In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme

BMC Genomics

Volumn 9, Issue SUPPL. 2, 2008, Pages

  Yuan, Jiazheng ^a   Zhu, Mengxia ^a   Lightfoot, David A ^a   Javed, M Javed ^a   Yang, Jack Y ^b   Meksem, Khalid ^a  

^a SOUTHERN ILLINOIS UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; COMPUTER MODEL; CONFERENCE PAPER; CONTROLLED STUDY; FUNGAL PLANT DISEASE; FUSARIUM; FUSARIUM VIRGULIFORME; GENE INTERACTION; GENETIC TRANSCRIPTION; HOST PATHOGEN INTERACTION; INFECTION RESISTANCE; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PLANT GENETICS; PLANT RESPONSE; SOYBEAN; ARTICLE; BIOLOGY; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; MICROBIOLOGY; PATHOGENICITY; PHYLOGENY; PLANT ROOT; SEQUENCE ALIGNMENT;

ARABIDOPSIS THALIANA; FUNGI; FUSARIUM; FUSARIUM SOLANI F. SP. GLYCINES; FUSARIUM VIRGULIFORME; GLYCINE MAX; NEMATODA;

PLANT RNA;

ARABIDOPSIS; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; FUSARIUM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PLANT ROOTS; RNA, PLANT; SEQUENCE ALIGNMENT; SOFTWARE; SOYBEANS;

EID: 52249100583     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-S2-S6     Document Type: Conference Paper

References (68)

1. Journot-Catalino N Somssich IE Roby D Kroj T The transcription factors WRKY11 and WRKY17 Act as negative regulators of basal resistance in Arabidopsis thaliana Plant Cell 2006, 18:3289-3302. 1693958 17114354 10.1105/tpc.106.044149
2. Schenk PM Kazan K Wilson I Anderson JP Richmond T Somerville SC Manners JM Coordinated plant defense responses in Arabidopsis revealed by microarray analysis Proc Natl Acad Sci USA 2000, 97:11655-11660. 17256 11027363 10.1073/pnas.97.21.11655
3. Wang R Guegler K LaBrie ST Crawford NM Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate Plant Cell 2000, 12:1491-1510. 149118 10948265 10.1105/tpc.12.8.1491
4. Wang R Tischner R Gutierrez RA Hoffman M Xing X Chen M Coruzzi G Crawford NM Genomic analysis of the nitrate response using a nitrate reductase null mutant of Arabidopsis Plant Physiol 2004, 136:2512-2522. 523318 15333754 10.1104/pp.104.044610
5. Lockhart DJ Winzeler EA Genomics, gene expression and DNA arrays Nature 2000, 405:827-836. 10.1038/35015701 10866209
6. Gutierrez RA Ewing RM Cherry JM Green PJ Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes Proc Natl Acad Sci USA 2002, 99:11513-11518. 123287 12167669 10.1073/ pnas.152204099
7. Lloyd JC Zakhleniuk OV Responses of primary and secondary metabolism to sugar accumulation revealed by microarray expression analysis of the Arabidopsis mutant, pho3 J Exp Bot 2004, 55:1221-1230. 10.1093/jxb/ erh143 15133053
8. Zhao B Ardales E Raymundo A Bai J Trick H Leach J Hulbert S The avrRxo1 gene from the rice pathogen Xanthomonas oryzae pv. oryzicola confers a nonhost defense reaction on maize with resistance gene Rxo1 Mol Plant-Microbe Interact 2004, 17:771-779. 10.1094/MPMI.2004.17.7.771 15242171
9. Iqbal MJ Yaegashi S Ahsan R Shopinski K Lightfoot DA Root response to F. solani f. sp. glycines: Temporal accumulation of transcripts in partially resistant and susceptible soybean Theor and Appl Genet 2005, 110:1429-1438. 10.1007/s00122-005-1969-9
10. Iqbal MJ Yaegashi S Njiti V Ahsan R Cryder KL Lightfoot DA Resistance locus pyramids alter transcript abundance in soybean roots inoculated by Fusarium solani f. sp. glycines Mol Genet and Genom 2002, 268:407-417. 10.1007/s00438-002-0762-6
11. Iqbal MJ Afzal AJ Yaegashi S Ruben E Triwitayakorn K Njiti V Ahsan R Wood AJ Lightfoot DA A pyramid of loci for partial resistance to Fusarium solani fsp Theor and Appl Genet 2002, 105:1115-1123. 10.1007/ s00122-002-0987-0
12. Dangl JL Ritter C Gibbon MJ Muir LA Wood JR Goss S Mansfield I Taylor JD Vivian A Functional homologs of the Arabidopsis RPM7 disease resistance gene in bean and pea Plant Cell 1992, 4:1359-1369. 10.1105/tpc.4.11.1359 1477552 160224
13. Innes RW Bisgrove SR Smith NM Bent AF Staskawicz BJ Liu YC Identification of a disease resistance locus in Arabidopsis that is functionally homologous to the Rpgl locus of soybean Plant J 1993, 4:813-820. 10.1046/j.1365-313X.1993.04050813.x 8275100
14. Simonich MT Innes RW A disease resistance gene in Arabidopsis with specificity for the avrPph3 gene of Pseudomonas syringae pv. phaseolicola Mol Plant Microbe lnteract 1995, 8:637-640.
15. Meyers BC Kaushik S Nandety RS Evolving disease resistance genes Curr Opin Plant Biol 2005, 8:129-134. 10.1016/j.pbi.2005.01.002 15752991
16. Labrador M Corces VG Setting the boundaries of chromatin domains and nuclear organization Cell 2002, 111:151-154. 10.1016/ S0092-8674(02)01004-8 12408858
17. Dixon RA Achnine L Kota P Liu CJ Reddy MSS Wang L The phenylpropanoid pathway and plant defense - a genomics perspective Mol Plant Pathol 2002, 3:371-390. 10.1046/j.1364-3703.2002.00131.x
18. Durner J Wendehenne D Klessig DF Defense gene induction in tobacco by nitric oxide, cyclic GMP, and cyclic ADP-ribose Proc Natl Acad Sci 1998, 95:10328-10333. 21508 9707647 10.1073/pnas.95.17.10328
19. McDowell JM Woffenden BJ Plant disease resistance genes: Recent insights and potential applications Trends in Biotechnology 2003, 21:178-183. 10.1016/S0167-7799(03)00053-2 12679066
20. Cochrane FC Davin LB Lewis NG The Arabidopsis phenylalanine ammonia lyase gene family: Kinetic characterization of the four PAL isoforms Phytochemistry 2004, 65:1557-1564. 10.1016/j.phytochem.2004.05.006 15276452
21. Pellegrini L Geoffroy P Fritig B Legrand M Molecular cloning and expression of a new class of ortho-diphenol-O-methyltransferases induced in tobacco (Nicotiana tabacum L.) leaves by infection or elicitor treatment Plant Physiol 1993, 103:509-517. 159010 7518088 10.1104/ pp.103.2.509
22. Pellegrin L Rohfritsch O Fritig B Legrand M Phenylalanine ammonia-lyase in tobacco. Molecular cloning and gene expression during the hypersensitive reaction to tobacco mosaic virus and the response to a fungal elicitor Plant Physiol 1994, 106:877-886. 159610 7824656 10.1104/ pp.106.3.877
23. Lozovaya V Lygin A Zernova O Li S Hartman G Widholm J Isoflavonoid accumulation in soybean hairy roots upon treatment with Fusarium solani Plant Physiol Biochem 2004, 42:671-679. 10.1016/j.plaphy.2004.06.007 15331097
24. Maher EA Bate NJ Ni W Elkind Y Dixon RA Lamb CJ Increased disease susceptibility of transgenic tobacco plants with suppressed levels of preformed phenylpropanoid products Proc Natl Acad Sci 1994, 91:7802-7806. 44490 8052663 10.1073/pnas.91.16.7802
25. Pallas JA Paiva NL Lamb CJ Dixon RA Tobacco plants epigenetically suppressed in phenylalanine ammonia-lyase expression do not develop systemic acquired resistance in response to infection by tobacco mosaic virus Plant J 1996, 10:281-293. 10.1046/j.1365-313X.1996.10020281.x
26. Mitchell HJ Hall SA Stratford R Hall JL Barber MS Differential induction of cinnamyl alcohol dehydrogenase during defensive lignification in wheat (Triticum aestivum L.): Characterisation of the major inducible form Planta 1999, 208:31-37. 10.1007/s004250050531
27. Buchanan BB Gruissem W Jones RL Biochemistry and molecular biology of plants American Society of Plant Physiologists 2000.
28. Humphreys JM Chapple C Rewriting the lignin roadmap Curr Opin Plant Biol 2002, 5:224-229. 10.1016/S1369-5266(02)00257-1 11960740
29. Boerjan W Ralph J Baucher M Lignin biosynthesis Annu Rev Plant Biol 2003, 54:519-546. 10.1146/annurev.arplant.54.031902.134938 14503002
30. Baucher M Halpin C Petit-Conil M Boerjan W Lignin: Genetic engineering and impact on pulping Crit Rev Biochem Mol Biol 2003, 38:305-350. 10.1080/10409230391036757 14551235
31. Davin LB Bedgar DL Katayama T Lewis NG On the stereospecific synthesis of (+) pinoresinol in Forsythia suspensa from its achiral precursor, coniferyl alcohol Phytochemistry 1992, 31:3869-3874. 10.1016/ S0031-9422(00)97544-7 11536515
32. Dean JFD LaFayette PR Rugh C Tristram AH Hoopes JT Eriksson K-EL Merkle SA Laccases associated with lignifying vascular tissue Lignin and Lignan Biosynthesis Washington, DC: American Chemical Society Lewis NG, Sarkanen S 1998:96-108.
33. Hong SP Leiper FC Woods A Carling D Carlson M Activation of yeast Snf1 and mammalian AMP-activated protein kinase by upstream kinases Proc Natl Acad Sci 2003, 100:8839-8843. 166400 12847291 10.1073/pnas.1533136100
34. Hardie DG Simon A Hawley SA Scott JW AMP-activated protein kinase - development of the energy sensor concept J Physiol 2006, 574:7-15. 1817788 16644800 10.1113/jphysiol.2006.108944
35. Halford NG Hardie DG SNF1-related protein kinases: Global regulators of carbon metabolism in plants? Plant Mol Biol 1999, 37:735-748. 10.1023/ A:1006024231305
36. Woods A Munday MR Scott J Yang X Carlson M Carling D Yeast SNF1 is functionally related to mammalian AMP-activated protein kinase and regulates acetyl-CoA carboxylase in vivo J Biol Chem 1994, 269:19509-19515. 7913470
37. Schwachtje J Minchin EHP Jahnke S van Dongen TJ Schittko U Baldwin TI SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots Proc Natl Acad Sci USA 2006, 103:12935-12940. 1568949 16912118 10.1073/pnas.0602316103
38. Tooley PW Grau CR Identification and quantitative characterization of rate-reducing resistance to Phytophthora megasperma f.sp. glycinea in soybean seedlings Phytopathology 1982, 72:727-733.
39. Njiti VN Gray LE Lightfoot DA Rate-reducing resistance to Fusarium solani f.sp. phaseoli underlies field resistance to soybean sudden death syndrome (SDS) Crop Sci 1997, 37:1-12.
40. Yu I Fengler KA Clough SJ Bent AF Identification of Arabidopsis mutants exhibiting an altered hypersensitive response in gene-for-gene disease resistance Mol Plant Microbe Interact 2000, 13:277-286. 10.1094/ MPMI.2000.13.3.277 10707353
41. Gebhardt C Valkonen JP Organization of genes controlling disease resistance in the potato genome Annu Rev Phytopathol 2001, 39:79-102. 10.1146/annurev.phyto.39.1.79 11701860
42. Piffanelli P Zhou F Casais C Orme J Jarosch B Schaffrath U Collins NC Panstruga R Schulze-Lefert P The barley MLO modulator of defense and cell death is responsive to biotic and abiotic stress stimuli Plant Physiol 2002, 129:1076-1085. 166502 12114562 10.1104/pp.010954
43. Schultheiss H Dechert C Kogel KH Huckelhoven Functional analysis of barley RAC/ROP G-protein family members in susceptibility to the powdery mildew fungus Plant J 2003, 36:589-601. 10.1046/j.1365-313X.2003.01905.x 14617061
44. Aoki T O'Donnell K Homma Y Lattanzi AR Sudden death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex - F. virguliforme in North America and F. tucumaniae in South America Mycologia 2003, 95:660-684. 10.2307/3761942
45. Jin H Hartman GL Nickell CD Widholm JM Characterization and purification of a phytotoxin produced by Fusarium solani, the causal agent of soybean sudden death syndrome Phytopathology 1996, 86:277-282. 10.1094/ Phyto-86-277
46. Achenbach LA Patrick J Gary L Use of RAPD markers as a diagnostic tool for the identification of Fusarium solani isolates that cause soybean sudden death syndrome Plant Disease 1999, 80:1228-1232.
47. Wrather JA Sleper DA Steven WE Shannon JG Wilson RF Planting date and cultivar effects on soybean yield, seed quality, and Phomopsis sp. seed infection Plant Dis 2003, 87:529-532. 10.1094/PDIS.2003.87.5.529
48. Shoemaker R Keim P Vodkin L Retzel E Clifton SW Waterson R Smoller D Coryell V Khanna A Erpelding J Gai X Brendel V Raph-Schmidt C Shoop EG Vielweber CJ Schmatz M Pape D Bowers Y Theising B Martin J Dante M Wylie T Granger C A compilation of soybean ESTs: Generation and analysis Genome 2002, 45:329-338. 10.1139/g01-150 11962630
49. Pevsner J Bioinformatics and Functional Genomics New York: John Wiley & Sons Inc 2003.
50. Thimm O Bläsing O Gibon Y Nagel A Meyer S Krüger P Selbig J Müller LA Rhee SY Stitt M MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metaboli pathways and other biological processes Plant J 2004, 37:914-939. 10.1111/ j.1365-313X.2004.02016.x 14996223
51. Wang Y Yun B Kwon Y Hong J Yoon J Loake G S-Nitrosylation: An emerging redox-based post-translational modification in plants J Exp Bot 2006, 57:1777-1784. 10.1093/jxb/erj211 16714306
52. Geisler-Lee J O'Toole N Ammar R Provart NJ Millar AH Geisler M A Predicted Interactome for Arabidopsis Plant Physiology 2007, 145:317-329. 2048726 17675552 10.1104/pp.107.103465
53. Schwachtje J Minchin PEH Jahnke S van Dongen JT Schittko U Balswin IT SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots Proc Natl Acad Sci USA 2006, 103:12935-12940. 1568949 16912118 10.1073/pnas.0602316103
54. Hawley SA Boudeau J Reid JL Mustard KJ Udd L Makela TP Alessi DR Hardie DG Complexes between the LKB1 tumor suppressor, STRADα/β and MO25α/β are upstream kinases in the AMP-activated protein kinase cascade J Biol 2003, 2:28. 333410 14511394 10.1186/1475-4924-2-28
55. Thompson JD Gibson TJ Plewniak F Jeanmougin F Higgins DG The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Nucl Acids Res 1997, 25:4876-4882. 147148 9396791 10.1093/nar/25.24.4876
56. Kumar S Tamura K Nei M MEGA 3: Integrated software for Molecular Evolutionary Genetics Analysis sequence alignment Brief Bioinform 2004, 5:150-163. 10.1093/bib/5.2.150 15260895
57. Shadle GL Wesley SV Korth KL Chen F Lamb C Dixon RA Phenylpropanoid compounds and disease resistance in transgenic tobacco with altered expression of L-phenylalanine ammonia-lyase Phytochemistry 2003, 64:153-161. 10.1016/S0031-9422(03)00151-1 12946414
58. Chong J Baltz R Schmitt C Beffa R Fritig B Saindrenan P Downregulation of a pathogen-responsive tobacco UDP-Glc:pHenylpropanoid glucosyltransferase reduces scopoletin glucoside accumulation, enhances oxidative stress, and weakens virus resistance Plant Cell 2002, 14:1093-1107. 150609 12034899 10.1105/tpc.010436
59. Way HM Kazan K Mitter N Goulter KC Birch RG Manners JM Constitutive expression of a phenylalanine ammonia-lyase gene from Stylosanthes humilis in transgenic tobacco leads to enhanced disease resistance but impaired plant growth Physiol and Mol Plant Pathol 2002, 60:275-282.
60. Tsuji J Jackson EP Gage DA Hammerschmidt R Somerville SC Phytoalexin accumulation in Arabidopsis thaliana during the hypersensitive reaction to Pseudomonas syringae Pv syringa Plant Physiol 1992, 98:1304-1309. 1080349 16668792
61. Buell CR Somerville SC Expression of defense-related and putative signaling genes during tolerant and susceptible interactions of Arabidopsis with Xanthomonas campestris pv. campestri Mol Plant-Microbe Interact 1995, 8:435-443.
62. Thibaud MC Gineste S Nussaume L Robaglia C Sucrose increases athogenesis-related PR-2 gene expression in Arabidopsis thaliana through an SAdependent but NPR1-independent signaling pathway Plant Physiol Biochem 2004, 42:81-88. 10.1016/j.plaphy.2003.10.012 15061088
63. Gaudet AD Laroche A Yoshida M Low temperature-wheat-fungal interactions: A carbohydrate connection Physiologia Plantarum 1999, 106:437-444. 10.1034/j.1399-3054.1999.106412.x
64. Polge C Thomas M SNF1/AMPK/SnRK1 kinases, global regulators at the heart of energy control? Trends Plant Sci 2007, 12:20-28. 10.1016/ j.tplants.2006.11.005 17166759
65. Meyer R Yuan J Afzal J Iqbal J Zhu M Garvey G Lightfoot DA Identification of Gsr1: A locus inferred to regulate gene expression in response to exogenous glutamine Euphytica 2006, 151:291-302. 10.1007/ s10681-006-9149-9
66. Njiti VN Johnson JE Torto TA Gray LE Lightfoot DA Inoculum rate influences selection for field resistance to soybean sudden death syndrome in the greenhouse Crop Science 2001, 41:1726-1731.
67. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13:2498-2504. 403769 14597658 10.1101/gr.1239303
68. Thompson JD Higgins DG Gibson TG CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gp penalties and weight matrix choice Nucl Acids Res 1994, 22:4673-4680. 308517 7984417 10.1093/nar/22.22.4673