# Conserved Plastid Genomes of _Pourthiaea_ Trees: Comparative Analyses and Phylogenetic Relationship
## 4 Discussion  
### Characteristics and Comparison of the Pourthiaea Plastomes  
The conserved plastomes in numerous plant lineages have been reported, namely Araceae [51], Asteraceae [52], Betulaceae [53], Fagaceae [54], etc. Here, we newly sequenced three plastomes of _Pourthiaea_ species, which are similar to formerly published Rosaceae plastomes in total length, gene number, and GC content [55]. While the total lengths of the three _Pourthiaea_ plastomes, ranging from 159,903 bp to 160,090 bp, were larger than some species within Rosaceae, such as _Alchemilla_ (152,427-152,438 bp) [56], _Rosa_ (156,405-156,749 bp) [57], and _Rubus_ (155,566-156,236 bp) [58]. The gene number in the three _Pourthiaea_ species (131) was fewer than _Alchemilla_ (133) [56] and _Rosa_ (134) [57], but  
Figure 6: Nucleotide diversity (Pi) in whole plastomes. Coding (**A**) and non-coding (**B**) regions. Figure 7: The phylogenetic tree generated by BI and ML analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences with _Photinia glomerata_ as outgroup. ML replicate values and BI posterior probability values are given at each node. _\"\"\"_ represents the highest support (100%/1). _#_” represents that the node does not occur in the ML tree. was identical to _Rubus_ (131) [58]. The GC content of three _Pourthiaea_ species (36.5%-36.6%) was lower than _Alchemilla_ (37.0%) [56], _Rosa_ (37.2%) [57], and _Rubus_ (37.0%-37.3%) [58]. Moreover, the total length of the three _Pourthiaea_ plastomes differs by only 187 bp. Perhaps this proves the conservatism of the _Pourthiaea_ plastomes from one aspect, which may be attributed to the conservatism of the IR region. Overall, the newly sequenced plastomes contribute to understanding the characteristics of plastomes of the members within _Pourthiaea_ and Rosaceae. The expansion and contraction of the IR regions are significant factors contributing to plastome length variations and evolutionary dynamics [59; 60; 61]. Our comparison of IR/SC boundary regions among the 13 _Pourthiaea_ plastomes revealed that the gene numbers and orders in these borders were identical, with only slight extensions of the IRa/LSC borders into _rpl2-trn_H, while other IR/SC borders have not shifted. This indicates that the IR regions are highly conserved with minimal structural variation in the 13 _Pourthiaea_ plastomes. There are differences in the IR/SC boundary regions between _Pourthiaea_ and other members of the Rosaceae, such as _Alchemilla_ [56], _Fragaria_ [56], _Rubus_ [62], etc. Moreover, highly conserved genomic structures have been observed in other tree species, such as _Quercus_ [63], _Tilia_ [64], and _Ehretia_ [65]. SSRs, often containing one to six nucleotides, are employed as molecular markers for biogeographic and population genetics studies [66; 67]. Consistent with previous studies on Rosaceae or other plant groups, our results found that SSRs in the 13 _Pourthiaea_ plastomes predominantly consist of polythymine (polyT) or polyadenine (polyA) repeats [62; 68; 69]. Additionally, the high polyT or polyA SSRs likely contribute to the overall AT richness in the plastomes [70; 71]. The uneven distribution of SSRs observed in the 13 _Pourthiaea_ plastomes is similar to findings in _Cridium monnieri_ [71] and _Oryzaa minuta_ [72]. Our study provides essential molecular resources for the conservation of _Pourthiaea_ germplasm, offering SSRs that can be used in breeding programs and population genetic studies aimed at preserving the genetic diversity of this genus. It is well known that repeat sequences play a major role in mutation, rearrangement, and recombination events in plastomes [73; 74; 75]. Among the identified 992 long repeat sequences, those with 30-40 bp and 40-50 bp were the most common (99.1%), consistent with many plant plastomes [64; 76]. The palindromic and forward repeats were the most universal repeat types, while the reverse and complementary repeats were the less universal, as reported in prior studies [64; 76; 77].