*Article* **Structural and Comparative Analysis of the Complete Chloroplast Genome of** *Pyrus hopeiensis***—"Wild Plants with a Tiny Population"—and Three Other** *Pyrus* **Species**

#### **Yongtan Li 1,2,†, Jun Zhang 1,2,†, Longfei Li <sup>3</sup> , Lijuan Gao <sup>3</sup> , Jintao Xu <sup>3</sup> and Minsheng Yang 1,2,\***


Received: 2 October 2018; Accepted: 16 October 2018; Published: 20 October 2018

**Abstract:** *Pyrus hopeiensis* is a valuable wild resource of *Pyrus* in the Rosaceae. Due to its limited distribution and population decline, it has been listed as one of the "wild plants with a tiny population" in China. To date, few studies have been conducted on *P. hopeiensis*. This paper offers a systematic review of *P. hopeiensis*, providing a basis for the conservation and restoration of *P. hopeiensis* resources. In this study, the chloroplast genomes of two different genotypes of *P. hopeiensis*, *P. ussuriensis* Maxin. cv. Jingbaili, *P. communis* L. cv. Early Red Comice, and *P. betulifolia* were sequenced, compared and analyzed. The two *P. hopeiensis* genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy (LSC) region, and a small single copy (SSC) region. The length of the chloroplast genome of *P. hopeiensis* HB-1 was 159,935 bp, 46 bp longer than that of the chloroplast genome of *P. hopeiensis* HB-2. The lengths of the SSC and IR regions of the two *Pyrus* genotypes were identical, with the only difference present in the LSC region. The GC content was only 0.02% higher in *P. hopeiensis* HB-1. The structure and size of the chloroplast genome, the gene species, gene number, and GC content of *P. hopeiensis* were similar to those of the other three *Pyrus* species. The IR boundary of the two genotypes of *P. hopeiensis* showed a similar degree of expansion. To determine the evolutionary history of *P. hopeiensis* within the genus *Pyrus* and the Rosaceae, 57 common protein-coding genes from 36 Rosaceae species were analyzed. The phylogenetic tree showed a close relationship between the genera *Pyrus* and *Malus*, and the relationship between *P. hopeiensis* HB-1 and *P. hopeiensis* HB-2 was the closest.

**Keywords:** *Pyrus hopeiensis*; cp genome; IR boundary; phylogeny
