Genome wide analysis of nucleotide-binding site disease resistance genes in Brachypodium distachyon

Comparative and Functional Genomics

Volumn 2012, Issue , 2012, Pages

  Tan, Shenglong ^a,b   Wu, Song ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b HUBEI UNIVERSITY OF ECONOMICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BRACHYPODIUM; CHROMOSOMAL LOCALIZATION; COMPUTER MODEL; DATA BASE; DNA SEQUENCE; GENE; GENE DUPLICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ASSOCIATION; NONHUMAN; NUCLEOTIDE BINDING SITE; NUCLEOTIDE BINDING SITE LEUCINE RICH REPEAT RESISTANCE GENE; PHYLOGENY; PLANT GENOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF;

EID: 84862301146     PISSN: 15316912     EISSN: 15326268     Source Type: Journal    
DOI: 10.1155/2012/418208     Document Type: Article

References (50)

1. Flor H. H., Current status of the gene-for-gene concept Annual Review of Phytopathology 1971 9 275 296
2. Dangl J. L., Dietrich R. A., Richberg M. H., Death don't have no mercy: cell death programs in plant-microbe interactions Plant Cell 1996 8 10 1793 1807 (Pubitemid 27012405)
3. Heath M. C., Hypersensitive response-related death Plant Molecular Biology 2000 44 3 321 334 (Pubitemid 32143033)
4. Hulbert S. H., Webb C. A., Smith S. M., Sun Q., Resistance gene complexes: evolution and utilization Annual Review of Phytopathology 2001 39 285 312 (Pubitemid 32965187)
5. Belkhadir Y., Nimchuk Z., Hubert D. A., Mackey D., Dangl J. L., Arabidopsis RIN4 negatively regulates disease resistance mediated by RPS2 and RPM1 downstream or independent of the NDR1 signal modulator and is not required for the virulence functions of bacterial type III effectors AvrRpt2 or AvrRpm1 Plant Cell 2004 16 10 2822 2835 (Pubitemid 41071365)
6. Ellis J. G., Lawrence G. J., Luck J. E., Dodds P. N., Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity Plant Cell 1999 11 3 495 506
7. Meyers B. C., Dickerman A. W., Michelmore R. W., Sivaramakrishnan S., Sobral B. W., Young N. D., Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily Plant Journal 1999 20 3 317 332 (Pubitemid 129515914)
8. Pan Q., Wendel J., Fluhr R., Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes Journal of Molecular Evolution 2000 50 3 203 213 (Pubitemid 30429973)
9. Richly E., Kurth J., Leister D., Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution Molecular Biology and Evolution 2002 19 1 76 84 (Pubitemid 34008049)
10. Meyers B. C., Kozik A., Griego A., Kuang H., Michelmore R. W., Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis Plant Cell 2003 15 4 809 834 (Pubitemid 36453281)
11. Zhou T., Wang Y., Chen J. Q., Araki H., Jing Z., Jiang K., Shen J., Tian D., Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes Molecular Genetics and Genomics 2004 271 4 402 415 (Pubitemid 38824034)
12. Kohler A., Rinaldi C., Duplessis S., Baucher M., Geelen D., Duchaussoy F., Meyers B. C., Boerjan W., Martin F., Genome-wide identification of NBS resistance genes in Populus trichocarpa Plant Molecular Biology 2008 66 6 619 636
13. Yang S. H., Zhang X. H., Yue J. X., Tian D. C., Chen J. Q., Recent duplications dominate NBS-encoding gene expansion in two woody species Molecular Genetics and Genomics 2008 280 3 187 198
14. Ameline-Torregrosa C., Wang B. B., O'Bleness M. S., Deshpande S., Zhu H., Roe B., Young N. D., Cannon S. B., Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula Plant Physiology 2008 146 1 5 21 (Pubitemid 351380033)
15. Porter B. W., Paidi M., Ming R., Alam M., Nishijima W. T., Zhu Y. J., Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family Molecular Genetics and Genomics 2009 281 6 609 626
16. Li X. Y., Cheng H. Y., Ma W., Zhao Y., Jiang H., Zhang M., Identification and characterization of NBS-encoding disease resistance genes in Lotus japonicus Plant Systematics and Evolution 2010 289 1-2 101 110
17. Tamura M., Tachida H., Evolution of the number of LRRs in plant disease resistance genes Molecular Genetics and Genomics 2011 285 5 393 402
18. Li J., Ding J., Zhang W., Zhang Y., Tang P., Chen J. Q., Tian D., Yang S., Unique evolutionary pattern of numbers of gramineous NBS-LRR genes Molecular Genetics and Genomics 2010 283 5 427 438
19. Draper J., Mur L. A., Jenkins G., Ghosh-Biswas G. C., Bablak P., Hasterok R., Routledge A. P. M., Brachypodium distachyon. A new model system for functional genomics in grasses Plant Physiology 2001 127 4 1539 1555 (Pubitemid 34050024)
20. Opanowicz M., Vain P., Draper J., Parker D., Doonan J. H., Brachypodium distachyon: making hay with a wild grass Trends in Plant Science 2008 13 4 172 177
21. Kellogg E. A., Evolutionary history of the grasses Plant Physiology 2001 125 3 1198 1205 (Pubitemid 32224610)
22. Bevan M. W., Garvin D. F., Vogel J. P., Brachypodium distachyon genomics for sustainable food and fuel production Current Opinion in Biotechnology 2010 21 2 211 217
23. Vogel J. P., Garvin D. F., Mockler T. C., Schmutz J., Rokhsar D., Bevan M. W., Barry K., Lucas S., Harmon-Smith M., Lail K., Tice H., Grimwood J., McKenzie N., Huo N., Gu Y. Q., Lazo G. R., Anderson O. D., You F. M., Luo M. C., Dvorak J., Wright J., Febrer M., Idziak D., Hasterok R., Lindquist E., Wang M., Fox S. E., Priest H. D., Filichkin S. A., Givan S. A., Bryant D. W., Chang J. H., Wu H., Wu W., Hsia A. P., Schnable P. S., Kalyanaraman A., Barbazuk B., Michael T. P., Hazen S. P., Bragg J. N., Laudencia-Chingcuanco D., Weng Y., Haberer G., Spannagl M., Mayer K., Rattei T., Mitros T., Lee S. J., Rose J. K. C., Mueller L. A., York T. L., Wicker T., Buchmann J. P., Tanskanen J., Schulman A. H., Gundlach H., Beven M., Costa De Oliveira A., Da L., Belknap W., Jiang N., Lai J., Zhu L., Ma J., Sun C., Pritham E., Salse J., Murat F., Abrouk M., Bruggmann R., Messing J., Fahlgren N., Sullivan C. M., Carrington J. C., Chapman E. J., May G. D., Zhai J., Ganssmann M., Gurazada S. G. R., German M., Meyers B. C., Green P. J., Tyler L., Wu J., Thomson J., Chen S., Scheller H. V., Harholt J., Ulvskov P., Kimbrel J. A., Bartley L. E., Cao P., Jung K. H., Sharma M. K., Vega-Sanchez M., Ronald P., Dardick C. D., De Bodt S., Verelst W., Inzé D., Heese M., Schnittger A., Yang X., Kalluri U. C., Tuskan G. A., Hua Z., Vierstra R. D., Cui Y., Ouyang S., Sun Q., Liu Z., Yilmaz A., Grotewold E., Sibout R., Hematy K., Mouille G., Hfte H., Micheel T., Pelloux J., O'Connor D., Schnable J., Rowe S., Harmon F., Cass C. L., Sedbrook J. C., Byrne M. E., Walsh S., Higgins J., Li P., Brutnell T., Unver T., Budak H., Belcram H., Charles M., Chalhoub B., Baxter I., Genome sequencing and analysis of the model grass Brachypodium distachyon Nature 2010 463 7282 763 768
24. Eddy S. R., Profile hidden Markov models Bioinformatics 1998 14 9 755 763 (Pubitemid 28552108)
25. Thompson J. D., Higgins D. G., Gibson T. J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 1994 22 22 4673 4680 (Pubitemid 24354800)
26. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J., Basic local alignment search tool Journal of Molecular Biology 1990 215 3 403 410
27. Lupas A., Van Dyke M., Stock J., Predicting coiled coils from protein sequences Science 1991 252 5010 1162 1164 (Pubitemid 21917026)
28. Bailey T. L., Elkan C., The value of prior knowledge in discovering motifs with MEME. Proceedings of the International Conference on Intelligent Systems for Molecular Biology 1995 3 21 29
29. Gu Z., Cavalcanti A., Chen F. C., Bouman P., Li W. H., Extent of gene duplication in the genomes of Drosophila, nematode, and yeast Molecular Biology and Evolution 2002 19 3 256 262 (Pubitemid 34184598)
30. Castresana J., Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Molecular Biology and Evolution 2000 17 4 540 552 (Pubitemid 30210700)
31. Tamura K., Dudley J., Nei M., Kumar S., MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 Molecular Biology and Evolution 2007 24 8 1596 1599 (Pubitemid 47236692)
32. Higo K., Ugawa Y., Iwamoto M., Korenaga T., Plant cis-acting regulatory DNA elements (PLACE) database: 1999 Nucleic Acids Research 1999 27 1 297 300 (Pubitemid 29209466)
33. Jang C. S., Kamps T. L., Skinner D. N., Schulze S. R., Vencill W. K., Paterson A. H., Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression Plant Physiology 2006 142 3 1148 1159 (Pubitemid 44764638)
34. Dong J., Chen C., Chen Z., Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response Plant Molecular Biology 2003 51 1 21 37 (Pubitemid 36189133)
35. Sakuma Y., Maruyama K., Qin F., Osakabe Y., Shinozaki K., Yamaguchi-Shinozaki K., Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression Proceedings of the National Academy of Sciences of the United States of America 2006 103 49 18822 18827 (Pubitemid 44913494)
36. Ohme-Takagi M., Suzuki K., Shinshi H., Regulation of ethylene-induced transcription of defense genes Plant and Cell Physiology 2000 41 11 1187 1192 (Pubitemid 32003656)
37. Cannon S. B., Zhu H., Baumgarten A. M., Spangler R., May G., Cook D. R., Young N. D., Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies Journal of Molecular Evolution 2002 54 4 548 562 (Pubitemid 34271135)
38. Yang S., Feng Z., Zhang X., Jiang K., Jin X., Hang Y., Chen J. Q., Tian D., Genome-wide investigation on the genetic variations of rice disease resistance genes Plant Molecular Biology 2006 62 1-2 181 193 (Pubitemid 44372896)
39. Houb E. B., The arms race is ancient history in Arabidopsis, the wildflower Nature Reviews Genetics 2001 2 7 516 527 (Pubitemid 33674025)
40. Gowacki S., Macioszek V. K., Kononowicz A. K., R proteins as fundamentals of plant innate immunity Cellular and Molecular Biology Letters 2011 16 1 1 24
41. Takken F. L., Albrecht M., Tameling W. I., Resistance proteins: molecular switches of plant defence Current Opinion in Plant Biology 2006 9 4 383 390 (Pubitemid 44202280)
42. Muge Sayar-Turet S. D., Braun H. J., Hede A., Dreisigacker S., MacCormack R., Boyd L. A., Genetic variation within and between winter wheat genotypes from Turkey, Kazakhstan, and Europe as determined by nucleotide-binding-site profiling Genome 2011 54 5 419 430
43. Kajava A. V., Structural diversity of leucine-rich repeat proteins Journal of Molecular Biology 1998 277 3 519 527 (Pubitemid 28190855)
44. Bella J., Hindle K. L., McEwan P. A., Lovell S. C., The leucine-rich repeat structure Cellular and Molecular Life Sciences 2008 65 15 2307 2333
45. Stange C., Matus J. T., Domnguez C., Perez-Acle T., Arce-Johnson P., The N-homologue LRR domain adopts a folding which explains the TMV-Cg-induced HR-like response in sensitive tobacco plants Journal of Molecular Graphics and Modelling 2008 26 5 850 860 (Pubitemid 350213443)
46. Kobe B., Kajava A. V., When protein folding is simplified to protein coiling: the continuum of solenoid protein structures Trends in Biochemical Sciences 2000 25 10 509 515
47. Ratnaparkhe M. B., Wang X., Li J., Compton R. O., Rainville L. K., Lemke C., Kim C., Tang H., Paterson A. H., Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny New Phytologist 2011 192 1 164 178
48. Monosi B., Wisser R. J., Pennill L., Hulbert S. H., Full-genome analysis of resistance gene homologues in rice Theoretical and Applied Genetics 2004 109 7 1434 1447 (Pubitemid 40059266)
49. Yu D., Chen C., Chen Z., Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression Plant Cell 2001 13 7 1527 1539 (Pubitemid 32675718)
50. Li J., Brader G., Palva E. T., The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense Plant Cell 2004 16 2 319 331 (Pubitemid 38192692)