Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq

Gene

Volumn 512, Issue 2, 2013, Pages 259-266

  Zhu, Qian Hao ^a   Stephen, Stuart ^a   Kazan, Kemal ^a   Jin, Gulei ^b   Fan, Longjiang ^b   Taylor, Jennifer ^a   Dennis, Elizabeth S ^a   Helliwell, Chris A ^a   Wang, Ming Bo ^a  

^a CSIRO   (Australia)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

Arabidopsis; Fusarium oxysporum; Innate immune response; NADPH oxidase; Transcriptome sequencing

Indexed keywords

REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE OXIDASE; TRANSCRIPTOME;

ARABIDOPSIS; ARTICLE; DOWN REGULATION; FUSARIUM OXYSPORUM; FUSARIUM WILT; GENE LIBRARY; GENETIC ANALYSIS; NONHUMAN; PLANT DISEASE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; STRAND SPECIFIC RNA SEQUENCING; UPREGULATION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; FUSARIUM; GENE EXPRESSION REGULATION; HOST-PARASITE INTERACTIONS; NADPH OXIDASE; PLANT DISEASES; PLANT IMMUNITY; TRANSCRIPTOME;

ARABIDOPSIS; FUSARIUM OXYSPORUM;

EID: 84870359630     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.10.036     Document Type: Article

References (48)

1. Anderson J.P., et al. Antagonistic interaction between abscisic acid and jasmonate-ethylene signaling pathways modulates defense gene expression and disease resistance in Arabidopsis. Plant Cell 2004, 16:3460-3479.
2. Andreasson E., Ellis B. Convergence and specificity in the Arabidopsis MAPK nexus. Trends Plant Sci. 2010, 15:106-113.
3. Asai T., et al. MAP kinase signaling cascade in Arabidopsis innate immunity. Nature 2002, 415:977-983.
4. Bae H., Kim M.S., Sicher R.C., Bae H.J., Bailey B.A. Necrosis- and ethylene-inducing peptide from Fusarium oxysporum induces a complex cascade of transcripts associated with signal transduction and cell death in Arabidopsis. Plant Physiol. 2006, 141:1056-1067.
5. Bednarek P., et al. A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense. Science 2009, 323:101-106.
6. Berrocal-Lobo M., Molina A. Ethylene response factor 1 mediates Arabidopsis resistance to the soilborne fungus Fusarium oxysporum. Mol. Plant Microbe Interact. 2004, 17:763-770.
7. Berrocal-Lobo M., Molina A. Arabidopsis defense response against Fusarium oxysporum. Trends Plant Sci. 2008, 13:145-150.
8. Bu Q., et al. Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses. Cell Res. 2008, 18:756-767.
9. Chen C., et al. Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes. BMC Plant Biol. 2010, 10:280.
10. Clay N.K., Adio A.M., Denoux C., Jander G., Ausubel F.M. Glucosinolate metabolites required for an Arabidopsis innate immune response. Science 2009, 323:95-101.
11. Czechowski T., Bari R.P., Stitt M., Scheible W., Udvardi M.K. Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific gene. Plant J. 2004, 38:366-379.
12. Davies D.R., Bindschedler L.V., Strickland T.S., Bolwell G.P. Production of reactive oxygen species in Arabidopsis thaliana cell suspension cultures in response to an elicitor from Fusarium oxysporum: implications for basal resistance. J. Exp. Bot. 2006, 57:1817-1827.
13. Edgar C.I., et al. Salicylic acid mediates resistance to the vascular wilt pathogen Fusarium oxysporum in the model host Arabidopsis thaliana. Aust. Plant Pathol. 2006, 35:581-591.
14. Filichkin S.A., et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 2010, 20:45-58.
15. Gigolashvili T., Berger B., Mock H.P., Müller C., Weisshaar B., Flügge U.I. The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana. Plant J. 2007, 50:886-901.
16. Godiard L., et al. CYP76C2, an Arabidopsis thaliana cytochrome P450 gene expressed during hypersensitive and developmental cell death. FEBS Lett. 1998, 438:245-249.
17. Kidd B.N., et al. The Mediator complex subunit PFT1 is a key regulator of jasmonate-dependent defense in Arabidopsis. Plant Cell 2009, 21:2237-2252.
18. Kidd B.N., et al. Auxin signaling and transport promote susceptibility to the root-infecting fungal pathogen Fusarium oxysporum in Arabidopsis. Mol. Plant Microbe Interact. 2011, 24:733-748.
19. Kim K.H., et al. RNA-Seq analysis of a soybean near-isogenic line carrying bacterial leaf pustule-resistant and -susceptible alleles. DNA Res. 2011, 18:483-497.
20. Li Y., Zhang Q., Zhang J., Wu L., Qi Y., Zhou J.M. Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol. 2010, 152:2222-2231.
21. Liu J., Elmore J.M., Coaker G. Investigating the functions of the RIN4 protein complex during plant innate immune responses. Plant Signal. Behav. 2009, 4:1107-1110.
22. Liu F., et al. The Arabidopsis P450 protein CYP82C2 modulates jasmonate-induced root growth inhibition, defense gene expression and indole glucosinolate biosynthesis. Cell Res. 2010, 20:539-552.
23. (-Delta Delta C(t)) method. Methods 2001, 25:402-408.
24. Lu T., et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 2010, 20:1238-1249.
25. Lu D., et al. Direct ubiquitination of pattern recognition receptor FLS2 attenuates plant innate immunity. Science 2011, 332:1439-1442.
26. Maleck K., et al. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat. Genet. 2000, 26:403-410.
27. Miller G., et al. The plant NADPH oxidase RBOHD mediates rapid systemic signaling in response to diverse stimuli. Sci. Signal. 2009, 2:ra45.
28. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
29. Pfalz M., Vogel H., Kroymann J. The gene controlling the indole glucosinolate modifier1 quantitative trait locus alters indole glucosinolate structures and aphid resistance in Arabidopsis. Plant Cell 2009, 21:985-999.
30. Pogány M., et al. Dual roles of reactive oxygen species and NADPH oxidase RBOHD in an Arabidopsis-Alternaria pathosystem. Plant Physiol. 2009, 151:1459-1475.
31. Proels R.K., Oberhollenzer K., Pathuri I.P., Hensel G., Kumlehn J., Hückelhoven R. RBOHF2 of barley is required for normal development of penetration resistance to the parasitic fungus Blumeria graminis f. sp. Hordei. Mol. Plant Microbe Interact. 2010, 23:1143-1150.
32. Ren D., et al. A fungal-responsive MAPK cascade regulates phytoalexin biosynthesis in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:5638-5643.
33. Schenk P.M., et al. Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:11655-11660.
34. Sunkar R. MicroRNAs with macro-effects on plant stress responses. Semin. Cell Dev. Biol. 2010, 21:805-811.
35. Tarazona S., García-Alcalde F., Dopazo J., Ferrer A., Conesa A. Differential expression in RNA-seq: a matter of depth. Genome Res. 2011, 21:2213-2223.
36. Tay Y., et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 2011, 147:344-357.
37. Thatcher L.F., Manners J.M., Kazan K. Fusarium oxysporum hijacks COI1-mediated jasmonate signaling to promote disease development in Arabidopsis. Plant J. 2009, 58:927-939.
38. Torres M.A., Dangl J.L. Functions of the respiratory burst oxidase in biotic interactions, abiotic stress and development. Curr. Opin. Plant Biol. 2005, 8:397-403.
39. Torres M.A., Dangl J.L., Jones J.D. Arabidopsis gp91phox homologues AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:517-522.
40. Torres M.A., Jones J.D., Dangl J.L. Pathogen-induced, NADPH oxidase-derived reactive oxygen intermediates suppress spread of cell death in Arabidopsis thaliana. Nat. Genet. 2005, 37:1130-1134.
41. Torres M.A., Jones J.D., Dangl J.L. Reactive oxygen species signaling in response to pathogens. Plant Physiol. 2006, 141:373-378.
42. van Breusegem F., Bailey-Serres J., Mittler R. Unraveling the tapestry of networks involving reactive oxygen species in plants. Plant Physiol. 2008, 147:978-984.
43. Wang D., Amornsiripanitch N., Dong X. A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog. 2006, 2:e123.
44. Xu L., et al. Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. J. Exp. Bot. 2011, 62:5607-5621.
45. Yang H., Lu P., Wang Y., Ma H. The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process. Plant J. 2011, 65:503-516.
46. Zenoni S., et al. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 2010, 152:1787-1795.
47. Zhang G., et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 2010, 20:646-654.
48. Zhang W., et al. Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol. Biol. 2011, 75:93-105.