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| Status |
Public on Aug 21, 2023 |
| Title |
The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA385363] |
| Organism |
Capsicum annuum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. In addition, we obtained existing transcriptome datasets in response to abiotic and biotic stressors, phytohormones, and various developmental stages. From 428 total samples comprising 841.49 Gb, we identified the AS landscape in C. annuum. We further uncovered 1,704,387 AS events through differential AS analysis and identified 6,280 differential alternative splicing (DAS) genes related to environmental stressors, developmental stages, and phytohormones. This information and approach will enable comparative analysis of differential AS from RNA-seq datasets. Additionally, our findings provide useful data for basic-research programs focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.
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| Overall design |
Identify changes in transcriptome based on biotic stress, abiotic stress, signal molecule and tissue RNA-seq samples of chilli.
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| Contributor(s) |
Kim N, Lee J, Yeom S |
| Citation missing |
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| BioProject |
PRJNA385363 |
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| Submission date |
Aug 16, 2023 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Seon-In Yeom |
| E-mail(s) |
[email protected]
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| Organization name |
Gyeongsang National University
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| Street address |
501, Jinjou-daero
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| City |
Jinju |
| ZIP/Postal code |
52828 |
| Country |
South Korea |
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| Platforms (1) |
| GPL26789 |
Illumina HiSeq 2500 (Capsicum annuum) |
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| Samples (39)
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| This SubSeries is part of SuperSeries: |
| GSE240949 |
The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper |
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| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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