Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide DNA Methylation Patterns in Response to Low-P Stress
2.2. DNA Methylation Patterns in Gene and TE Regions
2.3. Association Analyses of DNA Methylation Status and Gene Expression
2.4. Identification of DMR and DMR-Associated Genes in Response to Low-P Stress
2.5. Abundant TE Genes Are Hypomethylated in Response to Low-P Stress
2.6. Conjoint Analysis of Methylome and Transcriptome Alterations in Low-P Stress
2.7. Association Analyses of DNA Methylation and Small RNA Expression
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Treatment
4.2. Bisulfite Sequencing Library Construction
4.3. Read Mapping and Methylation Level Analysis
4.4. Differentially Methylated Regions (DMRs) Analysis
4.5. RNA Sequencing and Transcriptome Profiling Analysis
4.6. Small RNA Sequencing and Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
P | Phosphorus |
TE | Transposable element |
RdDM | RNA-directed DNA methylation |
NN | Nannong 94-156 |
BG | Bogao |
LP | Low-P |
HP | High-P |
DMRs | Differentially methylated regions |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
DMGs | Differentially methylated genes |
TFs | Transcription factors |
DEGs | Differentially expressed genes |
SiRNAs | Small interfering RNAs |
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Sample | Raw Reads | Clean Reads | Mapped Reads | Mapped Ratio (%) | Sequence Depth | Bisulfite Conversion Efficiency Ratio (%) |
---|---|---|---|---|---|---|
NN_HP | 444676244 | 438763364 | 387477437 | 88.31% | 59.40 | 99.62% |
NN_LP | 366193864 | 360336480 | 316853049 | 87.93% | 48.57 | 99.64% |
BG_HP | 522038932 | 515810512 | 458006046 | 88.79% | 70.21 | 99.65% |
BG_LP | 404607624 | 398836454 | 350842529 | 87.97% | 53.78 | 99.66% |
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Chu, S.; Zhang, X.; Yu, K.; Lv, L.; Sun, C.; Liu, X.; Zhang, J.; Jiao, Y.; Zhang, D. Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress. Int. J. Mol. Sci. 2020, 21, 6817. https://doi.org/10.3390/ijms21186817
Chu S, Zhang X, Yu K, Lv L, Sun C, Liu X, Zhang J, Jiao Y, Zhang D. Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress. International Journal of Molecular Sciences. 2020; 21(18):6817. https://doi.org/10.3390/ijms21186817
Chicago/Turabian StyleChu, Shanshan, Xiangqian Zhang, Kaiye Yu, Lingling Lv, Chongyuan Sun, Xiaoqian Liu, Jinyu Zhang, Yongqing Jiao, and Dan Zhang. 2020. "Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress" International Journal of Molecular Sciences 21, no. 18: 6817. https://doi.org/10.3390/ijms21186817