*2.3. Chloroplast Gene Gain–Loss Events*

The chloroplast genome structure of most higher plants is stable, and the number, sequence, and composition of genes are conserved. However, the loss of chloroplast genome genes is common. For example, the chloroplast genome of the sweet orange has lost the *infA* gene [8]; the *ycf1*, *ycf2*, and *accD* genes have been lost in Gramineae [9], and the chloroplast genome of some legumes has been recombined several times, resulting in the deletion of a copy of the IR region [10]. The *rpl22* gene was detected in the chestnut nuclear genome [11], presumably having derived from the chloroplast genome. In addition, the *rpl32* gene was transferred to the nuclear genome in the poplar [12], and 17 similar chloroplast regions were found in the mitochondrial genome of papaya, suggesting that the chloroplast gene may have transferred to the mitochondria [13]. However, there have been few studies on how these genes are lost, transferred, and integrated into the nuclear and mitochondrial genomes.

In this study, we compared the gain–loss events of eight *Pyrus* species (five *Pyrus* species that were sequenced in this study and three other *Pyrus* species, *P. pyrifolia*, *P. spinose*, and *P. pashia*, which were downloaded from NCBI) (Tables 4 and 5). The *psbL*, *psbl*, *trnI-GAU*, *trnA*, *trnL*, and *trnY-AUA* genes were most readily lost through evolution, followed by *trnA-UGC*, *trnG-UCC*, *trnI-AAU*, *trnI-GAU*, *trnK-UUU*, *trnN-AUU*, and *trnV-UAC*. *P. hopeiensis* HB-1 contained one less *MATK* gene than *P. hopeiensis* HB-2. Compared with the other three sequenced *Pyrus* species, *trnI-AAU* was only present in *P. hopeiensis* HB-1 and *P. hopeiensis* HB-2. The *atpB* gene was only lost in *P. ussuriensis* Maxin. cv. Jingbaili and *P. communis* L. cv. Early Red Comice, and *petB*, *petD*, *rps16* and *trnL-UAA* were present in the five *Pyrus* species sequenced here, but missing in *P. pyrifolia*, *P. spinosa*, and *P. pashia*.
