Omics · study · 2026
RNA-seq data of SR30-overexpression transgenic tomato leaves
Listed in NCBI GEO
Alternative splicing (AS) plays a vital role in plant responses to biotic and abiotic stress.
Description
The modulation of host precursor-mRNA (pre-mRNA) AS is a common pathogenic strategy among distinct pathogens. However, the underlying mechanism by which how plants respond to pathogen-modulated AS remains largely elusive.
Here, we fished out a serine/arginine-rich RNA splicing factor (SR) family protein gene, SR30, that promotes tomato susceptibility to P. infestans. To explore the effect of SR30 on host pre-mRNA AS, we examine AS change in SR30 overexpression (SR30-OE) Solanum lycopersicum leaves compared to wild type using paired-end illumina RNA-seq. A large number of AS events are identified, indicating SR30 regulates the AS of tomato pre-mRNA.
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The overlap between differentially expression genes (DEGs) and differentially alternative splicing genes (DASGs) was low, indicating that most genes were unique to either pre-mRNA splicing or DEGs. SR30 overexpression represses the AS of tomato defense-related genes. Moreover, we also demonstrated that SR30 is upregulated and forms nuclear speckles through phase separation driven by intrinsically disordered regions (IDRs) during Phytophthora infestans.
IDR2 and IDR5 deletion mutant SR30ΔIDR2&5 failed to phase separate and promote P. infestans infection. Importantly, the association between SR30 and tomato spliceosome components and the alternative splicing of host defense-related genes are altered in the SR30 in a phase-separate-dependent manner.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE271nnn/GSE271386 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE271386 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1131286 ncbi.nlm.nih.gov/bioproject/PRJNA1131286 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- Agricultural biotechnology 71% · RNA sequencing 65%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE271386 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].anzsrc:group:3001 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (71%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |