Transcriptomic Analysis Provides New Insights into the Tolerance Mechanisms of Green Macroalgae Ulva prolifera to High Temperature and Light Stress
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Algal Strain Collection and Culture Conditions
2.2. Temperature Treatment and Tissue Sampling
2.3. RNA Extraction
2.4. Transcriptome Sequencing and Quality Control
2.5. Assembly and Annotation
2.6. Differential Expression Analysis
2.7. Validation of the Genes
3. Results
3.1. Transcriptome Analysis
3.2. Analysis of DEGs and Identification of Temperature-Responsive Genes
3.3. Functional Classification
3.4. Enrichment and Pathway Analysis and Comparison of the Group
3.5. Analysis of Major Pathway-Related Differentially Express Genes (DEGs) in Different Comparison Groups
3.6. Validation of RNA-seq Results with RT-qPCR
4. Discussion
4.1. Ribosome Metabolism
4.2. Spliceosome Pathway
4.3. Peroxisome Metabolism
4.4. Autophagy Pathway
4.5. Energy Metabolism
4.6. Glutathione Pathway
4.7. Carbon Fixation in Photosynthetic Organisms
4.8. Alanine, Aspartate, and Glutamate Metabolism
4.9. Differentially Expressed Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Group | Average Logcpm | Mean Fold Change Differentially Expressed Genes | Differentially Expressed Genes DEGs p-Value (Average) | DEG | Up-Regulated DEGs | Down-Regulated DEGs |
---|---|---|---|---|---|---|
H24 vs. C | 1.177248 | −6.896698 | 0.017459 | 49,796 | 26,253 | 23,543 |
H48 vs. C | 0.983384 | −14.470383 | 0.22426397 | 47,066 | 25,250 | 21,816 |
MH24 vs. C | 1.276447 | −20.981178 | 0.004089 | 44,468 | 23,210 | 21,258 |
MH48 vs. C | 1.287536 | −16.937280 | 0.001698 | 44,169 | 23,180 | 20,989 |
GO Term | % Unigenes | Number of Unigenes |
---|---|---|
Molecular functions | 30.84% | 19,214 |
Biological processes | 28.84% | 17,967 |
Cellular components | 14.91% | 9287 |
Total unigenes | 46,468 |
H24 vs. C | H48 vs. C | MH24 vs. C | MH48 vs. C | |
---|---|---|---|---|
Total enriched pathway | 434 | 434 | 432 | 431 |
Total enriched genes | 1207 | 1166 | 1115 | 1108 |
Significantly up-regulated or down-regulated genes in ribosome pathway | 131 | 130 | 129 | 130 |
Significantly up-regulated or down-regulated Genes in the peroxisome pathway | 47 | 48 | 41 | 44 |
Significantly up-regulated or down-regulated genes in the autophagy pathway | 17 | 16 | 15 | 16 |
Significantly up-regulated or down-regulated genes in spliceosome pathway | 89 | 85 | 78 | 78 |
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Jahan, K.; Supty, M.S.A.; Lee, J.-S.; Choi, K.-H. Transcriptomic Analysis Provides New Insights into the Tolerance Mechanisms of Green Macroalgae Ulva prolifera to High Temperature and Light Stress. Biology 2024, 13, 725. https://doi.org/10.3390/biology13090725
Jahan K, Supty MSA, Lee J-S, Choi K-H. Transcriptomic Analysis Provides New Insights into the Tolerance Mechanisms of Green Macroalgae Ulva prolifera to High Temperature and Light Stress. Biology. 2024; 13(9):725. https://doi.org/10.3390/biology13090725
Chicago/Turabian StyleJahan, Kifat, Mst Shamim Ara Supty, Jun-Seok Lee, and Keun-Hyung Choi. 2024. "Transcriptomic Analysis Provides New Insights into the Tolerance Mechanisms of Green Macroalgae Ulva prolifera to High Temperature and Light Stress" Biology 13, no. 9: 725. https://doi.org/10.3390/biology13090725
APA StyleJahan, K., Supty, M. S. A., Lee, J. -S., & Choi, K. -H. (2024). Transcriptomic Analysis Provides New Insights into the Tolerance Mechanisms of Green Macroalgae Ulva prolifera to High Temperature and Light Stress. Biology, 13(9), 725. https://doi.org/10.3390/biology13090725