Dual RNAseq analysis of the interaction between the plant pathogen Pythium myriotylum and the mycoparasite Pythium oligandrum
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ABSTRACT:
PROVIDER: PRJNA743526 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15035089.fastq.gz | Fastqsanger.gz | |||
| SRR15035090.fastq.gz | Fastqsanger.gz | |||
| SRR15035091.fastq.gz | Fastqsanger.gz | |||
| SRR15035092.fastq.gz | Fastqsanger.gz | |||
| SRR15035093.fastq.gz | Fastqsanger.gz |
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Project description:Biological control is a promising approach to control diseases caused by Pythium species. Unusually for a single genus, the Pythium genus also includes species that can antagonise Pythium plant pathogens, such as Pythium oligandrum. These Pythium plant pathogens are commonly found in the soil such as the broad host-range pathogen Pythium myriotylum and cause various diseases of important crops. While P. oligandrum genes expressed in the interaction with oomycete plant pathogens have been identified previously, the transcriptional response of an oomycete plant pathogen to P. oligandrum has not been investigated. An isolate of P. oligandrum, GAQ1, recovered from soil could antagonise P. myriotylum in a plate-based confrontation assay. The P. oligandrum isolate had a strong disease control effect on soft-rot of ginger caused by P. myriotylum. We investigated the transcriptional interaction between P. myriotylum and P. oligandrum. As part of the transcriptional response of P. myriotylum to the presence of P. oligandrum, putative effector genes such as a sub-set of Kazal-type protease inhibitors were strongly upregulated. P. myriotylum cellulases and elicitin-like putative effectors were also upregulated. In P. oligandrum, cellulases, peroxidases, proteases and NLP effectors were upregulated. The transcriptional response of P. myriotylum suggests clear features of a counter-attacking strategy that may contribute to the variable success and durability of biological attempts to control diseases caused by Pythium species. Whether aspects of this counter-attack could inhibit aspects of this virulence of P. myriotylum is another interesting aspect for future studies.
2021-10-28 | GSE179387 | GEO
Project description:The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycetes-caused diseases such as Pythium myriotylum-caused rhizome rot in ginger leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using N. benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass content. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones, and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stress and the mechanisms of action of P. oligandrum as a biocontrol agent.
2023-06-22 | GSE235182 | GEO
Project description:Oomycetes, such as the broad host-range necrotrophic plant pathogen Pythium myriotylum, cause devastating crop losses. We have previously identified P. myriotylum as the major pathogen infecting ginger (Zingiber officinale) rhizomes in China with symptoms of Pythium soft rot (PSR) disease. Ginger is an important crop with global production estimated at approximately three million metric tonnes with about 20% of this production in China. To better understand how P. myriotylum infects ginger, transcriptomic analysis was performed on two P. myriotylum isolates (SWQ7 and SL2) infecting ginger leaves. From both of the isolates, there was a clear separation between the transcriptome replicates from the mycelial control condition and those from the infection of the ginger leaf. In SWQ7 and SL2, there were 2,110 and 2,513 genes upregulated during infection of ginger, respectively. Of the putative effectors, a subset of the NEP1-like toxin protein (NLP) effectors were highly induced during the infection of ginger leaves. Insights from the transcriptome highlight the important role of a subset of plant cell wall degrading enzymes (PCWDEs) and effectors in the pathogenicity of P. myriotylum towards ginger. The surprisingly large numbers of P. myriotylum PCWDEs and effectors within the genome may be due to the broad host-range of P. myriotylum whereby particular subsets of the PCWDEs and effectors are required for pathogenicity towards particular hosts.
2022-07-22 | GSE174557 | GEO
Project description:The oomycete P. oligandrum is a soil-inhabiting parasite and predator of both fungi and oomycetes and uses hydrolytic enzymes extensively to penetrate and hydrolyze its host or prey. Other mechanisms have been overlooked, and we investigated whether P. oligandrum-produced volatile organic compounds (VOCs) could also be contributing to antagonism. VOCs have diverse functions, including contributing to antagonism in ecological interactions and potential applications in biocontrol. The growth-inhibiting activity of P. oligandrum VOCs was tested on P. myriotylum – a host or prey of P. oligandrum – coupled with electron microscopy, biochemical assays and transcriptomic analysis. The total VOCs produced by P. oligandrum reduced P. myriotylum growth by 80% and zoospore levels by 60%. GC-MS identified twenty-three VOCs, and methyl heptenone, D-limonene, 2-undecanone and 1-octanal were potent inhibitors of P. myriotylum growth and led to increased production of reactive oxygen species at a concentration that did not inhibit P. oligandrum growth. Exposure to the total VOCs of P. oligandrum led to shrinkage of P. myriotylum hyphae, and lysis of the cellular membranes and organelles. Transcriptomic analysis of P. myriotylum exposed to the P. oligandrum VOCs at increasing levels of growth inhibition showed initially a strong upregulation of putative detoxification related genes that was not maintained later during exposure to the VOCs. The inhibition of P. myriotylum growth continued after the exposure to the VOCs was discontinued and led to reduced leaf lesion size during P. myriotylum infection of its plant host. The VOCs produced by P. oligandrum could be another factor alongside hydrolytic enzymes contributing to its ecological role as a microbial antagonist where the concentration of the VOCs may be inhibitory in particular ecological niches such as in soil. The VOCs analyzed here may also be contributing to the biocontrol of diseases using P. oligandrum commercial preparations.
2022-12-31 | GSE214639 | GEO
Project description:Pythium oligandrum genome sequencing
| PRJNA379110 | ENA
Project description:Pythium myriotylum isolate:SL2 Raw sequence reads
| PRJNA701145 | ENA
Project description:Pythium myriotylum strain:CBS25470 Raw sequence reads
| PRJNA353159 | ENA
Project description:Biological control is a promising approach to suppress diseases caused by Pythium spp. such as Pythium soft rot of ginger caused by P. myriotylum. Unusually for a single genus, it also includes species that can antagonize Pythium plant pathogens, such as Pythium oligandrum. We investigated if a new isolate of P. oligandrum could antagonize P. myriotylum, what changes occurred in gene expression when P. oligandrum (antagonist) and P. myriotylum (host) interacted, and whether P. oligandrum could control soft-rot of ginger caused by P. myriotylum. An isolate of P. oligandrum, GAQ1, recovered from soil could antagonize P. myriotylum in a plate-based confrontation assay whereby P. myriotylum became non-viable. The loss of viability of P. myriotylum coupled with how P. oligandrum hyphae could coil around and penetrate the hyphae of P. myriotylum, indicated a predatory interaction. We investigated the transcriptional responses of P. myriotylum and P. oligandrum using dual-RNAseq at a stage in the confrontation where similar levels of total transcripts were measured from each species. As part of the transcriptional response of P. myriotylum to the presence of P. oligandrum, genes including a subset of putative Kazal-type protease inhibitors were strongly upregulated along with cellulases, elicitin-like proteins and genes involved in the repair of DNA double-strand breaks. In P. oligandrum, proteases, cellulases, and peroxidases featured prominently in the upregulated genes. The upregulation along with constitutive expression of P. oligandrum proteases appeared to be responded to by the upregulation of putative protease inhibitors from P. myriotylum, suggesting a P. myriotylum defensive strategy. Notwithstanding this P. myriotylum defensive strategy, P. oligandrum had a strong disease control effect on soft-rot of ginger caused by P. myriotylum. The newly isolated strain of P. oligandrum is a promising biocontrol agent for suppressing the soft-rot of ginger. The dual-RNAseq approach highlights responses of P. myriotylum that suggests features of a defensive strategy, and are perhaps another factor that may contribute to the variable success and durability of biological attempts to control diseases caused by Pythium spp.
| S-EPMC8637047 | biostudies-literature