A phylogenetic tree was used to reveal homologous relationships and evolutionary roots of TPS from Arabidopsis, rice, poplar (Yang et al., 2012), and soybean (Yang et al., 2012). The amino acid sequence alignment of TPS in these plants was conducted for phylogenetic tree construction using MEGA 5.1 (Figure 5). According to the phylogenetic tree and previous division of Arabidopsis and rice TPS genes, these TPS genes are divided into two subfamilies (I and II; Vandesteene et al., 2010; Zang et al., 2011). Arabidopsis, rice, soybean, and poplar contain four (AtTPS1, 2, 3, and 4), one (OsTPS1), four (GmTPS1, 2, 3, and 4), and one (PtTPS1) subfamily I TPS, respectively. However, no lotus TPS subfamily I members was found. It should be noted that the absence of subfamily I TPS in lotus might be due to incomplete genome sequencing coverage (86.5%). However, we cannot exclude the possibility that these genes have been fatally lost in evolution, as the number of TPS genes in subfamily I is far less than TPS genes in subfamily II in previous reported species (Zang et al., 2011). In order to describe paralogous and orthologous relations among this family, the subfamily II TPS genes were further divided into five group (II-1, 2, 3, 4, and 5) with high bootstrap support, suggesting that genes in each subgroup might share a similar origin. In most cases, subgroups are duplicates of at least one lineage. For example, subgroup II-2 and II-3 were duplicated after the separation between dicot and monocots. We identified nodes that lead to dicots (lotus, Arabidopsis, poplar, and soybeans)-specific and monocots (rice)-specific subfamilies. Group II-2 only contained lotus, Arabidopsis, and poplar Class II TPS genes, indicating that genes might have been lost from the rice genome. Subfamily I-1 only contained three Arabidopsis Class I TPS. Moreover, most proteins in lotus TPS family were contained in paralogous pairs, including 4 pairs of NnTPS accounting for 89% NnTPSs. This result indicated that most lotus TPS genes expanded in a species-specific manner.