*2.1. Basic Characteristics of Chloroplast Genome of P. hopeiensis*

The chloroplast genome of *P. hopeiensis* has a typical tetrad structure, including paired IRa and IRb sequences, encoding in opposite directions, and large and small single copy regions (Figure 1). The total chloroplast genome of *P. hopeiensis* HB-1 was 159,935 bp in length, 46 bp smaller than that of *P. hopeiensis* HB-2. The large single copy (LSC) region was 87,961 bp long, 46 bp smaller than that of *P. hopeiensis* HB-2. The length of the small single copy (SSC) region was 19,200 bp and the IR region was 26,387 bp, the same as those of *P. hopeiensis* HB-2. There was little difference in length between the two *P. hopeiensis* genotypes, and what difference existed was in the LSC region.

A total of 117 genes (Table 1) from the chloroplast genome of *P. hopeiensis* HB-1 were annotated, including 77 protein coding genes, 31 tRNAs, eight rRNAs, and two pseudogenes (*clpP* and *atpF*). *P. hopeiensis* HB-1 lacked only the *MATK* protein-coding gene that was associated with biosynthesis in *P. hopeiensis* HB-2. These 77 protein-coding genes can be divided into four categories. The first contains 28 self-replicating genes, including three subunits encoding the synthesis of chloroplast RNA polymerase. The second category contains 40 genes related to photosynthesis, including light systems I and II, a cytochrome b 6/f protein complex, and ATP synthase and other biosynthesis genes, including

bp.

cytochrome-related genes (*P. hopeiensis* HB-1 contains three genes and *P. hopeiensis* HB-2 contains four genes). The fourth category contains five unknown genes, such as the *ycf* gene. The IR region of *P. hopeiensis* contains 32 genes, of which the *ndhB* gene is present only in the IRb region and is absent in the IRa region. In addition, *rps12* is a mitotic gene with its 50 terminal located at the LSC region and 30 end with a copy is located in each of the two IR regions. This phenomenon is common in higher plants. contains four genes). The fourth category contains five unknown genes, such as the *ycf* gene. The IR region of *P. hopeiensis* contains 32 genes, of which the *ndhB* gene is present only in the IRb region and is absent in the IRa region. In addition, *rps12* is a mitotic gene with its 5' terminal located at the LSC region and 3' end with a copy is located in each of the two IR regions. This phenomenon is common in higher plants.

including cytochrome-related genes (*P. hopeiensis* HB-1 contains three genes and *P. hopeiensis* HB-2

**Figure 1.** Gene maps of *Pyrus hopeiensis* HB-1chloroplast genomes. **Figure 1.**Gene maps of *Pyrus hopeiensis* HB-1chloroplast genomes.

The chloroplast genome of *P. hopeiensis* HB-1 contains 11 genes that harbor introns and one more *trnI-TAT* gene than *P. hopeiensis* HB-2. Of these 11 genes, two are tRNA genes (*trnI-TAT* and *trnI-AAT*) and nine are protein-coding genes (*rpoC1*, *rpl22*, *rpl22*, *ndhA, rpl2*, *rpl2*, *rps12*, *rps12*, *rps12*, *ycf3*), of which *ycf3* contains two introns. Excepting the intron length of the *trnI-AAT* gene, *P. hopeiensis* HB-2 is larger than *P. hopeiensis* HB-1. The exon and intron lengths of the two *P. hopeiensis* genotypes are identical. Among the coding genes, *ndhA* was the longest at 1125 bp, and rpl22 was the shortest at 63 The chloroplast genome of *P. hopeiensis* HB-1 contains 11 genes that harbor introns and one more *trnI-TAT* gene than *P. hopeiensis* HB-2. Of these 11 genes, two are tRNA genes (*trnI-TAT* and *trnI-AAT*) and nine are protein-coding genes (*rpoC1*, *rpl22*, *rpl22*, *ndhA, rpl2*, *rpl2*, *rps12*, *rps12*, *rps12*, *ycf3*), of which *ycf3* contains two introns. Excepting the intron length of the *trnI-AAT* gene, *P. hopeiensis* HB-2 is larger than *P. hopeiensis* HB-1. The exon and intron lengths of the two *P. hopeiensis* genotypes are identical. Among the coding genes, *ndhA* was the longest at 1125 bp, and rpl22 was the shortest at 63 bp.


*Int. J. Mol. Sci.* **2018**, *19*, 3262
