## 2 Results
### Comparative Analysis of the TPS Family in R. chinensis  
Among the 12 Rosales species examined, _R. chinensis_ hosts the most extensive TPS gene family. We constructed a phylogenetic tree of 54 RcTPS genes, which grouped into three main clades as depicted in Figure 4A. The predominant clade comprises 36 genes from the TPS-a subgroup, significantly larger than the others, which include eight TPS-b  
Figure 3: Phylogenetic relationships of TPS-c and TPS-e/f subgroups across 115 angiosperm species. The TPS-c clades are shown in purple, and the TPS-e/f clades are shown in green. The phylogenetic tree was constructed using the TPS-c and TPS-e/f members from 115 angiosperms (Table S1). The clades are highlighted in different colors: super-rosids (light orange), monocots (light green), super-asterids (light blue), basal-eudicots (light purple), basal-angiogenesis and magnolids (light gray). and five TPS-g members in the second clade, and two TPS-c and three TPS-e/f members in the third clade. Detailed phylogenetic analysis revealed two sub-clades within the TPS-a subgroup, characterized by notably diverse branch lengths, indicating a significant expansion relative to other subgroups (Figure 4A). We further explored the chromosomal distribution of these 54 RcTPS genes, finding a pronounced uneven distribution across the seven chromosomes of _R. chinensis_ (Figure 4B). Notably, chromosome 5 (Chr5) harbors 20 RcTPS genes, whereas chromosome 4 (Chr4) contains only one. All members of the TPS-g and TPS-c subfamilies are localized to Chr5 and Chr6, respectively. Except for Chr2, TPS-a gene clusters are present on six chromosomes. This genomic architecture, combined with our phylogenetic findings, underscores the expansion of the TPS-a genes. Additionally, gene structure analysis provides further evolutionary insights; for instance, most TPS-a, TPS-b, and TPS-g subgroup members feature seven exons, while TPS-c and TPS-e/f subgroup members typically have 13 to 15 exons (Figure S3). These structural patterns, similar to those observed in _A. thaliana, E. grandis_, and _M. domestica_[21; 23; 41], suggest a relative conservation of exon features across these species. We explored the syntenic relationships of 54 identified RcTPSs across 115 angiosperms, finding that 27 of these genes are syntenic homologs with TPSs from other species. The relationships involving RcTPSs were individually illustrated, with each RcTPS positioned centrally in the diagrams (Figure 5A). Notably, two RcTPSs (RchiOBHmChr5g0023471 and RchiOBHmChr2g0160561) demonstrated extensive syntenic connections. The majority of RcTPSs (23 out of 27) predominantly showed synteny with TPSs from species within the super-rosid and super-asterid groups. Moreover, two RcTPSs (RchiOBHmChr1g0326251 and RchiOBHmChr5g0004801) appeared as Rosaceae-specific syntelogs, indicating unique syntenic relationships confined to this family. Additionally, three distinct pairs of syntenic genes were identified between _R. chinensis_ and _V. vinifera_, highlighting specific evolutionary links (items 9, 10, and 11 in Figure 5A). Figure 4: Phylogenetic and chromosomal distribution of RcTPSs in _R. chinensis_. (**A**) This panel shows a phylogenetic tree of TPS proteins from _R. chinensis_, constructed using the maximum-likelihood method with 1000 bootstrap replicates via RAxML. The tree segregates TPS proteins into six subgroups, each indicated by a distinct color. The composition and relationships of these subgroups are detailed in Table S7. (**B**) Chromosomal distribution of putative functional terpene synthase genes across the chromosomes (denoted as Chr) of _R. chinensis_. Each gene is represented by a small dot, color-coded by subfamily: TPS-a (orange), TPS-b (yellow), TPS-c (purple), TPS-e/f (green), and TPS-g (blue), providing a visual representation of gene location and subgroup prevalence. We analyzed the gene expression patterns of _RcTPSs_ using RNA-seq data from various rose tissues and across four critical developmental stages of petals.