HM, Vision T, Liu J and Tanksley SD (2000). Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA 97: 9121-9126.
36. Kumar S, Tamura K and Nei M (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163.
37. Lambais MR (2001). In silico differential display of defense-related expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes. Genet. Mol. Biol. 24: 1-4.
38. Lawrence GJ, Finnegan EJ, Ayliffe MA and Ellis JG (1995). The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene RPS2 and the tobacco viral resistance gene N. Plant Cell 7: 1195-1206.
39. Lee S, Reth A, Meletzus D, Sevilla M, et al. (2000). Characterization of a major cluster of nif, fix, and associated genes in a sugarcane endophyte, Acetobacter diazotrophicus. J. Bacteriol. 182: 7088-7091.
40. Liu JJ and Ekramoddoullah AK (2003). Isolation, genetic variation and expression of TIR-NBS-LRR resistance gene analogs from western white pine (Pinus monticola Dougl. ex. D. Don.). Mol. Genet. Genomics 270: 432-441.
41. Loh YT and Martin GB (1995). The Pto bacterial resistance gene and the Fen insecticide sensitivity gene encode functional protein kinases with serine/threonine specificity. Plant Physiol. 108: 1735-1739.
42. Lu YH, D'Hont A, Paulet F, Grivet L, et al. (1994). Molecular diversity and genome structure in modern sugarcane varieties. Euphytica 78: 217-226.
43. McDowell JM, Dhandaydham M, Long TA, Aarts MG, et al. (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.
44. Mestre P and Baulcombe DC (2006). Elicitor-mediated oligomerization of the tobacco N disease resistance protein. Plant Cell 18: 491-501.
45. Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, et al. (1999). Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 20: 317-332.
46. Meyers BC, Kozik A, Griego A, Kuang H, et al. (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809-834.
47. Meyers BC, Kaushik S and Nandety RS (2005). Evolving disease resistance genes. Curr. Opin. Plant Biol. 8: 129-134.
48. Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, et al. (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: 1307-1319.
49. Mindrinos M, Katagiri F, Yu GL and Ausubel FM (1994). The A. thaliana disease resistance gene RPS2 encodes a protein containing a nucleotide-binding site and leucine-rich repeats. Cell 78: 1089-1099.
50. Monosi B, Wisser RJ, Pennill L and Hulbert SH (2004). Full-genome analysis of resistance gene homologues in rice. Theor. Appl. Genet. 109: 1434-1447.
51. National Center for Biotechnology Information (NCBI). http://www.ncbi.nlm.nih.gov. Accessed June 7, 2006.
52. Nelson RR (1972). Stabilizing racial populations of plant pathogens by use of resistance genes. J. Environ. Qual. 3: 220-227.
53. Nogueira EM, Vinagre F, Masuda HP, Vargas C, et al. (2001). Expression of sugarcane genes induced by inoculation with Gluconacetobacter diazotrophicus and Herbaspirillum rubrisubalbicans. Genet. Mol. Biol. 24: 1-4.
54. Ohtsuki A and Sasaki A (2006). Epidemiology and disease-control under gene-for-gene plant-pathogen interaction. J. Theor. Biol. 238: 780-794.
55. Ori N, Eshed Y, Paran I, Presting G, et al. (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.
56. Page RD (1996). TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357-358.
57. 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.
58. Parker JE, Coleman MJ, Szabo V, Frost LN, et al. (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.
59. Piffanelli P, Zhou F, Casais C, Orme J, et al. (2002). The barley MLO modulator of defense and cell death is responsive to biotic and abiotic stress stimuli. Plant Physiol. 129: 1076-1085.
60. Pryor T and Ellis J (1993). The genetic complexity of fungal resistance genes in plants. Adv. Plant Pathol. 10: 281-305.
61. Rehmany AP, Gordon A, Rose LE, Allen RL, et al. (2005). Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. Plant Cell 17: 1839-1850.
62. Reinhold-Hurek B and Hurek T (1998). Life in grasses: diazotrophic endophytes. Trends Microbiol. 6: 139-144.
63. Richter TE and Ronald PC (2000). The evolution of disease resistance genes. Plant Mol. Biol. 42: 195-204.
64. Rommens CM and Kishore GM (2000). Exploiting the full potential of disease-resistance genes for agricultural use. Curr. Opin. Biotechnol. 11: 120-125.
65. Rose LE, Langley CH, Bernal AJ and Michelmore RW (2005). Natural variation in the Pto pathogen resistance gene within species of wild tomato (Lycopersicon). I. Functional analysis of Pto alleles. Genetics 171: 345-357.
66. Rossi M, Araujo PG, Paulet F, Garsmeur O, et al. (2003). Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol. Genet. Genomics 269: 406-419.
67. Salmeron JM, Oldroyd GE, Rommens CM, Scofield SR, et al. (1996). Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster. Cell 86: 123-133.
68. Salvaudon L, Heraudet V and Shykoff JA (2005). Parasite-host fitness trade-offs change with parasite identity: genotype-specific interactions in a plant-pathogen system. Evol. Int. J. Org. Evol. 59: 2518-2524.
69. Sevilla M, Burris RH, Gunapala N and Kennedy C (2001). Comparison of benefit to sugarcane plant growth and 15N2 incorporation following inoculation of sterile plants with Acetobacter diazotrophicus wild-type and Nifmutants strains. Mol. Plant Microbe Interact. 14: 358-366.
70. Song WY, Wang GL, Chen LL, Kim HS, et al. (1995). A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270: 1804-1806.
71. Song WY, Pi LY, Wang GL, Gardner J, et al. (1997). Evolution of the rice Xa21 disease resistance gene family. Plant Cell 9: 1279-1287.
72. Sugarcane EST Genome Project (SUCEST). http://sucest.lad.dcc.unicamp.br. Accessed May 2, 2006.
73. Tang X, Xie M, Kim YJ, Zhou J, et al. (1999). Overexpression of Pto activates defense responses and confers broad resistance. Plant Cell 11: 15-29.
74. The Arabidopsis Genome Iniciative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
75. The Rice Chromosomes 11 and 12 Sequencing Consortia (2005). The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol. 3: 20.
76. União dos Produtores de Bioenergia (UDOP). http://www.udop.com.br. Accessed February 12, 2007.
77. Urquiaga S, Cruz HS and Boddey RM (1992). Contribution of nitrogen fixation to sugarcane: nitrogen-15 and nitrogen balance estimates. Soil Sci. Soc. Am. J. 56: 105-114.
78. Vallad G, Rivkin M, Vallejos C and McClean P (2001). Cloning and homology modeling of a Pto-like protein kinase family of common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 103: 1046-1058.
79. van der Biezen EA, Freddie CT, Kahn K, Parker JE, et al. (2002). Arabidopsis RPP4 is a member of the RPP5 multigene family of TIR-NB-LRR genes and confers downy mildew resistance through multiple signalling components. Plant J. 29: 439-451.
80. Vettore AL, da Silva FR, Kemper EL and Arruda P (2001). The libraries that made SUCEST. Genet. Mol. Biol. 24: 1-7.
81. Wang GL, Holsten TE, Song WY, Wang HP, et al. (1996). Construction of a rice bacterial artificial chromosome library and identification of clones linked to the Xa21 disease resistance locus. Plant J. 7: 525-533.
82. Wang ZX, Yano M, Yamanouchi U, Iwamoto M, et al. (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.
83. Whitham S, Dinesh-Kumar SP, Choi D, Hehl R, et al. (1994). The product of the tobacco mosaic virus resistance gene N: similarity to toll and the interleukin-1 receptor. Cell 78: 1101-1115.
84. Whitham 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: 8776-8781.
85. Winter P, Benko-Iseppon AM, Hüttel B, Pfaff T, et al. (2000). A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum x C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5. Theor. Appl. Genet. 101: 1155-1163.
86. Xu WH, Wang YS, Liu GZ, Chen X, et al. (2006). The autophosphorylated Ser686, Thr688, and Ser689 residues in the intracellular juxtamembrane domain of XA21 are implicated in stability control of rice receptor-like kinase. Plant J. 45: 740-751.
87. Yoshimura S, Yamanouchi U, Katayose Y, Toki S, et al. (1998). Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc. Natl. Acad. Sci. USA 95: 1663-1668.
88. Zhou T, Wang Y, Chen JQ, Araki H, et al. (2004). Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol. Genet. Genomics 271: 402-415.