## 2 Results
### Comparative Sequence Alignments of Rice Trans-Preuyltransferases in the Highly Conservative Regions  
To support the phylogenetically predicted functions by matching them with known conserved motifs, multiple alignment of rice _trans_-PTs along with representatives of other _trans_-PTs in each subgroup showed relatively good conservation. However, there were several exceptions in four regions (I-IV), including core sites in regions I (GKR) and II (H/QX\({}_{(15-17)}\)RR) for IPP-binding, aspartate-rich motifs in regions II (FARM, DDX\({}_{(2-4)}\)D) and IV (SARM, DDX\({}_{2}\)D) for catalytic activity, which have been reported as three highly conserved regions for critical function as common PTs, and two CxxxC motifs in regions I and IV for forming the heteromeric complex of GGPS_LSU and __SSU (Figure 2A, Supplementary Table S4). The first IPP-binding site showed major variation only in Group I PTs (Figure 2A): Monocot families containing OsGRP (GGPS_SSU-II, subgroup F) had the insertion of seven amino acids between the first G and the third K residues, but dicot families of GGPS_SSUs contained one X insertion between G and K residues (GGPS_SSU-II) or no GKR motif (GGPS_SSU-I), suggesting that these peculiar properties might be largely responsible for their differential roles of GGPS_SSUs. Group II PTs displayed conservation (GKR/Q) between subgroup A and B as no insertion and all of Group III PTs contained the same motif (GKR. ), as shown in Figure 2B,C. The second IPP-binding site was well conserved within Group I (HX\({}_{17}\)RR), Group II (HX\({}_{15}\)RR) and Group III (QX\({}_{15}\)RR). These results suggest that the first IPP-binding site might have crucial roles for the differential functions among plant PTs containing GGPS_SSU families. In cases of two aspartate-rich motifs, there are also major variations only in Group I: A Mp AAF08792 in subgroup E was defective in both FARM and SARM, and all of PTs belonged to subgroup F, including an OsGRP, have no fully conserved SARM due to absence of the last D residue, supporting lack of catalytic activity of GGPS_SSUs alone as the second representative characteristic. Lastly, two CxxxC motifs were presented only in Group I, but not in Groups II and III (Figure 2). In particular, the first C residue of a CxxxC motif in a region I was varied in three monocot PTs, including an OsGPS in subgroup C as an AxxxC motif, supposing a different type of physical interaction, but the second CxxxC motif in a region IV conservatively existed expectedly only in subgroups E and F. Collectively, two rice PTs in Group I showed remarkably different patterns: The first IPP binding motif (GKR) of OsGRP had additional amino acid residues between the G and K residues and OsGPS contained an AxxxC motif in region I, instead of a CxxxC motif (Figure 2A). In contrast, the other rice PTs had no modified residues in those highly conserved domains to show the general patterns of plant PT families. To infer the biochemical function of rice _trans_-PTs on using the \"three floors\" model suggested by [PERSON] et al. [13], the determinant amino acid residues corresponding to Floor 1, Floor 2 and Floor 3 in the elongation channels were individually displayed as green, red and yellow (Figure 2 and Supplementary Table S5). To derive the specified patterns using the three floor motifs among plant _trans_-PTs, we constructed color-based HeatMap graphs according to the ranges of the molecular weights of amino acid residues (Figure 3). Figure 2: Multiple sequence alignment for plant _trans_-PIs. The deduced amino acids of the representative PIs in subgroups I-III were aligned using the standard parameters of the ClustalW algorithm, as shown in (**A**–**C**), respectively, and four kinds of highly conserved regions (**I**-**IV**) were displayed using GeneDoc program. The conserved amino acids are presented below with the blue letter, and the conserved sequences of FARM (first aspartate-rich motif) and SARM (second aspartate-rich motif) are marked with red letters.