Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis

Abstract

The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem.

A genomics perspective on cucurbit-oomycete interactions

“…To better understand the pathogen and its life cycle at a molecular level, previous research has characterized the infection stages using and combination of microscopy and next-generation sequencing (Adhikari et al 2012;Savory et al 2012b). To this end, the transcriptomes of Ps.…”

“…To this end, the transcriptomes of Ps. cubensis and 'Vlaspik,' a susceptible C. sativus cultivar, have been sequenced at 1, 2, 3, 4, 6, and 8 days post inoculation (dpi) using next generation Illumina technology (Adhikari et al 2012;Savory et al 2012b). These 35-42 bp single end reads from the Illumina Genome Analyzer II platform were then mapped to the Ps.…”

“…These 35-42 bp single end reads from the Illumina Genome Analyzer II platform were then mapped to the Ps. cubensis genome using Bowtie and TopHat and were processed and quantified using Cufflinks (Adhikari et al 2012;Savory et al 2012b). Out of the approximately 23,000 genes in the 67.9 Mb genome of Ps.…”

“…Out of the approximately 23,000 genes in the 67.9 Mb genome of Ps. cubensis, 7,821 genes were expressed within the time course (Adhikari et al 2012;Savory et al 2012b). The expression of differentially expressed genes was evaluated using the Pearson correlation coefficient, and early, middle and late phases of infection were determined (Adhikari et al 2012;Savory et al 2012b).…”

“…cubensis, 7,821 genes were expressed within the time course (Adhikari et al 2012;Savory et al 2012b). The expression of differentially expressed genes was evaluated using the Pearson correlation coefficient, and early, middle and late phases of infection were determined (Adhikari et al 2012;Savory et al 2012b). These phases correlated well with the expression of orthologous genes in another oomycete pathogen, Phytophthora infestans, especially at 4 dpi during which haustoria formation and pathogen colonization is occurring in both oomycetes (Adhikari et al 2012;Savory et al 2012b).…”