SpongoRNASeq
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR863837_1.fastq.gz | Fastqsanger.gz | |||
| ERR863837_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Spongospora subterranea is an obligate biotrophic pathogen, causing a tremendous economic loss in the potato industry. Currently, there are no effective chemical or biological strategies for the control of S. subterranea. Understanding the gene regulation of pathogens in their host is dependent on multidimensional datasets. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen inside the susceptible and resistant potato cultivars. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 14 proteins significantly changed in comparison between resistant and susceptible cultivars. The transcriptome analysis uncovered the gene regulatory modules underlying virulence. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivars suggesting a remarkable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of identified proteins were related to the metabolic processes. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea germination and growth in planta and illuminates the role of host immunity in affecting pathogen responses.
2022-02-17 | PXD027266 | Pride
Project description:The potato powdery scab agent Spongospora subterranea causes damage on the skin of tubers and induces root gall formation, precipitating considerable yield and quality losses. Currently, there are no effective chemical treatments for the control of powdery scabs. Understanding the inducible defence responses in roots of potato plants in the resistant and susceptible host environment, particularly during colonisation of the root by S. subterranea is required for the breeding of novel resistant cultivars. Here, we integrated transcriptomics, proteomics and metabolomics datasets to uncover the mechanisms underlying of the potato resistance to powdery scab. This multi-omics approach identified upregulation of glutathione metabolism at the levels of RNA, protein and metabolite in the resistant cultivar but not in the susceptible cultivar. Upregulation of the lignin metabolic process was also specific to in the resistant cultivar at the transcriptome level. In addition, Tthe inositol phosphate pathway was differentially expressed between two cultivars in response to S. subterranea infection, where it was upregulated in the susceptible cultivar but downregulated in the resistant cultivar. We provide, for the first time, large-scale multi-omics data of Spongospora-potato interaction, thereby suggesting the signaling role of glutathione metabolism in the potato resistance against powdery scab
2022-08-12 | PXD029381 | Pride
Project description:Illumina assembly of Spongospora subterranea genome
| PRJEB26377 | ENA
Project description:This project is aiming to identify specific root surface proteins from susceptible and resistant potato strains and identify those factors responsible for Spongospora subterranea zoospore binding.
2022-10-13 | PXD022502 | Pride
Project description:Spongospora subterranea f. sp. subterranea strain:SssMN22-1 | cultivar:Russet Burbank potato plant Genome sequencing
| PRJNA988890 | ENA
Project description:The protozoan Spongospora subterranea is an obligate biotrophic soil-borne pathogen, causing powdery scab and root disease of potato. Spores of S. subterranea can remain in their dormant states for years, but exposure to germination stimulants can cause dormant spores to re-enter the mitotic cell cycle. The soil-borne and plant-associated nature of S. subterranea has hindered a detailed study of this pathogen. The regulatory pathways driving the germination processes of S. subterranea are still unknown. In order to better understand the mechanisms that control the transition from cellular dormancy to germination, protein profiles between germinating and resting spores were compared using label-free quantitative proteomics. A total of 681 proteins were identified using shotgun proteomics. These proteins, functioning in carbohydrate metabolism, binding activity, metabolomic process and hydrolyse activity. Twenty proteins were found to be differentially expressed during the germination of S. subterranea resting spores. It is worth noting that not only the upregulation of proteins involved protein synthetase was confirmed also we showed that transcription occurs during the germination of S. subterranea. Elongation factor Tu, histones (H2A and H1), proteasome and DJ-1_PfpI, which are involved in transcription and translation, were upregulated during the germination of spores. Protein such as superoxide dismutase that was constitutively high in both germinating and spores may contribute to the ability of S. subterranea virulence and provide spores with protection from the oxidative stress. Our findings provide the first insights into the basic protein components of S. subterranea spores and provide a better understanding of S. subterranea biology and might lead to the development of novel approaches for the management of persistent soil inoculum.
2026-02-23 | PXD022089 | Pride
Project description:Potato is one of the most important food crops for human consumption. The obligate biotrophic pathogen Spongospora subterranea infects potato roots and tubers, resulting in considerable loss of potato tuber yield and quality. A comprehensive understanding of how potato plants respond to S. subterranea infection is essential for the development of pathogen-resistant crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses of the susceptible and resistant potato cultivars in response to S. subterranea. A total of 2669 proteins and 1498 phosphoproteins were quantified in the leaf samples of the different treatment groups. Following statistical analysis of the proteomic data, oxidoreductase activity, electron transfer, and photosynthesis were identified as significant processes that differentially changed upon infection specifically in the resistant cultivar and not in the susceptible cultivar. The phosphoproteomics results indicated increased activity of signal transduction and defence response functions in the resistant cultivar. In contrast, the majority of increased phosphoproteins in the susceptible cultivar were related to transporter activity and localisation. This study provides new insight into the molecular mechanisms involved in potato resistance to S. subterranea infection and has highlighted the critical roles of protein phosphorylation in the regulation of potato immune response.
2022-04-07 | PXD031529 | Pride
Project description:We report the application of RNA- sequencing technology for high-throughput profiling of histone modifications in mammalian cellsor identification of expressed genes upon infection by Spongospora subterranea. Using RNA-sequencing (RNA-seq), 2058 differentially expressed genes (DEGs) were identified from two potato cultivars (tolerant and susceptible) in response to Sss infection. Analysis of the expression patterns of ten selected defense-response genes was carried out at two different stages of tuber growth using RT-qPCR to validate the RNA-seq data. Several defense related genes showed contrasting expression patterns between the tolerant and susceptible cultivars, including marker genes involved in the salicylic acid hormonal response pathway (StMRNA, StUDP and StWRKY6). Induction of six defense related genes (StWRKY6, StTOSB, StSN2, StLOX, StUDP and StSN1) persisted until harvest of the tubers, while three other genes (StNBS, StMRNA and StPRF) were highly up-regulated during the initial stages of disease development. The results of this study suggested that the tolerant potato cultivar employs quantitative resistance and salicylic acid pathway hormonal responses against tuber infection by Sss. The identified genes have the potential to be used in the development of molecular markers for selection of powdery scab resistant potato lines in marker assisted breeding programs.
2018-12-11 | GSE123545 | GEO