Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum
Abstract
:1. Introduction
2. Results
2.1. Phenotype Characters Effected by Different Concentrations of Ammonium
2.2. Effect of Ammonium on Amino Acid Content in Leaves
2.3. Differential Expression of Genes to Different Concentrations of Ammonium
2.4. Gene Clustering Analysis
2.5. Gene Ontology and Pathway Analysis of DEGs
2.6. Differential Expression Behavior of Genes Involved in Nitrogen and Carbohydrate Metabolisms
2.7. Identification of Differentially Expressed TFs
2.8. Weighted Gene Co-Expression Network Analysis
2.9. Validation of Differentially Expressed Genes
3. Discussion
3.1. Nitrogen Metabolism and Amino Acid Synthesis
3.2. Carbohydrate and Energy Pathways
3.3. Involvement of TF Families and Protein Kinases in the Ammonium Mediated Signalling Response
3.4. Regulation of Secondary Metabolite Pathways at Different Ammonium Conditions
4. Materials and Methods
4.1. Experimental Design
4.2. Phenotype Characters Analysis
4.3. RNA Extraction, Sequencing, and Annotation
4.4. Gene Differential Expression and Enrichment Analysis
4.5. Weighted Gene Correlation Network Analysis of Nitrogen Responding Genes
4.6. Gene Expression Validation
4.7. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Groups | Ammonium Concentration (ug g−1 FW) | RGR (g d−1 FW) | Fv/Fm | Root Length (cm) | Root Number |
---|---|---|---|---|---|
LNC | 44.752 ± 8.037 d | 0.044 ± 0.008 c | 0.805 ± 0.006 b | 17.12 ± 1.343 a | 29 ± 2 a |
L1 | 57.655 ± 7.134 d | 0.08 ± 0.017 abc | 0.818 ± 0.006 ab | 18.243 ± 1.136 a | 30 ± 3 a |
L2 | 100.94 ± 8.316 c | 0.113 ± 0.034 a | 0.833 ± 0.004 a | 12.183 ± 0.949 b | 20 ± 3 b |
L3 | 212.258 ± 13.871 b | 0.088 ± 0.004 ab | 0.832 ± 0.004 a | 7.397 ± 0.728 c | 8 ± 4 c |
L4 | 464.647 ± 44.995 a | 0.056 ± 0.031 bc | 0.779 ± 0.018 c | 5.693 ± 1.696 c | 4 ± 3 c |
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Wang, R.; Xu, S.; Jiang, C.; Sun, H.; Feng, S.; Zhou, S.; Zhuang, G.; Bai, Z.; Zhuang, X. Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum. Int. J. Mol. Sci. 2019, 20, 1587. https://doi.org/10.3390/ijms20071587
Wang R, Xu S, Jiang C, Sun H, Feng S, Zhou S, Zhuang G, Bai Z, Zhuang X. Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum. International Journal of Molecular Sciences. 2019; 20(7):1587. https://doi.org/10.3390/ijms20071587
Chicago/Turabian StyleWang, Rui, Shengjun Xu, Cancan Jiang, Haishu Sun, Shugeng Feng, Sining Zhou, Guoqiang Zhuang, Zhihui Bai, and Xuliang Zhuang. 2019. "Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum" International Journal of Molecular Sciences 20, no. 7: 1587. https://doi.org/10.3390/ijms20071587