## 5 Conclusions  
In this study, a global transcriptomic analysis on _M. aquaticum_ in response to a serial of ammonium treatments was performed to investigate the mechanism behind high NUE and ammonium assimilation by _M. aquaticum_. Ammonium was efficiently assimilated into key amino acids in different treatment groups, especially in groups of high concentrations of ammonium. A number of genes involved in nitrogen-transport, assimilation, and remobilization in response to various ammonium conditions made the dominant contributions to high NUE in these groups. Meanwhile, genes involved in the carbohydrate, TFs, and secondary metabolism also played important roles in regulating for high NUE. In addition, the co-expression network analysis of DEGs identified several ammonium regulatory modules that might be associated with phenylpropanol and amino acid metabolism in _M. aquaticum_. Future work will focus on functionally characterizing the ammonium responsive transcripts, especially from high NUE groups, which may be the potential candidates to improve NUE of _M. aquaticum_ and related wetland plant species.  
Supplementary materials can be found at [[http://www.mdpi.com/1422-0067/20/7/1587/s1](http://www.mdpi.com/1422-0067/20/7/1587/s1)]([http://www.mdpi.com/1422-0067/20/7/1587/s1](http://www.mdpi.com/1422-0067/20/7/1587/s1)). Figure S1: Principal component analysis of the gene expression of _Myriophyllum aquaticum_ at different concentrations of ammonium. Figure S2: Volcano plots of the differentially expressed genes (DEGs) between the control and treated _Myriophyllum aquaticum_. Figure S3: Heatmap of correlation analysis among 10 modules. Figure S4: Scatterplot of top 30 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment for differentially expressed genes (DEGs) in the positive and negative modules. Figure S5: qRT-PCR validation of differentially expressed genes in _Myriophyllum aquaticum_ at different concentrations of ammonium. Table S1: RNA-seq data analysis of _Myriophyllum aquaticum_. Table S2: Change of expression and annotation of all the DEGs in the treated groups of _Myriophyllum aquaticum_. Table S3: Downregulated or upregulated differentially expressed genes (DEGs) of _Myriophyllum aquaticum_ in all four treated groups. Table S4: Genes expression and annotation in the nine clusters of _Myriophyllum aquaticum_. Table S5: Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs enriched in ammonium treated groups. Table S6: Differentially regulated transcription factors of _Myriophyllum aquaticum_. Table S7: Differentially expressed genes (DEGs) of _Myriophyllum aquaticum_ enriched in different modules. Table S8: Gene Ontology (GO) analysis of differentially expressed genes (DEGs) enriched in the positive and negative modules. Table S9: Primers used for qRT-PCR in _Myriophyllum aquaticum_ at different concentrations of ammonium. Table S10: Nutrient solution formulation of 50% modified Hoagland solution.  
**Author Contributions:** [PERSON], [PERSON], and [PERSON] conceived and designed the project. [PERSON], [PERSON], [PERSON], and [PERSON] performed the experiments. [PERSON] and [PERSON] analyzed the data. [PERSON], [PERSON], and [PERSON] wrote the manuscript. All authors have read the final manuscript and approved it.  
**Funding:** This research was supported by the Key Research Program of Chinese Academy of Sciences (ZDRW-ZS-2016-5), the Interdisciplinary Innovation Team Program of the Chinese Academy of Sciences (2015, Team of Directional Biotransformation of Environmental Pollutants), and the Major Science and Technology Program for Water Pollution Control and Treatment of China (2015 ZX07206-006).  
**Acknowledgments:** We thank Shanghai Majorbio Bio-pharm Technology Co., Ltd., China for their help with the data analysis.  
**Conflicts of Interest:** The authors declare no conflict of interests.