Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis

BMC Plant Biology

Volumn 7, Issue , 2007, Pages

  Tan, Xiaoping ^a   Meyers, Blake C ^b   Kozik, Alexander ^a   West, Marilyn Al ^a   Morgante, Michele ^c   St Clair, Dina A ^a   Bent, Andrew F ^d   Michelmore, Richard W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

^c UNIVERSITY OF UDINE   (Italy)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS;

COMPLEMENTARY DNA; LEUCINE; NUCLEOTIDE;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BINDING SITE; CHEMISTRY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ARABIDOPSIS; BINDING SITES; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENES, PLANT; LEUCINE; NUCLEOTIDES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPETITIVE SEQUENCES, AMINO ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 38049074926     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-7-56     Document Type: Article

References (141)

1. Plant Disease Resistance Genes. KE Hammond-Kosack JD Jones, Annu Rev Plant Physiol Plant Mol Biol 1997 48 575 607 10.1146/annurev.arplant.48.1.575 15012275
2. Plant pathogens and integrated defence responses to infection. JL Dangl JD Jones, Nature 2001 411 6839 826 833 10.1038/35081161 11459065
3. Common and contrasting themes of plant and animal diseases. BJ Staskawicz MB Mudgett JL Dangl JE Galan, Science 2001 292 5525 2285 2289 10.1126/science.1062013 11423652
4. Understanding the functions of plant disease resistance proteins. GB Martin AJ Bogdanove G Sessa, Annual review of plant biology 2003 54 23 61 10.1146/annurev.arplant.54.031902.135035 14502984
5. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. BC Meyers AW Dickerman RW Michelmore S Sivaramakrishnan BW Sobral ND Young, Plant J 1999 20 3 317 332 10.1046/j.1365-313X.1999.t01-1-00606.x 10571892
6. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. Q Pan J Wendel R Fluhr, Journal of molecular evolution 2000 50 3 203 213 10754062
7. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. BC Meyers A Kozik A Griego H Kuang RW Michelmore, The Plant cell 2003 15 4 809 834 12671079 10.1105/tpc.009308
8. Plant NBS-LRR proteins: adaptable guards. L McHale X Tan P Koehl RW Michelmore, Genome biology 2006 7 4 212 16677430 10.1186/gb-2006-7-4-212
9. TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. BC Meyers M Morgante RW Michelmore, Plant J 2002 32 1 77 92 10.1046/j.1365-313X. 2002.01404.x 12366802
10. Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. E Richly J Kurth D Leister, Mol Biol Evol 2002 19 1 76 84 11752192
11. Full-genome analysis of resistance gene homologues in rice. B Monosi RJ Wisser L Pennill SH Hulbert, Theor Appl Genet 2004 109 7 1434 1447 10.1007/s00122-004-1758-x 15309302
12. Plant disease-resistance proteins and the gene-for-gene concept. EA Van der Biezen JD Jones, Trends in biochemical sciences 1998 23 12 454 456 10.1016/S0968-0004(98)01311-5 9868361
13. Guarding the goods. New insights into the central alarm system of plants. RW Innes, Plant physiology 2004 135 2 695 701 15208416 10.1104/pp.104.040410
14. Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. PN Dodds GJ Lawrence AM Catanzariti T Teh CI Wang MA Ayliffe B Kobe JG Ellis, Proceedings of the National Academy of Sciences of the United States of America 2006 103 23 8888 8893 16731621 10.1073/pnas.0602577103
15. The plant immune system. JD Jones JL Dangl, Nature 2006 444 7117 323 329 10.1038/nature05286 17108957
16. Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. QH Shen Y Saijo S Mauch C Biskup S Bieri B Keller H Seki B Ulker IE Somssich P Schulze-Lefert, Science 2007 315 5815 1098 1103 10.1126/science.1136372 17185563
17. Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. M Parniske KE Hammond-Kosack C Golstein CM Thomas DA Jones K Harrison BB Wulff JD Jones, Cell 1997 91 6 821 832 10.1016/S0092-8674(00)80470-5 9413991
18. Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9. CM Thomas DA Jones M Parniske K Harrison PJ Balint-Kurti K Hatzixanthis JD Jones, The Plant cell 1997 9 12 2209 2224 9437864 10.2307/3870580
19. Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. MA Botella JE Parker LN Frost PD Bittner-Eddy JL Beynon MJ Daniels EB Holub JD Jones, The Plant cell 1998 10 11 1847 1860 9811793 10.2307/3870908
20. Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. JM McDowell M Dhandaydham TA Long MG Aarts S Goff EB Holub JL Dangl, The Plant cell 1998 10 11 1861 1874 9811794 10.2307/3870909
21. Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. BC Meyers KA Shen P Rohani BS Gaut RW Michelmore, The Plant cell 1998 10 11 1833 1846 9811792 10.2307/3870907
22. Xa21D encodes a receptor-like molecule with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution. GL Wang DL Ruan WY Song S Sideris L Chen LY Pi S Zhang Z Zhang C Fauquet BS Gaut MC Whalen PC Ronald, The Plant cell 1998 10 5 765 779 9596635 10.2307/3870663
23. Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. JG Ellis GJ Lawrence JE Luck PN Dodds, The Plant cell 1999 11 3 495 506 10072407 10.2307/3870876
24. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. L Noel TL Moores EA van Der Biezen M Parniske MJ Daniels JE Parker JD Jones, The Plant cell 1999 11 11 2099 2112 10559437 10.2307/3871012
25. 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. PN Dodds GJ Lawrence JG Ellis, The Plant cell 2001 13 1 163 178 11158537 10.2307/3871161
26. Domain swapping and gene shuffling identify sequences required for induction of an Avr-dependent hypersensitive response by the tomato Cf-4 and Cf-9 proteins. BB Wulff CM Thomas M Smoker M Grant JD Jones, The Plant cell 2001 13 2 255 272 11226184 10.2307/3871275
27. Leucine-rich repeat-mediated intramolecular interactions in nematode recognition and cell death signaling by the tomato resistance protein Mi. CF Hwang VM Williamson, Plant J 2003 34 5 585 593 10.1046/j.1365-313X.2003.01749.x 12787241
28. Regions outside of the leucine-rich repeats of flax rust resistance proteins play a role in specificity determination. JE Luck GJ Lawrence PN Dodds KW Shepherd JG Ellis, The Plant cell 2000 12 8 1367 1377 10948256 10.2307/3871136
29. A mutation within the leucine-rich repeat domain of the Arabidopsis disease resistance gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes. RF Warren A Henk P Mowery E Holub RW Innes, The Plant cell 1998 10 9 1439 1452 9724691 10.2307/3870609
30. Interaction between domains of a plant NBS-LRR protein in disease resistance-related cell death. P Moffett G Farnham J Peart DC Baulcombe, The EMBO journal 2002 21 17 4511 4519 12198153 10.1093/emboj/cdf453
31. Plant disease resistance protein signaling: NBS-LRR proteins and their partners. Y Belkhadir R Subramaniam JL Dangl, Current opinion in plant biology 2004 7 4 391 399 10.1016/j.pbi.2004.05.009 15231261
32. Plant innate immunity - direct and indirect recognition of general and specific pathogen-associated molecules. DA Jones D Takemoto, Current opinion in immunology 2004 16 1 48 62 10.1016/j.coi.2003.11.016 14734110
33. The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals. EA van der Biezen JD Jones, Curr Biol 1998 8 7 R226 7 10.1016/S0960-9822(98)70145-9 9545207
34. The tomato R gene products I-2 and MI-1 are functional ATP binding proteins with ATPase activity. WI Tameling SD Elzinga PS Darmin JH Vossen FL Takken MA Haring BJ Cornelissen, The Plant cell 2002 14 11 2929 2939 12417711 10.1105/tpc.005793
35. Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. WI Tameling JH Vossen M Albrecht T Lengauer JA Berden MA Haring BJ Cornelissen FL Takken, Plant physiology 2006 140 4 1233 1245 16489136 10.1104/pp.105.073510
36. A constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development. A Faigon-Soverna FG Harmon L Storani E Karayekov RJ Staneloni W Gassmann P Mas JJ Casal SA Kay MJ Yanovsky, The Plant cell 2006 18 11 2919 2928 10.1105/tpc.105.038810 17114357
37. cAMP acts as a second messenger in pollen tube growth and reorientation. A Moutinho PJ Hussey AJ Trewavas R Malho, Proceedings of the National Academy of Sciences of the United States of America 2001 98 18 10481 10486 11517303 10.1073/pnas.171104598
38. Expression of the Fusarium resistance gene I-2 colocalizes with the site of fungal containment. JJ Mes AA van Doorn J Wijbrandi G Simons BJ Cornelissen MA Haring, Plant J 2000 23 2 183 193 10.1046/j.1365-313x.2000.00765.x 10929112
39. The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. SE Clark RW Williams EM Meyerowitz, Cell 1997 89 4 575 585 10.1016/S0092-8674(00)80239-1 9160749
40. A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. J Li J Chory, Cell 1997 90 5 929 938 10.1016/S0092-8674(00)80357-8 9298904
41. The Arabidopsis CLAVATA2 gene encodes a receptor-like protein required for the stability of the CLAVATA1 receptor-like kinase. S Jeong AE Trotochaud SE Clark, The Plant cell 1999 11 10 1925 1934 10521522 10.2307/3871087
42. BRI1 is a critical component of a plasma-membrane receptor for plant steroids. ZY Wang H Seto S Fujioka S Yoshida J Chory, Nature 2001 410 6826 380 383 10.1038/35066597 11268216
43. Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. MR Grant L Godiard E Straube T Ashfield J Lewald A Sattler RW Innes JL Dangl, Science 1995 269 5225 843 846 10.1126/science.7638602 7638602
44. The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. MS Dixon DA Jones JS Keddie CM Thomas K Harrison JD Jones, Cell 1996 84 3 451 459 10.1016/S0092-8674(00)81290-8 8608599
45. 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. JM Salmeron GE Oldroyd CM Rommens SR Scofield HS Kim DT Lavelle D Dahlbeck BJ Staskawicz, Cell 1996 86 1 123 133 10.1016/S0092-8674(00)80083-5 8689679
46. The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and L6. JE Parker MJ Coleman V Szabo LN Frost R Schmidt EA van der Biezen T Moores C Dean MJ Daniels JD Jones, The Plant cell 1997 9 6 879 894 9212464 10.1105/tpc.9.6.879
47. 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. SB Milligan J Bodeau J Yaghoobi I Kaloshian P Zabel VM Williamson, The Plant cell 1998 10 8 1307 1319 9707531 10.2307/3870642
48. Dm3 is one member of a large constitutively expressed family of nucleotide binding site-leucine-rich repeat encoding genes. KA Shen DB Chin R Arroyo-Garcia OE Ochoa DO Lavelle T Wroblewski BC Meyers RW Michelmore, Mol Plant Microbe Interact 2002 15 3 251 261 10.1094/MPMI.2002.15.3.251 11952128
49. Analysis of alternative transcripts of the flax L6 rust resistance gene. MA Ayliffe DV Frost EJ Finnegan GJ Lawrence PA Anderson JG Ellis, Plant J 1999 17 3 287 292 10.1046/j.1365-313X.1999.00377.x 10097386
50. The tobacco mosaic virus resistance gene, N. R Marathe R Anandalakshmi Y Liu SP Dinesh-Kumar, Mol Plant Pathol 2002 3 3 167 172 10.1046/j.1364-3703.2002. 00110.x
51. Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. PA Anderson GJ Lawrence BC Morrish MA Ayliffe EJ Finnegan JG Ellis, The Plant cell 1997 9 4 641 651 9144966 10.2307/3870513
52. RPS4-mediated disease resistance requires the combined presence of RPS4 transcripts with full-length and truncated open reading frames. XC Zhang W Gassmann, The Plant cell 2003 15 10 2333 2342 14523247 10.1105/tpc.013474
53. The arabidopsis TIR-NB-LRR gene RAC1 confers resistance to Albugo candida (white rust) and is dependent on EDS1 but not PAD4. MH Borhan EB Holub JL Beynon K Rozwadowski SR Rimmer, Mol Plant Microbe Interact 2004 17 7 711 719 10.1094/MPMI.2004.17.7.711 15242165
54. The tomato resistance protein Bs4 is a predicted non-nuclear TIR-NB-LRR protein that mediates defense responses to severely truncated derivatives of AvrBs4 and overexpressed AvrBs3. S Schornack A Ballvora D Gurlebeck J Peart D Baulcombe M Ganal B Baker U Bonas T Lahaye, Plant J 2004 37 1 46 60 10.1046/j.1365-313X.2003.01937.x 14675431
55. Distinct post-transcriptional modifications result into seven alternative transcripts of the CC-NBS-LRR gene JA1tr of Phaseolus vulgaris. E Ferrier-Cana C Macadre M Sevignac P David T Langin V Geffroy, Theor Appl Genet 2005 110 5 895 905 10.1007/s00122-004-1908-1 15660237
56. Positional cloning of a gene for nematode resistance in sugar beet. D Cai M Kleine S Kifle HJ Harloff NN Sandal KA Marcker RM Klein-Lankhorst EM Salentijn W Lange WJ Stiekema U Wyss FM Grundler C Jung, Science 1997 275 5301 832 834 10.1126/science.275.5301.832 9012350
57. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. S Yoshimura U Yamanouchi Y Katayose S Toki ZX Wang I Kono N Kurata M Yano N Iwata T Sasaki, Proceedings of the National Academy of Sciences of the United States of America 1998 95 4 1663 1668 9465073 10.1073/pnas.95.4.1663
58. Powdery mildew-induced Mla mRNAs are alternatively spliced and contain multiple upstream open reading frames. DA Halterman F Wei RP Wise, Plant physiology 2003 131 2 558 567 12586880 10.1104/pp.014407
59. R gene expression induced by a type-III effector triggers disease resistance in rice. K Gu B Yang D Tian L Wu D Wang C Sreekala F Yang Z Chu GL Wang FF White Z Yin, Nature 2005 435 7045 1122 1125 10.1038/nature03630 15973413
60. Molecular characterization of the maize Rp1-D rust resistance haplotype and its mutants. N Collins J Drake M Ayliffe Q Sun J Ellis S Hulbert T Pryor, The Plant cell 1999 11 7 1365 1376 10402435 10.2307/3870755
61. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. ZX Wang M Yano U Yamanouchi M Iwamoto L Monna H Hayasaka Y Katayose T Sasaki, Plant J 1999 19 1 55 64 10.1046/j.1365-313X.1999.00498.x 10417726
62. Expression of the Pib rice-blast-resistance gene family is up-regulated by environmental conditions favouring infection and by chemical signals that trigger secondary plant defences. ZX Wang U Yamanouchi Y Katayose T Sasaki M Yano, Plant molecular biology 2001 47 5 653 661 10.1023/A:1012457113700 11725950
63. Comprehensive gene expression analysis by transcript profiling. J Donson Y Fang G Espiritu-Santo W Xing A Salazar S Miyamoto V Armendarez W Volkmuth, Plant molecular biology 2002 48 1-2 75 97 10.1023/A:1013722224489 11860215
64. Gene expression profiling: methodological challenges, results, and prospects for addiction research. JD Pollock, Chem Phys Lipids 2002 121 1-2 241 256 10.1016/S0009-3084(02)00160-3 12505704
65. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. MD Adams AR Kerlavage RD Fleischmann RA Fuldner CJ Bult NH Lee EF Kirkness KG Weinstock JD Gocayne O White G Sutton JA Blake RC Brandon MW Chiu RA Clayton RT Cline MD Cotton J Earle-Hughes LD Fine LM FitzGerald WM FitzHugh JL Fritchman NSM Geoghagen A Glodek CL Gnehm MC Hanna E Hedblom PS Hinkle Jr. JM Kelley KM Klimek, Nature 1995 377 6547 Suppl 3 174 7566098
66. Serial analysis of gene expression. VE Velculescu L Zhang B Vogelstein KW Kinzler, Science 1995 270 5235 484 487 10.1126/science.270.5235.484 7570003
67. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. S Brenner M Johnson J Bridgham G Golda DH Lloyd D Johnson S Luo S McCurdy M Foy M Ewan R Roth D George S Eletr G Albrecht E Vermaas SR Williams K Moon T Burcham M Pallas RB DuBridge J Kirchner K Fearon J Mao K Corcoran, Nature biotechnology 2000 18 6 630 634 10.1038/76469 10835600
68. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. S Brenner SR Williams EH Vermaas T Storck K Moon C McCollum JI Mao S Luo JJ Kirchner S Eletr RB DuBridge T Burcham G Albrecht, Proceedings of the National Academy of Sciences of the United States of America 2000 97 4 1665 1670 10677516 10.1073/pnas.97.4.1665
69. Microarray expression profiling resources for plant genomics. WA Rensink CR Buell, Trends in plant science 2005 10 12 603 609 10.1016/j.tplants.2005.10. 003 16275051
70. DNA microarray analyses in higher plants. DW Galbraith, Omics 2006 10 4 455 473 10.1089/omi.2006.10.455 17233557
71. Microarray data analysis: from hypotheses to conclusions using gene expression data. NJ Armstrong MA van de Wiel, Cell Oncol 2004 26 5-6 279 290 15623938
72. Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. JD Clarke T Zhu, Plant J 2006 45 4 630 650 10.1111/j.1365-313X.2006.02668.x 16441353
73. NibLrrs. http://niblrrs.ucdavis.edu
74. Arabidopsis MPSS database. http://mpss.udel.edu/at/
75. Arabidopsis MPSS. An online resource for quantitative expression analysis. BC Meyers DK Lee TH Vu SS Tej SB Edberg M Matvienko LD Tindell, Plant physiology 2004 135 2 801 813 15173564 10.1104/pp.104.039495
76. The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. BC Meyers SS Tej TH Vu CD Haudenschild V Agrawal SB Edberg H Ghazal S Decola, Genome research 2004 14 8 1641 1653 15289482 10.1101/gr.2275604
77. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. BC Meyers TH Vu SS Tej H Ghazal M Matvienko V Agrawal J Ning CD Haudenschild, Nature biotechnology 2004 22 8 1006 1011 10.1038/nbt992 15247925
78. Bacterial disease resistance in Arabidopsis through flagellin perception. C Zipfel S Robatzek L Navarro EJ Oakeley JD Jones G Felix T Boller, Nature 2004 428 6984 764 767 10.1038/nature02485 15085136
79. Genomic survey of gene expression diversity in Arabidopsis thaliana. DJ Kliebenstein MA West H van Leeuwen K Kim RW Doerge RW Michelmore DA St Clair, Genetics 2006 172 2 1179 1189 16204207 10.1534/genetics.105.049353
80. ELP. http://elp.ucdavis.edu/
81. Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. PS Springer WR McCombie V Sundaresan RA Martienssen, Science 1995 268 5212 877 880 10.1126/science.7754372 7754372
82. Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. V Sundaresan P Springer T Volpe S Haward JD Jones C Dean H Ma R Martienssen, Genes & development 1995 9 14 1797 1810 10.1101/gad.9.14.1797 7622040
83. Functional genomics: probing plant gene function and expression with transposons. RA Martienssen, Proceedings of the National Academy of Sciences of the United States of America 1998 95 5 2021 2026 9482828 10.1073/pnas.95.5.2021
84. Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis. S Parinov M Sevugan D Ye WC Yang M Kumaran V Sundaresan, The Plant cell 1999 11 12 2263 2270 10590156 10.2307/3870953
85. Arabidopsis Gene Trap Website at Cold Spring Harbor Lab. http://genetrap.cshl.org/
86. Institute of Molecular Agrobiology lines. http://www.arabidopsis.org/ abrc/ima.jsp
87. The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development. Q Gu C Ferrandiz MF Yanofsky R Martienssen, Development (Cambridge, England) 1998 125 8 1509 1517 9502732
88. Transposon tagging and the study of root development in Arabidopsis. R Tsugeki ML Olson NV Fedoroff, Gravit Space Biol Bull 1998 11 2 79 87 11540642
89. TAIR. http://www.arabidopsis.org/
90. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. K Maleck A Levine T Eulgem A Morgan J Schmid KA Lawton JL Dangl RA Dietrich, Nature genetics 2000 26 4 403 410 10.1038/82521 11101835
91. Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Y Tao Z Xie W Chen J Glazebrook HS Chang B Han T Zhu G Zou F Katagiri, The Plant cell 2003 15 2 317 330 12566575 10.1105/tpc.007591
92. A Novel Role for the TIR Domain in Association with Pathogen-Derived Elicitors. TM Burch-Smith M Schiff JL Caplan J Tsao K Czymmek SP Dinesh-Kumar, PLoS Biol 2007 5 3 e68 17298188 10.1371/journal.pbio.0050068
93. NRG1, a CC-NB-LRR protein, together with N, a TIR-NB-LRR protein, mediates resistance against tobacco mosaic virus. JR Peart P Mestre R Lu I Malcuit DC Baulcombe, Curr Biol 2005 15 10 968 973 10.1016/j.cub.2005.04.053 15916955
94. An NB-LRR protein required for HR signalling mediated by both extra- and intracellular resistance proteins. SH Gabriels JH Vossen SK Ekengren G van Ooijen AM Abd-El-Haliem GC van den Berg DY Rainey GB Martin FL Takken PJ de Wit MH Joosten, Plant J 2007 50 1 14 28 10.1111/j.1365-313X.2007.03027.x 17346268
95. Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. R Marathe Z Guan R Anandalakshmi H Zhao SP Dinesh-Kumar, Plant molecular biology 2004 55 4 501 520 10.1007/s11103-004-0439-0 15604696
96. Arabidopsis splicing variations at TIGR. http://www.tigr.org/tdb/e2k1/ ath1/altsplicing/splicing_variations.shtml
97. Genomewide comparative analysis of alternative splicing in plants. BB Wang V Brendel, Proceedings of the National Academy of Sciences of the United States of America 2006 103 18 7175 7180 16632598 10.1073/pnas.0602039103
98. Alternative splicing of transcripts encoding Toll-like plant resistance proteins - what's the functional relevance to innate immunity? T Jordan S Schornack T Lahaye, Trends in plant science 2002 7 9 392 398 10.1016/S1360-1385(02)02311-7 12234730
99. Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance. SP Dinesh-Kumar BJ Baker, Proceedings of the National Academy of Sciences of the United States of America 2000 97 4 1908 1913 10660679 10.1073/pnas.020367497
100. The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes. W Gassmann ME Hinsch BJ Staskawicz, Plant J 1999 20 3 265 277 10.1046/j.1365-313X.1999.t01-1-00600.x 10571887
101. The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. DC Boyes J Nam JL Dangl, Proceedings of the National Academy of Sciences of the United States of America 1998 95 26 15849 15854 9861059 10.1073/pnas.95.26.15849
102. Short communication: developmental control of Xa21-mediated disease resistance in rice. KS Century RA Lagman M Adkisson J Morlan R Tobias K Schwartz A Smith J Love PC Ronald MC Whalen, Plant J 1999 20 2 231 236 10.1046/j.1365-313x.1999.00589.x 10571882
103. The role of the 5' untranslated region of an mRNA in translation regulation during development. AW van der Velden AA Thomas, The international journal of biochemistry & cell biology 1999 31 1 87 106 10.1016/S1357- 2725(98)00134-4 10216946
104. Translational control of growth factor and proto-oncogene expression. AE Willis, The international journal of biochemistry & cell biology 1999 31 1 73 86 10.1016/S1357-2725(98)00133-2 10216945
105. The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria graminis f. sp. hordei in barley and wheat. D Halterman F Zhou F Wei RP Wise P Schulze-Lefert, Plant J 2001 25 3 335 348 10.1046/j.1365-313x.2001.00982.x 11208025
106. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, Journal of molecular biology 1990 215 3 403 410 2231712
107. Functional annotation of a full-length Arabidopsis cDNA collection. M Seki M Narusaka A Kamiya J Ishida M Satou T Sakurai M Nakajima A Enju K Akiyama Y Oono M Muramatsu Y Hayashizaki J Kawai P Carninci M Itoh Y Ishii T Arakawa K Shibata A Shinagawa K Shinozaki, Science 2002 296 5565 141 145 10.1126/science.1071006 11910074
108. TAIR BLAST. http://www.arabidopsis.org/Blast/
109. Improved tools for biological sequence comparison. WR Pearson DJ Lipman, Proceedings of the National Academy of Sciences of the United States of America 1988 85 8 2444 2448 3162770 10.1073/pnas.85.8.2444
110. Affymetrix. http://www.affymetrix.com
111. Raw array data for flagellin experiment. http://www.ebi.ac.uk/microarray- as/aer/dataselection?expid=295433876
112. ELP finder. http://elp.ucdavis.edu/parental_survey_ELP_finder.htm
113. Alkali treatment for rapid preparation of plant material for reliable PCR analysis. VI Klimyuk BJ Carroll CM Thomas JD Jones, Plant J 1993 3 3 493 494 10.1046/j.1365-313X.1993.t01-26-00999.x 8220456
114. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. RA Jefferson TA Kavanagh MW Bevan, The EMBO journal 1987 6 13 3901 3907 3327686
115. A Brassica S locus gene promoter directs sporophytic expression in the anther tapetum of transgenic Arabidopsis. K Toriyama MK Thorsness JB Nasrallah ME Nasrallah, Developmental biology 1991 143 2 427 431 10.1016/0012-1606(91) 90094-J 1991565
116. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. MM Bradford, Analytical biochemistry 1976 72 248 254 10.1016/0003-2697(76)90527-3 942051
117. Characterization and expression of two avirulence genes cloned from Pseudomonas syringae pv. glycinea. S Tamaki D Dahlbeck B Staskawicz NT Keen, Journal of bacteriology 1988 170 10 4846 4854 3049552
118. Identification and Molecular Mapping of a Single Arabidopsis-Thaliana Locus Determining Resistance to a Phytopathogenic Pseudomonas-Syringae Isolate. T Debener H Lehnackers M Arnold JL Dangl, Plant J 1991 1 3 289 302
119. NDR1, a locus of Arabidopsis thaliana that is required for disease resistance to both a bacterial and a fungal pathogen. KS Century EB Holub BJ Staskawicz, Proceedings of the National Academy of Sciences of the United States of America 1995 92 14 6597 6601 11607554 10.1073/pnas.92.14.6597
120. Characterization of eds1, a mutation in Arabidopsis suppressing resistance to Peronospora parasitica specified by several different RPP genes. JE Parker EB Holub LN Frost A Falk ND Gunn MJ Daniels, The Plant cell 1996 8 11 2033 2046 8953768 10.2307/3870410
121. RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. AF Bent BN Kunkel D Dahlbeck KL Brown R Schmidt J Giraudat J Leung BJ Staskawicz, Science 1994 265 5180 1856 1860 10.1126/science.8091210 8091210
122. The A. thaliana disease resistance gene RPS2 encodes a protein containing a nucleotide-binding site and leucine-rich repeats. M Mindrinos F Katagiri GL Yu FM Ausubel, Cell 1994 78 6 1089 1099 10.1016/0092-8674(94)90282-8 7923358
123. Molecular analysis of avirulence gene avrRpt2 and identification of a putative regulatory sequence common to all known Pseudomonas syringae avirulence genes. RW Innes AF Bent BN Kunkel SR Bisgrove BJ Staskawicz, Journal of bacteriology 1993 175 15 4859 4869 8335641
124. Identification of Pseudomonas syringae pathogens of Arabidopsis and a bacterial locus determining avirulence on both Arabidopsis and soybean. MC Whalen RW Innes AF Bent BJ Staskawicz, The Plant cell 1991 3 1 49 59 1824334 10.2307/3869199
125. Identification of a new Arabidopsis disease resistance locus, RPs4, and cloning of the corresponding avirulence gene, avrRps4, from Pseudomonas syringae pv. pisi. M Hinsch B Staskawicz, Mol Plant Microbe Interact 1996 9 1 55 61 8589423
126. Different requirements for EDS1 and NDR1 by disease resistance genes define at least two R gene-mediated signaling pathways in Arabidopsis. N Aarts M Metz E Holub BJ Staskawicz MJ Daniels JE Parker, Proceedings of the National Academy of Sciences of the United States of America 1998 95 17 10306 10311 9707643 10.1073/pnas.95.17.10306
127. Gene-for-gene interactions between Pseudomonas syringae pv. phaseolicola and Phaseolus. C Jenner E Hitchin J Mansfield K Walters P Betteridge D Teverson J Taylor, Mol Plant Microbe Interact 1991 4 6 553 562 1666524
128. A disease resistance gene in Arabidopsis with specificity for the avrPph3 gene of Pseudomonas syringae pv. phaseolicola. MT Simonich RW Innes, Mol Plant Microbe Interact 1995 8 4 637 640 8589418
129. Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. AP Rehmany A Gordon LE Rose RL Allen MR Armstrong SC Whisson S Kamoun BM Tyler PR Birch JL Beynon, The Plant cell 2005 17 6 1839 1850 15894715 10.1105/tpc.105.031807
130. Arabidopsis RPP4 is a member of the RPP5 multigene family of TIR-NB-LRR genes and confers downy mildew resistance through multiple signalling components. EA van der Biezen CT Freddie K Kahn JE Parker JD Jones, Plant J 2002 29 4 439 451 10.1046/j.0960-7412.2001.01229.x 11846877
131. Downy mildew (Peronospora parasitica) resistance genes in Arabidopsis vary in functional requirements for NDR1, EDS1, NPR1 and salicylic acid accumulation. JM McDowell A Cuzick C Can J Beynon JL Dangl EB Holub, Plant J 2000 22 6 523 529 10.1046/j.1365-313x.2000.00771.x 10886772
132. Members of the Arabidopsis HRT/RPP8 family of resistance genes confer resistance to both viral and oomycete pathogens. MB Cooley S Pathirana HJ Wu P Kachroo DF Klessig, The Plant cell 2000 12 5 663 676 10810142 10.2307/3870993
133. RCY1, an Arabidopsis thaliana RPP8/HRT family resistance gene, conferring resistance to cucumber mosaic virus requires salicylic acid, ethylene and a novel signal transduction mechanism. H Takahashi J Miller Y Nozaki M Takeda J Shah S Hase M Ikegami Y Ehara SP Dinesh-Kumar, Plant J 2002 32 5 655 667 10.1046/j.1365-313X.2002.01453.x 12472683
134. RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica. PD Bittner-Eddy IR Crute EB Holub JL Beynon, Plant J 2000 21 2 177 188 10.1046/j.1365-313x.2000.00664.x 10743658
135. The Arabidopsis downy mildew resistance gene, RPP13-Nd, functions independently of NDR1 and EDS1 and does not require the accumulation of salicylic acid. PD Bittner-Eddy JL Beynon, Mol Plant Microbe Interact 2001 14 3 416 421 10.1094/MPMI.2001.14.3.416 11277440
136. Host-parasite coevolutionary conflict between Arabidopsis and downy mildew. RL Allen PD Bittner-Eddy LJ Grenville-Briggs JC Meitz AP Rehmany LE Rose
137. Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. L Deslandes J Olivier F Theulieres J Hirsch DX Feng P Bittner-Eddy J Beynon Y Marco, Proceedings of the National Academy of Sciences of the United States of America 2002 99 4 2404 2409 11842188 10.1073/pnas.032485099
138. Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. L Deslandes J Olivier N Peeters DX Feng M Khounlotham C Boucher I Somssich S Genin Y Marco, Proceedings of the National Academy of Sciences of the United States of America 2003 100 13 8024 8029 12788974 10.1073/pnas.1230660100
139. Two TIR:NB:LRR genes are required to specify resistance to Peronospora parasitica isolate Cala2 in Arabidopsis. E Sinapidou K Williams L Nott S Bahkt M Tor I Crute P Bittner-Eddy J Beynon, Plant J 2004 38 6 898 909 10.1111/j.1365-313X.2004.02099.x 15165183
140. Targeted activation tagging of the Arabidopsis NBS-LRR gene, ADR1, conveys resistance to virulent pathogens. JJ Grant A Chini D Basu GJ Loake, Mol Plant Microbe Interact 2003 16 8 669 680 10.1094/MPMI.2003.16.8.669 12906111
141. Transgressive segregation reveals two Arabidopsis TIR-NB-LRR resistance genes effective against Leptosphaeria maculans, causal agent of blackleg disease. J Staal M Kaliff S Bohman C Dixelius, Plant J 2006 46 2 218 230 10.1111/j.1365-313X.2006.02688.x 16623885