Nitrogen Supply and Host-Plant Genotype Modulate the Transcriptomic Profile of Plasmodiophora brassicae (original) (raw)
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BMC genomics, 2018
Clubroot is an important disease caused by the obligate parasite Plasmodiophora brassicae that infects the Brassicaceae. As a soil-borne pathogen, P. brassicae induces the generation of abnormal tissue in the root, resulting in the formation of galls. Root infection negatively affects the uptake of water and nutrients in host plants, severely reducing their growth and productivity. Many studies have emphasized the molecular and physiological effects of the clubroot disease on root tissues. The aim of the present study is to better understand the effect of P. brassicae on the transcriptome of both shoot and root tissues of Arabidopsis thaliana. Transcriptome profiling using RNA-seq was performed on both shoot and root tissues at 17, 20 and 24 days post inoculation (dpi) of A. thaliana, a model plant host for P. brassicae. The number of differentially expressed genes (DEGs) between infected and uninfected samples was larger in shoot than in root. In both shoot and root, more genes wer...
Frontiers in plant science, 2015
Although Plasmodiophora brassicae is one of the most common pathogens worldwide, the causal agent of clubroot disease in Brassica crops, resistance mechanisms to it are still only poorly understood. To study the early defense response induced by P. brassicae infection, a global transcriptome profiling of the roots of two near-isogenic lines (NILs) of clubroot-resistant (CR BJN3-2) and clubroot-susceptible (BJN3-2) Chinese cabbage (Brassica rapa) was performed by RNA-seq. Among the 42,730 unique genes mapped to the reference genome of B. rapa, 1875, and 2103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 h after inoculation (hai). Functional annotation showed that most of the differently expressed genes are involved in metabolism, transport, signal transduction, and defense. Of the genes assigned to plant-pathogen interactions, 151 showed different expression patterns between two NILs, including genes associated with pat...
Transcriptome Analysis IdentifiesPlasmodiophora brassicaeSecondary Infection Effector Candidates
Journal of Eukaryotic Microbiology, 2020
Plasmodiophora brassicae (Wor.) is an obligate intracellular plant pathogen affecting Brassicas worldwide. Identification of effector proteins is key to understanding the interaction between P. brassicae and its susceptible host plants. To date, there is very little information available on putative effector proteins secreted by P. brassicae during a secondary infection of susceptible host plants, resulting in root gall production. A bioinformatics pipeline approach to RNA-Seq data from Arabidopsis thaliana (L.) Heynh. root tissues at 17, 20, and 24 d postinoculation (dpi) identified 32 small secreted P. brassicae proteins (SSPbPs) that were highly expressed over this secondary infection time frame. Functional signal peptides were confirmed for 31 of the SSPbPs, supporting the accuracy of the pipeline designed to identify secreted proteins. Expression profiles at 0, 2, 5, 7, 14, 21, and 28 dpi verified the involvement of some of the SSPbPs in secondary infection. For seven of the SSPbPs, a functional domain was identified using Blast2GO and 3D structure analysis and domain functionality was confirmed for SSPbP22, a kinase localized to the cytoplasm and nucleus. THE Rhizarian protist Plasmodiophora brassicae (Wor.), a soil-borne pathogen of the Order Plasmodiophorales, is responsible for clubroot, one of the most devastating diseases affecting Brassica plants, with billion-dollar losses worldwide (Burki et al. 2010; Dixon 2009). As an obligate biotrophic intracellular pathogen, P. brassicae depends on its host for propagation and only resting spores or shortlived zoospores occur outside of plant tissues (Kageyama and Asano 2009). The life cycle of P. brassicae starts in the soil, where resting spores, which can remain viable for up to 20 yr (Hwang et al. 2012), germinate in response to the presence of plant hosts. During the secondary infection, susceptible plants develop galls that disrupt water and nutrient uptake, leading to wilting, stunting, and, in some instances, death of the infected plant (Dixon 2009). Many details of the P. brassicae life cycle and the P. brassicae-Brassica host interaction are still unknown. In order to manipulate plant defenses and enable parasitic colonization, many eukaryotic biotrophic plant pathogens have evolved a repertoire of effector proteins that in some cases are responsible for the suppression of plant immunity or changes in plant morphology that can increase infection success (Dodds and Rathjen 2010; Jones and Dangl 2006; Sugio et al. 2011). The concept of an effector protein is very broad, but basically it can be considered as any small secreted protein that facilitates the pathogen infection process (Dodds and Rathjen 2010). Conserved pathogen-associated molecular patterns (PAMPs) induce PAMP-triggered immunity in a host (Dodds and Rathjen 2010). This is the first level of a host immune response that can be overcome by effector proteins produced by adapted pathogens (Dodds and Rathjen 2010). Putative effectors have been identified in the genomes or transcriptomes of biotrophic plant pathogens, such as oomycetes and fungi, based on the presence of putative small secreted proteins and the expression profiles of these candidates (Duplessis et al. 2011; Hacquard et al. 2012). A similar strategy has been followed to identify
The contribution of surrounding plant microbiota to disease development has led to the postulation of the ‘pathobiome’ concept, which represents the interaction between the pathogen, the host-plant, and the associated biotic microbial community, resulting or not in plant disease. The structure, composition and assembly of different plant-associated microbial communities (soil, rhizosphere, leaf, root) are more and more described, both in healthy and infected plants. A major goal is now to shift from descriptive to functional studies of the interaction, in order to gain a mechanistic understanding of how microbes act on plant growth and defense, and/or on pathogen development and pathogenicity. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, as well as the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Pla...
BMC genomics, 2016
The protist Plasmodiophora brassicae is a soil-borne pathogen of cruciferous species and the causal agent of clubroot disease of Brassicas including agriculturally important crops such as canola/rapeseed (Brassica napus). P. brassicae has remained an enigmatic plant pathogen and is a rare example of an obligate biotroph that resides entirely inside the host plant cell. The pathogen is the cause of severe yield losses and can render infested fields unsuitable for Brassica crop growth due to the persistence of resting spores in the soil for up to 20 years. To provide insight into the biology of the pathogen and its interaction with its primary host B. napus, we produced a draft genome of P. brassicae pathotypes 3 and 6 (Pb3 and Pb6) that differ in their host range. Pb3 is highly virulent on B. napus (but also infects other Brassica species) while Pb6 infects only vegetable Brassica crops. Both the Pb3 and Pb6 genomes are highly compact, each with a total size of 24.2 Mb, and contain l...
BMC genomics, 2014
The protist Plasmodiophora brassicae is a biotrophic soil-borne pathogen that causes clubroot on Brassica crops worldwide. Clubroot disease is a serious threat to the 8 M ha of canola (Brassica napus) grown annually in western Canada. While host resistance is the key to clubroot management, sources of resistance are limited. To identify new sources of clubroot resistance (CR), we fine mapped a CR gene (Rcr1) from B. rapa ssp. chinensis to the region between 24.26 Mb and 24.50 Mb on the linkage group A03, with several closely linked markers identified. Transcriptome analysis was conducted using RNA sequencing on a segregating F1 population inoculated with P. brassicae, with 2,212 differentially expressed genes (DEGs) identified between plants carrying and not carrying Rcr1. Functional annotation of these DEGs showed that several defense-related biological processes, including signaling and metabolism of jasmonate and ethylene, defensive deposition of callose and biosynthesis of indol...
Functional Plant Biology, 2013
Microarray analysis was used to investigate changes in host gene expression during the primary stages of the interaction between the susceptible plant Arabidopsis thaliana (L.) Heynh ecotype Col-0 and the biotrophic pathogen Plasmodiophora brassicae Woronin. Analyses were conducted at 4, 7 and 10 days after inoculation (DAI) and revealed significant induction or suppression of a relatively low number of genes in a range of functional categories. At 4 DAI, there was induced expression of several genes known to be critical for pathogen recognition and signal transduction in other resistant host–pathogen interactions. As the pathogen further colonised root tissue and progressed through the primary plasmodium stage to production of zoosporangia at 7 and 10 DAI, respectively, fewer genes showed changes in expression. The microarray results were validated by examining a subset of induced genes at 4 DAI by quantitative real-time reverse transcriptase PCR (RT-qPCR) analysis all of which cor...
A Proteome-Level Investigation Into Plasmodiophora brassicae Resistance in Brassica napus Canola
Frontiers in Plant Science
Clubroot of Brassicaceae, an economically important soil borne disease, is caused by Plasmodiophora brassicae Woronin, an obligate, biotrophic protist. This disease poses a serious threat to canola and related crops in Canada and around the globe causing significant losses. The pathogen is continuously evolving and new pathotypes are emerging, which necessitates the development of novel resistant canola cultivars to manage the disease. Proteins play a crucial role in many biological functions and the identification of differentially abundant proteins (DAP) using proteomics is a suitable approach to understand plant–pathogen interactions to assist in the development of gene specific markers for developing clubroot resistant (CR) cultivars. In this study, P. brassicae pathotype 3 (P3H) was used to challenge CR and clubroot susceptible (CS) canola lines. Root samples were collected at three distinct stages of pathogenesis, 7−, 14−, and 21-days post inoculation (DPI), protein samples we...
Identification of Plasmodiophora brassicae effectors — A challenging goal
Virulence, 2018
Clubroot is an economically important disease affecting Brassica plants worldwide. Plasmodiophora brassicae is the protist pathogen associated with the disease, and its soil-borne obligate parasitic nature has impeded studies related to its biology and the mechanisms involved in its infection of the plant host. The identification of effector proteins is key to understanding how the pathogen manipulates the plant's immune response and the genes involved in resistance. After more than 140 years studying clubroot and P. brassicae, very little is known about the effectors playing key roles in the infection process and subsequent disease progression. Here we analyze the information available for identified effectors and suggest several features of effector genes that can be used in the search for others. Based on the information presented in this review, we propose a comprehensive bioinformatics pipeline for effector identification and provide a list of the bioinformatics tools available for such.
Journal of Phytopathology, 2002
The soil‐borne obligate pathogen Plasmodiophora brassicae causes clubroot disease in species of Brassicaceae, including Arabidopsis thaliana. The host–pathogen interaction was studied with respect to the age of the plant at the time point of inoculation and to different infection pressures in order to establish a standardization of infection parameters and evaluation of disease extent for A. thaliana lines. Spore number per root weight, root and shoot weight of inoculated and non‐inoculated plants as well as infection rate and disease index (DI) were analysed and correlated. The disease extent of different lines was comparable as measured by the relation of root weight of inoculated and non‐inoculated plants (Ri/Rni index) and the DI. Most of the 71 screened A. thaliana lines turned out to be susceptible. However, the mutant lines tu8, tu3, det1‐1, and rhd3‐1 showed a certain degree of tolerance under specific culture conditions. The reactions of rhd3‐1 indicate that hypertrophy is ...