**4. Conclusions**

Next generation whole genome shotgun sequences of plant species often contain numerous reads that are derived from the cp genomes, which provides a unique opportunity to assemble complete cp genomes. This method of using low coverage of the whole genome sequencing data to recover highly repetitive genome regions such as organelle genomes is called the "whole genome skimming approach". In the present study, we determined and characterized the complete cp genomes of three *P. granatum* cultivars using the whole genome sequencing data. Sequence diversity analysis revealed that cp genome sequences may not be suitable for investigating the genetic diversity of pomegranate genotypes. The genome sequencing data of three different cultivars are valuable resources for pomegranate breeding programs. The complete cp genome sequences that were newly assembled in our study could provide valuable information for understanding the evolutionary relationships among the Myrtales.

**Author Contributions:** Data curation, M.Y., J.Z., and Y.D.; Formal analysis, M.Y., J.Z., and Y.H.; Funding acquisition, Z.Y.; Methodology, Z.Y.; Visualization, M.Y.; Writing—original draft, M.Y. and X.Z.; Writing—review and editing, X.Z., J.Z., and Z.Y.

**Funding:** This work was supported by the Initiative Project for Talents of Nanjing Forestry University (GXL2014070, GXL2018032), the Priority Academic Program Development of Jiangsu High Education Institutions (PAPD), and the Natural Science Foundation of Jiangsu Province (BK20180768).

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