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Spongospora subterranea SSUBK13 draft genome

ABSTRACT: Illumina assembly of Spongospora subterranea genome

PROVIDER: PRJEB26377 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR2541706_1.fastq.gz	Fastqsanger.gz
	ERR2541706_2.fastq.gz	Fastqsanger.gz

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Spongospora subterranea

Project description:Spongospora subterranea overview

| PRJNA1237457 | ENA

Spongospora subterranea de novo genome assembly project

Project description:Spongospora genome

| PRJEB25390 | ENA

Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea f. sp. subterranea tuber infection

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

Identification of root surface proteins from potato strains susceptible and resistant to Spongospora subterranea infection

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

Spongospora subterranea f. sp. subterranea strain:SssMN22-1 | cultivar:Russet Burbank potato plant

Project description:Spongospora subterranea f. sp. subterranea strain:SssMN22-1 | cultivar:Russet Burbank potato plant Genome sequencing

| PRJNA988890 | ENA

Draft Genome Resource for the Potato Powdery Scab Pathogen Spongospora subterranea.

Project description:The Plasmodiophorida (Phytomyxea, Rhizaria) are a group of protists that infect plants. Of this group, Spongospora subterranea causes major problems for the potato industry by causing powdery scab and root galling of potatoes and as vector for the Potato mop-top virus (PMTV) (genus Pomovirus, family Virgaviridae). A single tuber isolate (SSUBK13) of this uncultivable protist was used to generate DNA for Illumina sequencing. The data were assembled to a draft genome of 28.08 Mb consisting of 2,340 contigs and an L50 of 280. A total of 10,778 genes were predicted and 93% of the BUSCO genes were detected. The presented genome assembly is only the second genome of a plasmodiophorid. The data will accelerate functional genomics to study poorly understood interaction of plasmodiophorids and their hosts.

| S-EPMC6443038 | biostudies-literature

In planta transcriptome and proteome profiles of Spongospora subterranea illuminates regulatory principles underlying host-pathogen interaction

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

Large-scale protein and phosphoprotein profiling to explore potato resistance mechanisms to Spongospora subterranea infection

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

Optimisation of sporosori purification and protein extraction techniques for the biotrophic protozoan plant pathogen Spongospora subterranea

Project description:Spongospora subterranea is a soil-borne plant pathogen responsible for economically significant root and powdery scab diseases of potato. However, Tthe obligate biotrophic nature of S. subterranea has made detailed study of the pathogen problematic. Here, we first compared the benefits of sporosori partial purification utilizing Ludox gradient centrifugation. We then undertook optimization efforts for protein isolation comparing the use of a urea buffer followed by Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) and a sodium dodecyl sulfate (SDS) buffer followed by suspension-trapping (S-Trap). Label-free, quantitative proteomics was then used to evaluate the efficiency of sporosori purification and protein preparation methods. The purification protocol produced a highly purified suspension of S. subterranea sporosori without affecting the viability of the spores. Results indicated that the use of a combination of SDS and S-Trap for sample clean-up and digestion obtained a significantly higher number of identified proteins compare to using urea and SP3, with 218 and 652 proteins identified using SP3 and S-Trap methods, respectively. Analysis of proteins by mass spectrometry showed that the number of identified proteins increased by approximately 40% after the purification of spores by Ludox. These results suggested a potential use of the described spore purification and protein preparation methods for proteomics study of obligate biotrophic pathogens such as S. subterranea.

2021-09-09 | PXD019776 | Pride

Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea f. sp. subterranea tuber infection

Project description:Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea f. sp. subterranea tuber infection

| PRJNA509159 | ENA

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