Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions
Abstract
:1. Introduction
2. Materials and Methods
2.1. Datasets and Treatments
2.2. Reference-Based Transcriptome Structure Assembly
2.3. AS Detection and Identification of Drought Stress-Responsive AS Events
2.4. Differential Gene Expression Analysis
2.5. Gene Ontology and Pathway Enrichment Analysis
3. Results
3.1. Overview of the Sequencing Quality of RNA-seq Data for Identifying AS Events
3.2. Identification of AS Events in Soybean Roots under Various Drought Treatments
3.3. Identification of Drought Stress-Responsive AS Events in Soybean Root
3.4. Identification of Potential Drought Regulators via Analyzying Novel Drought-Responsive DSGs and DEGs
3.5. Comparative Analysis of the Biological Functions of All DSGs Regulated at AS and Transcription Levels
3.6. Comparative Analysis of the Selected Differentially Expressed and Alternatively Spliced Genes
4. Discussion
4.1. Many AS Events Occurred in Soybean Roots under Various Drought Conditions
4.2. A3SS and SE Were the Main AS Types in Soybean Roots in Response to Drought Stress
4.3. A Number of Key GO Terms and Pathways Were Enriched in DSGs
4.4. The Complexity of the Steady State Transcriptome in Soybean Roots under Drought Conditions
4.5. AS Has an Important Regulatory Role during Plant Development and Response to Abiotic Stress
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviation
AS | alternative splicing |
A5SS | alternative 5′ splicing site |
A3SS | alternative 3′ splicing site |
DAS | stress-responsive AS events |
DREB2B | dehydration-responsive element binding protein 2B |
DSGs | drought spliced genes |
PTC | premature translation termination codon |
FDR | false discovery rate calculated from p-value |
GO | Gene Ontology |
hnRNPs | heterogeneous nuclear ribonucleoproteins |
IEPs | isoform expression percentage changes |
IR | intron retention |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
MXE | mutually exclusive exon |
MS | mild drought stress |
NMD | nonsense-mediated decay |
rMATs | replicate multivariate analysis of transcript splicing |
SE | skipped exon |
SS | severe drought stress |
SR | recovery after severe drought |
SPFs | splicing regulatory factors |
UPF3 | UP FRAMESHIFT1 |
VMS | very mild drought stress |
WW | well-watered control |
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Song, L.; Pan, Z.; Chen, L.; Dai, Y.; Wan, J.; Ye, H.; Nguyen, H.T.; Zhang, G.; Chen, H. Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions. Genes 2020, 11, 1520. https://doi.org/10.3390/genes11121520
Song L, Pan Z, Chen L, Dai Y, Wan J, Ye H, Nguyen HT, Zhang G, Chen H. Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions. Genes. 2020; 11(12):1520. https://doi.org/10.3390/genes11121520
Chicago/Turabian StyleSong, Li, Zhenzhi Pan, Lin Chen, Yi Dai, Jinrong Wan, Heng Ye, Henry T. Nguyen, Guozheng Zhang, and Huatao Chen. 2020. "Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions" Genes 11, no. 12: 1520. https://doi.org/10.3390/genes11121520