**5. Conclusions**

In this study, we reported the de novo sequencing results of *P. hopeiensis* chloroplast genomes. The length of the chloroplast genome of *P. hopeiensis* HB-1 is 159,935 bp, which is 46 bp longer than that of *P. hopeiensis* HB-2. The SSC and IR regions of the two Pyrus genotypes were the same length, with the only difference present in the LSC region. A total of 118 genes were identified in *P. hopeiensis* HB-1, and it only lacked the *MATK* protein-coding gene that was associated with biosynthesis in *P. hopeiensis* HB-2. The GC content of *P. hopeiensis* HB-1 was only 0.02% higher than that of *P. hopeiensis* HB-2. A total of 11 genes in the chloroplast genome of *P. hopeiensis* HB-1 contained introns, and an additional *trnI-TAT* gene not present in *P. hopeiensis* HB-2. *ycf3* is the only gene that contained two introns. The chloroplast genome structure and size, gene species, gene number, and GC content of *P. hopeiensis* were similar to those of the other three *Pyrus* species investigated. Almost all of the protein coding sequences and amino acid codons showed an obvious codon preference. Selection pressure analysis revealed that the chloroplast genomes of different pears were affected by different environmental pressures during the evolutionary process, which may account for the differences in gene numbers among the five *Pyrus* species. Phylogenetic analysis strongly supports the status of *Pyrus* in the Rosaceae. This study adds to our knowledge of the molecular evolution of *Pyrus*, and will be of use for the genetic breeding and chloroplast engineering of *Pyrus*.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/19/10/ 3262/s1.

**Author Contributions:** M.Y. designed the research; Y.L., J.Z. and J.X. collected the samples; Y.L., L.L. and L.G. performed the experiments and analysis; Y.L. and J.Z. wrote the manuscript; all authors revised the manuscript.

**Funding:** This research received no external funding.

**Acknowledgments:** This research was supported by the National Key Research and Development Plan "Research on protection and restoration of typical small populations of wild plants" (Grant No. 2016YFC0503106).

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