## 5 Conclusions  
We demonstrate the power of an optimized Oxford Nanopore adaptive sampling (AS) protocol for integrated mitochondrial genomic and epigenomic analysis in adipose-derived mesenchymal stem cells. This amplification-free, long-read sequencing approach uniquely enables the simultaneous characterization of genetic variants--including heteroplasmy and haplotypes--and native DNA base modifications from the same single molecules. By preserving the crucial phase relationship between sequence and epigenetic marks, AS facilitates direct correlation analyses and provides a comprehensive view of mitochondrial heterogeneity and regulation. This study validates AS for effective mtDNA enrichment and linked geno-epigenomic profiling, highlighting its significant potential to advance investigations into mitochondrial biology, disease mechanisms, aging, and pharmacogenomics.  
**Supplementary Materials:** The following supporting information can be downloaded at: [[https://www.mdpi.com/article/10.3390/app15115822/s1](https://www.mdpi.com/article/10.3390/app15115822/s1)]([https://www.mdpi.com/article/10.3390/app15115822/s1](https://www.mdpi.com/article/10.3390/app15115822/s1)), Figure S1: Comparison of sequencing coverage metrics for selected ADME genes; Figure S2: Variants and heteroplasmies summary from Jar (A) and from AdMSC (B); Figure S3: Summary and statistics from the experiments (A) for mDNA from Jar (B) for mtDNA from AdMSCs; Figure S4: Phylogenetic trees of Jar (A) and AdMSC (B); Figure S5: Summary of the polymorphisms. Found_Polys represent the variants that were identified in the sample and matched the expected haplogroup-specific polymorphisms. RemainingPolys represent these that were not found or did not match the expected patterns for the haplogroup, or polymorphisms still to be confirmed; Figure S6. Different number of AS and WGS detected reads.  
**Author Contributions:** Conceptualization, S.H. and K.T.; methodology, A.G., S.H. and K.T.; software, S.H.; validation, D.P.-D. and K.T.; formal analysis, K.T.; investigation, A.G. and X.M.; resources, K.T.; data curation, A.G., K.T. and S.H.; writing--original draft preparation, A.G. and K.T.; writing--review and editing, S.H.; visualization, A.G. and S.H.; supervision, K.T.; project administration, K.T.; funding acquisition, K.T., D.P.-D. and S.H. All authors have read and agreed to the published version of the manuscript.  
**Funding:** This research was funded by the European Union-NextGenerationEU, through the National Recovery and Resilience Plan of the Republic of Bulgaria, grant number BG-RRP-2.004-0003 and utilized equipment funded by National Roadmap for Research Infrastructure of the Ministry of Education and Science of Republic of Bulgaria, grant number DO1-178/29.07.2022 and grant number DOI-352/13.12.2023.  
**Institutional Review Board Statement:** Not applicable.  
**Informed Consent Statement:** Not applicable.  
**Data Availability Statement:** Sequencing data are currently unavailable.  
**Conflicts of Interest:** The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.