## 3 Discussion
americana_ uniquely showed the presence of a reverse repeat, which was not observed in other species. Reverse repeats may contribute to structural variations by influencing recombination events, potentially affecting the genome architecture in species-specific ways. Overall, the distribution of SSRs and tandem repeats across the LSC, SSC, and IR regions indicated a well-conserved genomic structure in _Phytplacca_ species. Analysis of the IR expansion and contraction in _Phytplacca_ species revealed a largely conserved cp genome structure, consistent with patterns observed in other angiosperms. In this study, comparisons of the cp genome boundaries among six _Phytplacca_ species and _A.__clematiate_ revealed distinct patterns of the IR region contraction and expansion among the species. Specifically, IR contraction has been observed in _P. americana_, whereas IR expansion has been observed in other _Phytplacca_ species. Despite these variations in IR size, the overall gene arrangement and location were mostly conserved across _Phytplacca_ species, indicating a stable genomic structure with some degree of flexibility at the IR boundaries. These findings indicate that although the cp genome of _Phytplacca_ has undergone evolutionary changes in certain regions, particularly at the IR boundaries, it remains highly conserved in terms of gene order, which aligns with the evolutionary trends seen in other plant lineages [19; 44]. The mVISTA comparison revealed that the cp genome of _Phylolaca_ is highly conserved overall, particularly in the genic regions, which are more conserved than the IGS regions. This is a common trend in angiosperms, as genic regions play essential roles in biological functions [63]. Sequence comparisons using _P. acinosa_ as a reference indicated high similarity between _P. insularis_ and _P. acinosa_, suggesting a closer evolutionary relationship, whereas _P. americana_ showed the greatest divergence in both the genic and IGS regions, particularly in genes such as _rps16-trnQ-UIUC_, _trn5-GCUI-trnG-UCC_, _pafl-trn5-GGA_, _pafl-cemA_, _psal-rpl33_, and _ycf1_, indicating greater genetic variability within the genus. Morphological analysis was also consistent with the genomic results. Based on reproductive characteristics, such as inflorescence and carpels, _P. americana_ is clearly different from other Korean _Phylolaca_ species. Furthermore, according to recent species concepts, _P. insularis_ is treated as a form of _P. acinosa_[4] or as a recognized synonym of _P. acinosa_[64]. According to the Korean Herbal Pharmacopoeia, the dried roots of _P. acinosa_ and _P. americana_, which are morphologically and genetically distinct, are used in the same herbal medicine Phytolaceae Radix. Our results and recent taxonomic concepts indicate that _P. insularis_ is closely related to _P. acinosa_. Phylogenetic analysis of medicinal plants has proven to be a valuable predictive tool for more focused strategies [65]. According to our results, _P. acinosa_ and _P. insularis_ clustered in monophyly would have a similar effect. Thus, an analysis of the pharmacological and chemical properties of _P. insularis_ is needed to clarify the medicinal properties and also the possibilities of the newly listed Korean Herbal Pharmacopoeia. In addition to the mVISTA comparison, the Pi values across the six _Phylolaca_ species revealed specific regions with elevated variability. Notably, regions such as _ccsA-tdhD_, _trnM-atpE_, and _rps16-trnQ_ exhibited high Pi values, marking these as hotspots of nucleotide diversity. These regions, primarily located in the LSC and SSC regions, may play an important role in the evolutionary dynamics of the cp genomes of these species [45]. Identifying these hotspot regions is particularly valuable because they can serve as molecular markers for phylogenetic and population genetic studies within the genus [19].