Skip to main content

Comparative RNA-Seq analysis of Nicotiana benthamiana in response to Phytophthora parasitica infection

Abstract

Phytophthora parasitica causes serious damage to a broad spectrum of agriculturally important crops and natural ecosystems. To investigate plant responses to P. p arasitica, differential gene expressions between inoculated and mock-treated Nicotiana benthamiana leaves were analyzed by RNA-Seq approach. A total of 5375 and 3614 N. b enthamiana genes were found to be upregulated and downregulated, respectively. Infection with P. p arasitica triggered massive metabolic reprogramming in the inoculated tissues. Genes related to photosynthesis, starch biosynthesis, and nitrogen assimilation were suppressed while sucrose degrading genes were induced. Notably, plant defense responses were activated, reflected by larger number of upregulated JA and ET signaling genes, receptor-like kinases, pathogenesis-related genes, and transcription factors. Collectively, these results provide broad insights into N. b enthamiana defense mechanisms against P. p arasitca and advance our understanding of plant-Phytophthora interactions.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  • Attard A, Gourgues M, Galiana E, Panabieres F, Ponchet M, Keller H (2008) Strategies of attack and defense in plant-oomycete interactions, accentuated for Phytophthora parasitica Dastur (syn. P. Nicotianae Breda de Haan). J Plant Physiol 165(1):83–94

    CAS  Article  PubMed  Google Scholar 

  • Berger S, Sinha AK, Roitsch T (2007) Plant physiology meets phytopathology: plant primary metabolism and plant-pathogen interactions. J Exp Bot 58(15–16):4019–4026

    CAS  Article  PubMed  Google Scholar 

  • Boller T, He SY (2009) Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 324(5928):742–744

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Bolton MD (2009) Primary metabolism and plant defense-fuel for the fire. Mol Plant Microbe In 22(5):487–497

    CAS  Article  Google Scholar 

  • Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA, Martin GB (2012) A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact 25(12):1523–1530

    CAS  Article  PubMed  Google Scholar 

  • Bos JIB, Prince D, Pitino M, Maffei ME, Win J, Hogenhout SA (2010) A functional genomics approach identifies candidate effectors from the aphid species Myzus persicae (Green Peach Aphid). PLoS Genet 6(11):e1001216

    Article  PubMed  PubMed Central  Google Scholar 

  • Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M (2010) Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res 20(10):1451–1458

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Chandran D, Inada N, Hather G, Kleindt CK, Wildermuth MC (2010) Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proc Natl Acad Sci USA 107(1):460–465

    CAS  Article  PubMed  Google Scholar 

  • Chapman S, Kavanagh T, Baulcombe D (1992) Potato virus X as a vector for gene expression in plants. Plant J 2(4):549–557

    CAS  PubMed  Google Scholar 

  • Chen XR, Li YP, Li QY, Xing YP, Liu BB, Tong YH, Xu JY (2015) SCR96, a small cysteine-rich secretory protein of Phytophthora cactorum, can trigger cell death in the Solanaceae and is important for pathogenicity and oxidative stress tolerance. Mol Plant Pathol. doi:10.1111/mpp.12303

    Google Scholar 

  • Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124(4):803–814

    CAS  Article  PubMed  Google Scholar 

  • Dou D, Kale SD, Wang X, Chen Y, Wang Q, Jiang RH, Arredondo FD, Anderson RG, Thakur PB, McDowell JM, Wang Y, Tyler BM (2008) Conserved C-terminal motifs required for avirulence and suppression of cell death by Phytophthora sojae effector Avr1b. Plant Cell 20(4):1118–1133

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y (2012) GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics 28(21):2782–2788

    CAS  Article  PubMed  Google Scholar 

  • Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43:205–227

    CAS  Article  PubMed  Google Scholar 

  • Goff KE, Ramonell KM (2007) The role and regulation of receptor-like kinases in plant defense. Gene Regul Syst Biol 1:167–175

    Google Scholar 

  • Gomez-Gomez L, Boller T (2000) FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol Cell 5(6):1003–1011

    CAS  Article  PubMed  Google Scholar 

  • Goodin MM, Zaitlin D, Naidu RA, Lommel SA (2008) Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions. Mol Plant Microbe Interact 21(8):1015–1026

    CAS  Article  PubMed  Google Scholar 

  • Jing SJ, Zhou X, Song Y, Yu DQ (2009) Heterologous expression of OsWRKY23 gene enhances pathogen defense and dark-induced leaf senescence in Arabidopsis. Plant Growth Regul 58(2):181–190

    CAS  Article  Google Scholar 

  • Jones JDG, Dangl JL (2006) The plant immune system. Nature 444(7117):323–329

    CAS  Article  PubMed  Google Scholar 

  • Jongedijk E, Tigelaar H, Vanroekel JSC, Bresvloemans SA, Dekker I, Vandenelzen PJM, Cornelissen BJC, Melchers LS (1995) Synergistic activity of chitinases and beta-1,3-glucanases enhances fungal resistance in transgenic tomato plants. Euphytica 85(1–3):173–180

    CAS  Article  Google Scholar 

  • Kamoun S, van West P, Vleeshouwers VGAA, de Groot KE, Govers F (1998) Resistance of Nicotiana benthamiana to Phytophthora infestans is mediated by the recognition of the elicitor protein INF1. Plant Cell 10(9):1413–1425

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Kamoun S, Furzer O, Jones JD, Judelson HS, Ali GS, Dalio RJ, Roy SG, Schena L, Zambounis A, Panabieres F, Cahill D, Ruocco M, Figueiredo A, Chen XR, Hulvey J, Stam R, Lamour K, Gijzen M, Tyler BM, Grunwald NJ, Mukhtar MS, Tome DF, Tor M, Van Den Ackerveken G, McDowell J, Daayf F, Fry WE, Lindqvist-Kreuze H, Meijer HJ, Petre B, Ristaino J, Yoshida K, Birch PR, Govers F (2015) The Top 10 oomycete pathogens in molecular plant pathology. Mol Plant Pathol 16(4):413–434

    Article  PubMed  Google Scholar 

  • Kroon LP, Brouwer H, de Cock AW, Govers F (2012) The genus Phytophthora anno 2012. Phytopathology 102(4):348–364

    Article  PubMed  Google Scholar 

  • Liu T, Ye W, Ru Y, Yang X, Gu B, Tao K, Lu S, Dong S, Zheng X, Shan W, Wang Y, Dou D (2011) Two host cytoplasmic effectors are required for pathogenesis of Phytophthora sojae by suppression of host defenses. Plant Physiol 155(1):490–501

    CAS  Article  PubMed  Google Scholar 

  • Liu D, Shi L, Han C, Yu J, Li D, Zhang Y (2012) Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR. PLoS ONE 7(9):e46451

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402–408

    CAS  Article  PubMed  Google Scholar 

  • Lopez MA, Bannenberg G, Castresana C (2008) Controlling hormone signaling is a plant and pathogen challenge for growth and survival. Curr Opin Plant Biol 11(4):420–427

    CAS  Article  PubMed  Google Scholar 

  • Lu X, Chen D, Shu D, Zhang Z, Wang W, Klukas C, Chen LL, Fan Y, Chen M, Zhang C (2013) The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiol 162(1):440–455

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Ma L, Lukasik E, Gawehns F, Takken FL (2012) The use of agroinfiltration for transient expression of plant resistance and fungal effector proteins in Nicotiana benthamiana leaves. Methods Mol Biol 835:61–74

    CAS  Article  PubMed  Google Scholar 

  • Meng Y, Zhang Q, Ding W, Shan W (2014) Phytophthora parasitica: a model oomycete plant pathogen. Mycology 5(2):43–51

    Article  PubMed  PubMed Central  Google Scholar 

  • Miedes E, Vanholme R, Boerjan W, Molina A (2014) The role of the secondary cell wall in plant resistance to pathogens. Front Plant Sci 5:358

    Article  PubMed  PubMed Central  Google Scholar 

  • Purkayastha A, Dasgupta I (2009) Virus-induced gene silencing: a versatile tool for discovery of gene functions in plants. Plant Physiol Bioch 47(11–12):967–976

    CAS  Article  Google Scholar 

  • Rojas CM, Senthil-Kumar M, Tzin V, Mysore KS (2014) Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense. Front Plant Sci 5:17

    Article  PubMed  PubMed Central  Google Scholar 

  • Scheideler M, Schlaich NL, Fellenberg K, Beissbarth T, Hauser NC, Vingron M, Slusarenko AJ, Hoheisel JD (2002) Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem 277(12):10555–10561

    CAS  Article  PubMed  Google Scholar 

  • Sels J, Mathys J, De Coninck BM, Cammue BP, De Bolle MF (2008) Plant pathogenesis-related (PR) proteins: a focus on PR peptides. Plant Physiol Bioch 46(11):941–950

    CAS  Article  Google Scholar 

  • Spoel SH, Dong X (2008) Making sense of hormone crosstalk during plant immune responses. Cell Host Microbe 3(6):348–351

    CAS  Article  PubMed  Google Scholar 

  • Teixeira PJ, Thomazella DP, Reis O, do Prado PF, do Rio MC, Fiorin GL, Jose J, Costa GG, Negri VA, Mondego JM, Mieczkowski P, Pereira GA (2014) High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa. Plant Cell 26(11):4245–4269

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37(6):914–939

    CAS  Article  PubMed  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Wang KL, Li H, Ecker JR (2002) Ethylene biosynthesis and signaling networks. Plant Cell 14(Suppl):S131–S151

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This research was supported by grants from the National Natural Science Foundation of China (31501589) and China Postdoctoral Science Foundation (2015M571769).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Daolong Dou.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shen, D., Chai, C., Ma, L. et al. Comparative RNA-Seq analysis of Nicotiana benthamiana in response to Phytophthora parasitica infection. Plant Growth Regul 80, 59–67 (2016). https://doi.org/10.1007/s10725-016-0163-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10725-016-0163-1

Keywords

  • Nicotiana benthamiana
  • RNA-Seq analysis
  • Plant-Phytophthora interaction
  • Plant defense