Open AccessTranscriptome and Small RNAome Dynamics during a Resistant and Susceptible Interaction between Cucumber and Downy Mildew
Author(s) -
Burkhardt Alyssa,
Day Brad
Publication year - 2016
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2015.08.0069
Subject(s) - biology , downy mildew , transcriptome , oomycete , gene , genetics , candidate gene , de novo transcriptome assembly , plant disease resistance , obligate , gene expression profiling , gene expression , computational biology , botany
Cucumber ( Cucumis sativus L.) downy mildew, caused by the obligate oomycete pathogen Pseudoperonospora cubensis (Berk. and Curt.) Rostov., is the primary factor limiting cucumber production. Although sources of resistance have been identified, such as plant introduction line PI 197088, the genes and processes involved in mediating resistance are still unknown. In the current study, we conducted a comprehensive transcriptome and small RNAome analysis of a resistant (PI 197088) and susceptible (‘Vlaspik’) cucumber during a time course of P. cubensis infection using Illumina sequencing. We identified significantly differentially expressed (DE) genes within and between resistant and susceptible cucumber leaves over a time course of infection. Weighted gene correlation network analyses (WGCNA) created coexpression modules containing genes with unique expression patterns between Vlaspik and PI 197088. Recurring data trends indicated that resistance to cucumber downy mildew is associated with earlier response to the pathogen, hormone signaling, and regulation of nutrient supply. Candidate resistance genes were identified from multiple transcriptome analyses and literature support. Additionally, parallel sequencing of small RNAs (sRNAs) from cucumber and P. cubensis during the infection time course was used to identify and quantify novel and existing microRNA (miRNA) in both species. Predicted miRNA targets of cucumber transcripts suggest a complex interconnectedness of gene expression regulation in this plant–pathogen system. This work bioinformatically uncovered gene expression patterns involved in the mediation of or response to P. cubensis resistance. Herein, we provide the foundation for future work to validate candidate resistance genes and miRNA‐based regulation proposed in this study.