# Conserved Plastid Genomes of _Pourthiaea_ Trees: Comparative Analyses and Phylogenetic Relationship
## 5 Conclusions  
Here, we sequenced three plastomes of _P. beauverdiana, P. parvifolia_, and _P. villosa_ using high-throughput technology, providing new genetic insights into this genus. The three newly obtained _Pourthiaea_ species had a typical tetrad structure and contained one hundred and thirteen unique genes, including four rRNA, thirty tRNA, and seventy-nine PCGs. We first revealed the conservatism of the 13 _Pourthiaea_ plastomes (including 10 published plastomes) through IR/SC boundary, mVISTA, Pi value, and genetic distance analyses. We identified 100-107 SSRs, 60-132 long repeat sequences, and three mutational hotspots among the 13 _Pourthiaea_ plastomes. The selection pressure analysis revealed positively selected sites on the _rb_CL gene. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences support the monophyletic origin of 13 _Pourthiaea_ species, providing a reliable phylogenetic framework for understanding the evolution of the _Pourthiaea_ species. The cytotoxic discordance observed may result from hybridization among _Pourthiaea_ species. This study not only contributes to coming population genetics, species delimitation, and evolutionary history studies of _Pourthiaea_ species, but also provides essential support for horticultural improvement and the conservation of the germplasm resources.  
The following supporting information can be downloaded at: [[https://www.mdpi.com/article/10.3390/f15101811/s1](https://www.mdpi.com/article/10.3390/f15101811/s1)]([https://www.mdpi.com/article/10.3390/f15101811/s1](https://www.mdpi.com/article/10.3390/f15101811/s1)), Figure S1. Gene map of _Plotinia glomera_ plastome. Table S1. Voucher information of four newly sequenced species. Table S2. Gene list of four newly sequenced plastomes. Table S3. SSRs comparison of 13 _Pourthiaea_ species. Table S4. Long repeat sequences comparison of 13 _Pourthiaea_ species. Table S5. Pi values of non-coding and coding regionsof 13 _Pourthiaea_ plastomes. Table S6. Genetic distance among 13 _Pourthiaea_ species. Table S7. The \(\omega\) (dN/dS) of 79 protein-coding genes among 13 _Pourthiaea_ species. Table S8. The LRT of the \(\omega\) under different models. Table S9. Species list used for constructing the phylogenetic tree.  
**Author Contributions:** Formal analysis, T.R. and C.P.; funding acquisition, T.R., Y.J. and B.L.; methodology, C.P. and Y.J.; project administration, T.R.; resources, T.R., C.P. and Y.L.; Software, Y.L. and Y.J.; validation, Y.L. and B.L.; writing--original draft, T.R.; writing--review and editing, T.R., C.P., Y.L., Y.J. and B.L. All authors have read and agreed to the published version of the manuscript.  
**Funding:** This research was supported by the Project of the Science and Technology Program of Shaanxi Academy of Science (2023K-48, 2023K-25, 2023K-14), National Natural Science Foundation of China (32300314).  
**Data Availability Statement:** Four annotated nrDNA sequences and plastomes have been submitted into NCBI with accession numbers: PQ117736-PQ117739 and PQ197388-PQ197391.  
**Acknowledgments:** We thank Novogene company for sequencing.  
**Conflicts of Interest:** We declare that we have no conflicts of interest.