Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root (original) (raw)
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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...
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...
Transcriptome Analysis of Arabidopsis Thaliana Clubroots
Acta horticulturae, 2006
Clubroot disease is a serious threat to cruciferous plants worldwide, especially to oilseed rape. However, knowledge on pathogenic molecular mechanisms and host interaction is limited. We presume that the recognition between Arabidopsis thaliana and Plasmodiophora brassicae occurs at the early stage of infection and within a relatively short period. In this study, we demonstrated changes on gene expression and pathways in A. thaliana during early infection with P. brassicae using transcriptome analysis. We identified 1,903 and 1,359 DEGs at 24 and 48 h post-inoculation (hpi), respectively. Flavonoids and the lignin synthesis pathways were enhanced, glucosinolates, terpenoids, and proanthocyanidins accumulated and many hormonal-and receptor-kinase related genes were expressed, caused by P. brassicae infection during its early phase. Therefore, the early interaction between A. thaliana and P. brassicae plays an important role in the entire infection process. The results provide a new contribution to a better understanding of the interaction between host plants and P. brassicae, as well as the development of future measures for the prevention of clubroot.
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...
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
Plant Science, 2008
Clubroot, caused by the obligate parasite Plasmodiophora brassicae, has emerged as an important new disease of canola (Brassica napus) in Alberta, Canada. Changes in the root protein profile were examined by two-dimensional gel electrophoresis at 12, 24, 48 and 72 h after inoculation of a susceptible canola genotype with the pathogen. A total of 20 protein spots were identified as either increasing (13 spots) or decreasing (7 spots) in intensity relative to water-treated controls. The identities of these proteins were established by MS/MS, and included proteins involved in lignin biosynthesis, cytokinin metabolism, glycolysis, intracellular calcium homeostasis, and the detoxification of ROS. Decreased abundance of adenosine kinase, which is involved in cytokinin homeostasis, supported previous reports indicating a key role for cytokinin in the early phases of clubroot infection. An approximately sixfold reduction in caffeoyl-CoA O-methyltransferase abundance suggested a reduction in host lignin biosynthesis after pathogen challenge, and is consistent with the compatible nature of the interaction examined. Interestingly, levels of enzymes involved in ROS metabolism declined sharply at 12 h after inoculation, but increased at 24-72 h. Collectively, these data suggest major changes in canola metabolism shortly after challenge by the pathogen, which may result in the susceptibility of the host.
Research Square (Research Square), 2022
Background and aim Clubroot is an infectious root disease caused by Plasmodiophora brassicae of Brassica crops, which can cause immeasurable losses. We aimed to explore the infection mechanism under P. brassicae integrating transcriptome, small RNA, degradome and phytohormone technology. Result In this study, root samples of B. rapa resistant line BrT24 (R-line) and susceptible line Y510-9 (S-line) were collected at four different time points for cytological, transcriptome, miRNA and degradome investigations. We found the critical period of disease resistance and infection at 0-3 days and 9-20 days, respectively. Based on this finding we further analyzed the data of 9 d vs 20 d of S-line and predicted the key genes ARF8, NAC1, NAC4, TCP10, SPL14, REV and ATHB related to clubroot disease development and regulating disease resistance mechanisms. These genes are mainly related to auxin, cytokinin, jasmonic acid and ethylene cycles. We proposed a regulatory model of plant hormones under the mRNA-miRNA regulation in the critical period of Plasmodiophora brassicae infection based on the combination of 2 the present data of integrative transcriptome, small RNA, degradome and phytohormone with our previously published results. Conclusion Our integrative analysis found that the bra-miR164/NAC1/4, bra-miR319/TCP10 and bra-miR167/ARF8 were associated with clubroot symptoms development, which provide new insights into the regulation relationship of miRNA and plant hormones during the process of disease infection.
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...
Frontiers in Microbiology, 2021
Nitrogen fertilization can affect the susceptibility of Brassica napus to the telluric pathogen Plasmodiophora brassicae. Our previous works highlighted that the influence of nitrogen can strongly vary regarding plant cultivar/pathogen strain combinations, but the underlying mechanisms are unknown. The present work aims to explore how nitrogen supply can affect the molecular physiology of P. brassicae through its life epidemiological cycle. A time-course transcriptome experiment was conducted to study the interaction, under two conditions of nitrogen supply, between isolate eH and two B. napus genotypes (Yudal and HD-018), harboring (or not harboring) low nitrogen-conditional resistance toward this isolate (respectively). P. brassicae transcriptional patterns were modulated by nitrogen supply, these modulations being dependent on both host-plant genotype and kinetic time. Functional analysis allowed the identification of P. brassicae genes expressed during the secondary phase of inf...