**5. Conclusions**

In conclusion, this study investigated the TPS gene family in eight sequenced Rosaceae species through classification, chromosomal location, orthologous relationships, and duplication analysis. The distribution of the TPS gene family among Rosaceae species revealed a diversity of family number and function; lineage-specific expansion of the TPSs accompanied by frequent domain loss were widely observed within different TPS clades. We further provided their tissue-specific expression pattern in *F. vesca*, *M. domestica*, and *P. persica*, revealing the expression differentiation of TPSs between paralogs/species. The findings

revealed the evolution of TPSs in Rosaceae and will be highly useful for further genetic improvement of Rosaceae species.

**Supplementary Materials:** The following supporting information can be downloaded at https: //www.mdpi.com/article/10.3390/plants11060736/s1. Table S1: Pfam domain distribution in the TPSs of eight Rosaceae species (sheet a); motif distribution in the TPSs of three Rosaceae species (sheet b); the alternative splicing transcripts of putative TPSs in *F. vesca*, *M. domestica*, and *P. persica* (sheet c). Table S2: Information of all TPSs analyzed in this study, (XLSX); Table S3: Ka/Ks ratio of TPSs in Rosaceae; Table S4: Expression values of TPSs in *F. vesca*, *M. domestica*, and *P. persica*. Figure S1. A Neighbor-joining phylogenetic tree of TPSs of the TPS proteins in three Rosaceae species (*P. persica, M. domestica, F. vesca*). Figure S2. A maximum-likelihood phylogenetic tree of six representative Rosaceae species TPS gene family. The branches of TPS-a, TPS-g, TPS-b, TPS-c, TPS-e and TPS-f clades are colored in blue, yellow-green, green, red, purple and cyan, respectively. Figure S3. Chromosomal locations of TPS family members in peach 'Lovell' genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S4. Chromosomal locations of TPS family members in *Prunus mume* genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S5. Chromosomal locations of TPS family members in *Prunus mira* genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S6. Chromosomal locations of TPS family members in *Malus x domestica* genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S7. Chromosomal locations of TPS family members in *Pyrus betulifolia* genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S8. Chromosomal locations of TPS family members in *Fragaria vesca* genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S9. Chromosomal locations of TPS family members in *Rosa chinensis* genome. The gene location visualize package of TBTools was used to exhibit chromosomal locations of the TPS genes. The number to the left of each chromosome represented the size of the chromosome in bp. Figure S10. Expression pattern of TPS genes in three Rosaceae plants (*P. persica, M. domestica, F. vesca*). The x-axis represents different samples (ripe fruit, immature fruit and leaf), the y-axis represents TPS genes. There are two replicates for each tissue. The phylogenetic tree is shown on the left panel, the root nodes of TPS-a, TPS-g, TPS-b, TPS-c and TPS-e, TPS-f clades are indicated by blue, green, yellowgreen, red, benzo, and purple, respectively.

**Author Contributions:** Conceptualization, X.Z. and A.Z.; methodology, X.J. and A.Z.; software, A.Z.; validation, Y.X., A.Z. and J.F.; formal analysis, T.W., K.L.; investigation, A.Z.; resources, Y.X.; data curation, A.Z.; writing—original draft preparation, A.Z.; writing—review and editing, A.Z., X.Z. and H.P.; visualization, X.Z.; supervision, X.Z.; project administration, X.Z.; funding acquisition, X.Z. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by the National Natural Science Foundation of China, grant number 32070682, the National Science & Technology Innovation Zone Project, grant numbers 1716315XJ00200303 and 1816315XJ00100216.

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** All raw reads used in this work were deposited in NCBI Bio-Project with the accession number PRJNA381300.

**Acknowledgments:** We would like to thank the members of the Bioinformatics Group of Wuhan Botanical Garden, Chinese Academy of Sciences, China for the discussion and suggestions to improve the manuscript.

**Conflicts of Interest:** The authors declare no conflict of interest.
