Integration of Transcriptomics and Metabolomics for Pepper (Capsicum annuum L.) in Response to Heat Stress
Abstract
:1. Introduction
2. Results
2.1. Phenotype and Physiology Responses of 17CL30 and 05S180 under HS
2.2. Overview of Transcriptomic Data for 17CL30 and 05S180
2.3. Identification of Differentially Expressed Genes (DEGs) under HS
2.4. The Common HS-Responsive Genes in 17CL30 and 05S180
2.5. Cultivar-Specific HS-Responsive Genes
2.6. Analysis of HS-Responsive TFs
2.7. Metabolomic Analsis during HS in 17CL30 and 05S180
2.8. Integrated Analysis between DEGs and DAMs
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Heat Treatments
4.2. mRNA-seq Library Constuction and RNA Sequencing
4.3. Read Alignment and Analysis
4.4. Sample Preparation and Metabolite Detection
4.5. Metabolite Profiling
4.6. Measurements of Total Soluble Sugar, MDA, Proline and Total Protein
4.7. Integrated Analysis between HS-Responsive Genes and Metabolites
4.8. Synthesis of cDNA and qRT-PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
HS | Heat stress |
DEGs | Differentially expressed genes |
DAMs | Differentially accumulated metabolites |
HSPs | Heat shock proteins |
HSFs | Heat shock transcription factors |
sHSPs | Small HSPs |
TFs | Transcription factors |
MDA | Malondialdehyde |
RCK | Control group of 17CL30 |
RT | Heat treatment group of 17CL30 |
SCK | Control group of 17CL30 |
ST | Heat treatment group of 05S180 |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
PCA | Principal component analysis |
QC | Quality control |
GSH | Glutathione |
FDR | False Discovery Rate |
ESI | Electrospray ionization |
QTRAP | Quadrupole-linear ion trap |
LIT | Linear ion trap |
QQQ | Triple quadrupole |
MRM | Multi-reaction monitoring |
DP | Declustering potential |
CE | Collision energy |
PLS-DA | Partial least squares-discriminant analysis |
VIP | Variable importance of the projection |
PCC | Pearson Correlation Coefficient |
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Wang, J.; Lv, J.; Liu, Z.; Liu, Y.; Song, J.; Ma, Y.; Ou, L.; Zhang, X.; Liang, C.; Wang, F.; et al. Integration of Transcriptomics and Metabolomics for Pepper (Capsicum annuum L.) in Response to Heat Stress. Int. J. Mol. Sci. 2019, 20, 5042. https://doi.org/10.3390/ijms20205042
Wang J, Lv J, Liu Z, Liu Y, Song J, Ma Y, Ou L, Zhang X, Liang C, Wang F, et al. Integration of Transcriptomics and Metabolomics for Pepper (Capsicum annuum L.) in Response to Heat Stress. International Journal of Molecular Sciences. 2019; 20(20):5042. https://doi.org/10.3390/ijms20205042
Chicago/Turabian StyleWang, Jing, Junheng Lv, Zhoubin Liu, Yuhua Liu, Jingshuang Song, Yanqing Ma, Lijun Ou, Xilu Zhang, Chengliang Liang, Fei Wang, and et al. 2019. "Integration of Transcriptomics and Metabolomics for Pepper (Capsicum annuum L.) in Response to Heat Stress" International Journal of Molecular Sciences 20, no. 20: 5042. https://doi.org/10.3390/ijms20205042