## 2 Results
### Conserved Domains and Gene Structural Analysis of EhFPS  
Cluster analysis showed that _EthFPS_ genes could be divided into three categories, of which _EhFPS2_ and _EhFPS4_ were clustered into one category, _EhFPS3_ alone was in one category, and the remaining five members were in one category (Figure 3A). The conserved domains of each _EhFPS_ gene were predicted using NCBI-CDD, and the results showed that each EhFPS protein contained a single polyprenyl synthase domain of a similar length (Figure 3B). The structures of _EhFPS_ genes were similar and contained more exons; among them, _EhFPS2_ and _EhFPS5_ had 12 exons, and the remaining members had 11 exons. However, only _EhFPS6_, _EhFPS1_, _EhFPS3_, and _EhFPS2_ had UTR ends,  
Figure 1: Genetic map of _E. hirta_ and chromosome mapping of _FPS_ genes on _E. hirta_ genome. The scale to the left is in megabase units (Mb). The chromosome number is indicated to the left of each chromosome. Red-colored letters indicate gene positions on each chromosome. Blue lines on chromosomes indicate gene density. The greater the density of genes, the denser the blue line area.  
Figure 2: Series replication and selection pressure analysis of _FPS_ genes. (**A**) Collinearity analysis of _FPS_ genes between _E. hirta_ and _H. brasiliensis_. Gray lines in the background highlight collinear blocks within the _E. hirta_ and other plant genomes, while collinear _FPS_ gene pairs are linked with red lines. (**B**) Selection pressure analysis of _FPS_ gene cluster. (**C**) Analysis of tandem replication of _FPS_ genes in the genome of _E. hirta_. Chromosomes 1–9 are represented by rectangles. Lines and histograms along the rectangle represent the gene density on the chromosome. The gray lines represent the isolinear blocks in the genome of _E. hirta_, while the red lines between chromosomes represent the gene pairs with fragment repeats.  
whereas the other four genes did not have UTR ends (Figure 3C). Comparing the conserved domains and motifs of all genes, except EhFPS8, the other seven members all contained the important functional domain motif II DDXXD, which binds Mg2+ to regulate enzyme activity, whereas Motif2 (DDYXD) was shared by all members (Figure 4). In addition, it contained GKLNR (Motif1), which binds to the substrate, and KT (Motif4), which is the active site of the enzyme. Through protein tertiary structure modelling, the sequence identity of the EhFPS protein and Eucommia farnesyl diphosphate synthase 1 chimera (template number: 7 bux.1.A) from the PDB database ([[https://www.rcsb.org/](https://www.rcsb.org/)]([https://www.rcsb.org/](https://www.rcsb.org/)), accessed on 7 May 2024) was 78.36%, the sequence similarity was 0.81, and the coverage was 0.86. Modelling based on this template showed that EhFPS is composed of homodimeric oligonucleotides formed by \(\alpha\)-helices and that the spatial structure contains a \"pocket\" for binding to the substrate. At the same time, comparisons revealed that _EhFPS1_, _EhFPS2_, _EhFPS5_, and _EhFPS6_ had seven \(\alpha\)-helical chains with similar overall structures, _EhFPS3_ and _EhFPS7_ had similar side chain structures, and _EhFPS4_ and _EhFPS8_ had similar tertiary structures (Figure 5), indicating that changes in the protein structure of members may lead to protein functional diversity.