In response to submergence and copper stress, the total transcript abundance of NnTPS did not show apparent difference (Figure 7B). Two NnTPS genes (NNU_0044229 and NNU_016432) were highly induced by submergence treatment. In contrast, most NnTPS genes (i.e., NNU_024672, NNU_014679, and NNU_022788) were down-regulated. The abundance of NNU_024672 decreased over 80%. Submergence leads to lower concentration of oxygen in a plant as a result of a lower diffusion rate of molecular oxygen in water as opposed to air, which would ultimately influence energy metabolism. The reaction of NNU_024672 to low oxygen demonstrates possible involvement in energy metabolism in the seedlings and that highly expressed NnTPS genes could play vital roles during this complicated biological process. Some plant metabolic processes contain copper as an essential micronutrient, functioning as a constituent of enzymes and other proteins, and in photosynthetic reactions (Maksymiec, 1998; Hall, 2002; Yruela, 2009; Martins et al., 2014). Excessive copper can lead to oxidative stress and be phytotoxic (Mithöfer et al., 2004). It can inhibit growth, influence plant metabolism and affect the function of several enzymes (Martins and Mourato, 2006; Mourato et al., 2009). Under copper stress, the transcript abundance of most NnTPS genes was not obviously changed, except two NnTPS genes (NNU_014679 and NNU_022788). It is interesting that abundance of two genes were apparently decreased in response to submergence while increased upon copper stress. We speculate that under copper stress more energy was needed to strengthen antioxidant system, while more energy was needed to be preserved under submergence as photosynthesis is inhibited. The contrasting expression pattern under submergence and copper stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Similar to previous work, TPS has been reported to play an important role in the regulation of carbohydrate metabolism and especially the perception of carbohydrate availability (Müller et al., 2001).