*2.4. Chromosomal Location, Synteny Analysis of TPS Family Members in Rosaceae*

The chromosomal location maps of the TPSs in Rosaceae species were constructed by TBtools, as shown in Figures S3–S9, which indicates the diversity of distribution on chromosomes. For *P. persica*, TPSs were mainly distributed on three chromosomes (chromosomes 3, 4, and 8). Most TPSs (39) were distributed on the 4th chromosome, while five and one TPSs were located on the 3rd and 8th chromosomes, respectively. For the Rosoideae and Maloideae species, TPSs were widely distributed on the 8th and 10th chromosomes, respectively. On the whole, plants from the same subfamily shared a similar chromosome distribution of TPSs. From the physical location maps, we observed that the tandem arrays of TPSs are quite extensive, as in *P. persica*, about 30 TPSs cluster across a stretch of 1051 kb on the 4th chromosome, in *M. domestica*, six TPSs occur in a 200 kb stretch on 10th chromosome. These tandem arrays are likely the consequence of duplication by unequal crossover; genes in tandem arrays are typically highly homologous to each other. For *P. persica*, *M. domestica*, and *F. vesca*, synteny analysis within genomes was conducted to determine their duplication events, as shown in Figure 4, which indicated that genome segmental and tandem duplication were together the driving force for the expansion of the TPS gene family in Rosaceae. For *M. domestica* and *P. persica*, segmental and tandem duplication both contributed to family expansion; for *F. vesca*, tandem duplication played the most important role in the family expansion. MCScanX was used to identify possible collinear blocks between genomes in Rosaceae; the syntenic map between them was constructed, as shown in Figure 5, which showed plenty of syntenic relationships resulting from genome duplication and recombination.

**Figure 4.** Inter-chromosomal relationships of TPSs in *P. persica* (**A**), *M. domestica* (**B**), and *F. vesca* (**C**). Grey lines in the circle indicate the collinear blocks in the *P. persica* or *M. domestica* genome. The red lines in the circle highlight the segmental duplicated TPS gene pairs, while the red curve outside the circle indicates the tandemly duplicated TPS gene pairs produced by MCSscanX.

**Figure 5.** Synteny analysis of TPSs among Rosaceae species. Grey lines in the background indicate the collinear blocks between different genomes, while the yellow lines highlight the syntenic TPS gene pairs. The chromosome is indicated by different colored boxes and labeled by Pr.pLo (*P. persica*), Pr. Mir (*P. mira*), Ma.dom (*M. domestica*), Fr.ves (*F. vesca*), Ro.chi (*R. chinensis*). Collinear relationships between *P. persica*-*P. mira*, *P. persica*-*M. domestica*, *P. persica*-*F. vesca*, *P. persica*-*R. chinensis*, *F. vesca*-*R. chinensis* are shown in (**A**–**E**), respectively.
