## 2 Results
### Synteny Analysis of TPS Gene Families Across 115 Plant Genomes  
To elucidate the evolutionary conservation and diversification of terpene synthase (TPS) genes, we constructed synteny networks for 115 plant genomes. Synteny networks are crucial for depicting homologous relationships between gene pairs and tracing the evolutionary paths of genes [37; 38]. In these networks, nodes represent TPS genes with syntenic relationships, while edges denote the evolutionary lineages connecting these genes. Our analysis identified 22,035 edges and 1618 nodes, which we organized into 127 distinct  
Figure 1: Phylogenetic distribution and genomic organization of TPS genes in angiosperms. (**Left**) Phylogenetic tree of 115 angiosperm species. Major clades are color-coded: super-asterids (light blue), super-rosids (light orange), basal eudicots (light purple), and monocots (light green). _Lriodendon chinense_ (magnolids) and _Ambrella trichopoda_ (basal angiosperm) are highlighted in light gray. Red asterisks mark whole-genome duplication (WGD) events, blue asterisks indicate whole-genome triplication (WGT) events based on published genomic data [35; 36]. (**Center**) The number of TPS genes identified per species, with color gradients indicating subgroup composition: TPS-a (orange), TPS-b (yellow), TPS-c (purple), TPS-e/f (green), TPS-g (blue). Complete data in Table S1. (**Right**) Comparative distribution of TPS subgroups gene counts across species. With column lengths representing subgroup member counts and color scheme corresponds to TPS subgroups as in center panel.  
communities or node clusters (Tables S3-S5). These clusters were subsequently mapped using phylogenetic profiling, which visually represents the presence or absence of specific syntenic TPS clusters across the 115 angiosperms (Figure S1, Table S6). Notably, Figure S1 reveals the presence of species-specific TPS clusters within particular families, such as Solanaceae, Brassicaceae, and Poaceae, suggesting these clusters may have originated from whole-genome duplication events. Conversely, the absence of specific TPS clusters in some clades may be attributed to the limited number of species examined, underscoring potential gaps in our current genomic coverage.  
Syntenic relationships among species are invaluable for evolutionary analysis, providing insights into gene conservation and divergence over time [39]. To further uncover the potential evolutionary stories of TPSs in angiosperms, we constructed five subgroup-specific networks whose nodes represent subgroups TPS-a, -b, -c, -e/f, and -g (Figure 2A-E, Table S5). Each subgroup showed a specific synteny pattern, and the synteny patterns of certain subgroups were unique to specific plants [40]. The TPS-a network was the largest group, with 71 clusters and nodes that were widespread across angiosperms. A similar pattern emerged for the TPS-b network: some small clusters had the same outer circle color (species group), with interconnected nodes within the same species categories (Figure 2A,B). As shown in Figure 2C, the TPS-c network was highly interconnected, with nodes belonging to super-asterids, super-rosids, and basal eudicots and several nodes from monocots distributed in the periphery. Several nodes from super-asterids and monocots form four small clusters. Both the TPS-e/f and TPS-g networks were small and distributed in super-rosids and monocot species. The synteny pattern of TPS-c was different from the other subgroups. The tight syntenic junctions of TPS-c indicated that this subgroup was highly conserved within eudicots.