Cucumber Project

Transcriptional dynamics during the cucurbit-downy mildew interaction.

Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew, is a devastating, obligate pathogen that in the last 10 years, has overcome resistance in commercial cucumber varieties, and is increasing in virulence and incidence of disease. For decades, cucurbit-producing regions in Europe and Asia have faced production pressures from P. cubensis, while in the United States, P. cubensis was successfully managed through plant resistance conferred by the cucumber recessive locus dm-1. The overarching goal of our work in this area is to define how resistance, susceptibility, and virulence are genetically regulated.


Project_Cucurbit Downy Mildew_1

The P. cubensis life cycle. A) Single sporangia differentiate upon contact with moisture into zoospores (B) within 24 h of host contact. C) Zoospores encyst and enter through stomata by 1 dpi, and grow through intracellular spaces 2-3 dpi (D & E). By 4 dpi (F) haustoria (‘h’) have formed, and colonization of the mesophyll continues through 8 dpi. By 8 dpi, disease symptoms are evident, with the presences of heavy sporulation on the underside of the leaves (G), and (H) confluent yellow angular lesions with necrotic centers on the upper leaf surface. Scale bars: C-F = 25 mm.


We have generated a draft genome assembly of P. cubensis isolate MSU-1, with a primary goal of generating genomic resources to inventory the virulence potential of the pathogen (i.e., effector discovery). In total, we have used RNA-Seq to profile genome-wide changes in gene expression during distinct stages of the growth and development of P. cubensis on susceptible plants, generating the most comprehensive RNA-Seq dataset of a time-course of infection by an oomycete pathogen. More recently, we have generated an additional 1.6 billion sequenced fragments, which has enabled us to define several key mechanisms associated with the transcriptional interplay between host and pathogen, including: 1) pathogen alternative splicing during infection, 2) the identification of differentially expressed host genes during resistance and susceptibility, and 3) the identification of the pathogen and host sRNAome during resistance and susceptibility.


Future work in this area is aimed at:

  1. Characterize differential patterns of pathogen and host gene expression changes during resistant and susceptible interactions.

2. Characterization of host and pathogen sRNAs expressed during a resistant and susceptible interaction


Relevant publications:

Burkhardt, A. and Day, B. (2015). Plant pathogenic oomycetes: Counterbalancing resistance, susceptibility, and adaptation. Can. J. Plant Pathol. DOI:10.1080/07060661.2016.1149519

Burkhardt, A. and Day, B. (2015). Transcriptome and small RNAome dynamics during a resistant and susceptible interaction between cucumber and downy mildew. Plant Genome. doi:       10.3835/plantgenome2015.08.0069

Burkhardt, A., Buchanan, A., Cumbie, J.S., Savory, E.A., Chang, J.H.*, and Day, B.* (2015). Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis. Mol. Plant-Microbe Interact28: 298-309. *co-corresponding authors.

Burkhardt, A., and Day, B. (2013). A genomics perspective on cucurbit-oomycete interactions. Plant Biotech. 30: 265-271.

Savory, E.A., Adhikari, B., Vaillancourt, B., Hamilton, J., Buell, C.R., and Day, B. (2012). RNA-seq     analysis of the Pseudoperonospora cubensis transcriptome during infection of cucumber (Cucumis sativus). PloS One.10.1371/journal.pone.0035796.

Adhikari, B., Savory, E.A., Vaillancourt, B., Hamilton, J., Day, B. and Buell, C.R. (2012). Transcriptomic      response of Cucumis sativus to Pseudoperonospora cubensis infection. PLoS One. 0.1371/journal.pone.0034954.

Savory, E.A., Zou, C., Adhikari, B., Hamilton, J., Buell, C.R., Shiu, S-H., and Day, B. (2012). Alternative splicing of a Pseudoperonospora cubensis multi-drug transporter generates a translocated RXLR    effector protein that elicits a rapid cell death in cucumber. PLoS One. 10.1371/journal.pone.0034701.

Runge, F., Telle, S., Ploch, S., Savory, E., Day, B., Sharma, R., and Thines, M. (2011). Phylogenetic         relationships of downy mildews and their relatives reveal a high degree of paraphyly in Phytophthora.   IMA Fungus. 2: 163-171.

Tian, M., Win, J., Savory, E., Burkhardt, A., Held, M., Brandizzi, F., and Day, B. (2011). 454 genome   sequencing of Pseudoperonospora cubensis reveals effector proteins with a putative QXLR     translocation motif. Mol. Plant-Microbe Interact. 24: 543-553.

Savory, E.A., Granke, L.L., Quesada-Ocampo, L.M., Varbanova, M., Hausbeck, M.K., and Day, B. (2011). The cucurbit downy mildew pathogen Pseudoperonospora cubensis. Mol. Plant Pathol. 12: 217-226.