Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Ribosome Profiling (Ribo-seq)
2.3. RNA Sequencing (RNA-Seq)
2.4. Ribo-seq and RNA-seq Data Processing
2.5. Analysis of Gene Expression at Transcriptional and Translational Levels
2.6. Calculation of Translational Efficiency
2.7. Analysis of Homoeolog Expression Bias (HEB)
3. Results
3.1. Transcriptional and Translational Profiling of Diploid and Allopolyploid Cotton
3.2. Concordantly Decreased Transcription and Translation Accompanying Allopolyploidization
3.3. Impact of Allopolyploidy on Translational Efficiency
3.4. Reduced amount of Homoeolog Expression Biases at the Translational Level
4. Discussion
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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A2D5 | AD1 | AD2 | |||||
---|---|---|---|---|---|---|---|
Number | Proportion | Number | Proportion | Number | Proportion | ||
RNA | Total | 5285 | 23.09% | 5237 | 22.88% | 8407 | 36.73% |
A > D | 2574 | 11.25% | 2576 | 11.25% | 4165 | 18.20% | |
A < D | 2711 | 11.84% | 2661 | 11.63% | 4242 | 18.53% | |
p-value * | 0.0595 | 0.2402 | 0.401 | ||||
Ribo | Total | 2224 | 9.72% | 1013 | 4.43% | 562 | 2.46% |
A > D | 1115 | 4.87% | 484 | 2.11% | 244 | 1.07% | |
A < D | 1109 | 4.85% | 529 | 2.31% | 318 | 1.39% | |
p-value * | 0.8988 | 0.1574 | 0.001799 | ||||
TE | Total | 1076 | 4.70% | 625 | 2.73% | 547 | 2.39% |
A > D | 391 | 1.71% | 320 | 1.40% | 237 | 1.04% | |
A < D | 685 | 2.99% | 305 | 1.33% | 310 | 1.35% | |
p-value * | 2.20 × 10−16 | 0.5485 | 0.001801 |
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Fu, G.; Luo, H.; Jia, J.; Hou, M.; Hu, G. Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton. Genes 2024, 15, 1130. https://doi.org/10.3390/genes15091130
Fu G, Luo H, Jia J, Hou M, Hu G. Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton. Genes. 2024; 15(9):1130. https://doi.org/10.3390/genes15091130
Chicago/Turabian StyleFu, Guiling, Haotian Luo, Juqing Jia, Mingming Hou, and Guanjing Hu. 2024. "Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton" Genes 15, no. 9: 1130. https://doi.org/10.3390/genes15091130