Table S1 Plant materials used in this study and cpDNA haplotypes determined by two large deletions

No. / Species* / Accession
or name of cultivars / Origin / Region / Haplotype
accD–psaI
(229bp) / rps16–trnQ
(151bp)
001 / P.ussuriensis / QSL1-1 / Inner Mongolia / – / – / A
002 / P.ussuriensis / QSL1-2 / Inner Mongolia / – / – / A
003 / P.ussuriensis / QSL1-3 / Inner Mongolia / – / – / A
004 / P.ussuriensis / QSL1-4 / Inner Mongolia / – / – / A
005 / P.ussuriensis / QSL1-5 / Inner Mongolia / – / – / A
006 / P.ussuriensis / QSL1-6 / Inner Mongolia / – / – / A
007 / P.ussuriensis / QSL1-7 / Inner Mongolia / – / – / A
008 / P.ussuriensis / QSL1-8 / Inner Mongolia / – / – / A
009 / P.ussuriensis / QSL1-9 / Inner Mongolia / – / – / A
010 / P.ussuriensis / QSL1-10 / Inner Mongolia / – / – / A
011 / P.ussuriensis / QSL1-11 / Inner Mongolia / – / – / A
012 / P.ussuriensis / QSL1-12 / Inner Mongolia / – / – / A
013 / P.ussuriensis / QSL1-13 / Inner Mongolia / – / – / A
014 / P.ussuriensis / QSL1-14 / Inner Mongolia / – / – / A
015 / P.ussuriensis / QSL1-15 / Inner Mongolia / – / – / A
016 / P.ussuriensis / QSL1-16 / Inner Mongolia / – / – / A
017 / P.ussuriensis / QSL1-17 / Inner Mongolia / – / – / A
018 / P.ussuriensis / QSL1-18 / Inner Mongolia / – / – / A
019 / P.ussuriensis / QSL1-19 / Inner Mongolia / – / – / A
020 / P.ussuriensis / QSL1-20 / Inner Mongolia / – / – / A
021 / P.ussuriensis / QSL2-1 / Inner Mongolia / – / – / A
022 / P.ussuriensis / QSL2-2 / Inner Mongolia / – / – / A
023 / P.ussuriensis / QSL2-3 / Inner Mongolia / – / – / As
024 / P.ussuriensis / QSL2-4 / Inner Mongolia / – / – / A
025 / P.ussuriensis / QSL2-5 / Inner Mongolia / – / – / A
026 / P.ussuriensis / QSL2-6 / Inner Mongolia / – / – / A
027 / P.ussuriensis / QSL2-7 / Inner Mongolia / – / – / A
028 / P.ussuriensis / QSL2-8 / Inner Mongolia / – / – / A
029 / P.ussuriensis / QSL2-9 / Inner Mongolia / – / – / A
030 / P.ussuriensis / QSL2-10 / Inner Mongolia / – / – / A
031 / P.ussuriensis / QSL2-11 / Inner Mongolia / – / – / A
032 / P.ussuriensis / QSL2-12 / Inner Mongolia / – / – / A
033 / P.ussuriensis / QSL2-13 / Inner Mongolia / – / – / A
034 / P.ussuriensis / QSL2-14 / Inner Mongolia / – / – / A
035 / P.ussuriensis / QSL2-15 / Inner Mongolia / – / – / A
036 / P.ussuriensis / QSL2-16 / Inner Mongolia / – / – / A
037 / P.ussuriensis / QSL2-17 / Inner Mongolia / – / – / A
038 / P.ussuriensis / QSL2-18 / Inner Mongolia / – / – / A
039 / P.ussuriensis / QSL2-19 / Inner Mongolia / – / – / A
040 / P.ussuriensis / QSL2-20 / Inner Mongolia / – / – / A
041 / P.ussuriensis / THL1-1 / Inner Mongolia / – / – / A
042 / P.ussuriensis / THL1-2 / Inner Mongolia / – / – / A
043 / P.ussuriensis / THL1-3 / Inner Mongolia / – / – / A
044 / P.ussuriensis / THL1-4 / Inner Mongolia / – / – / A
045 / P.ussuriensis / THL1-5 / Inner Mongolia / – / – / A
046 / P.ussuriensis / THL1-6 / Inner Mongolia / – / – / A
047 / P.ussuriensis / THL1-7 / Inner Mongolia / – / – / A
048 / P.ussuriensis / THL1-8 / Inner Mongolia / – / – / A
049 / P.ussuriensis / THL1-9 / Inner Mongolia / – / – / A
050 / P.ussuriensis / THL1-10 / Inner Mongolia / – / – / A
051 / P.ussuriensis / THL1-11 / Inner Mongolia / – / – / A
052 / P.ussuriensis / THL1-12 / Inner Mongolia / – / – / A
053 / P.ussuriensis / THL1-13 / Inner Mongolia / – / – / A
054 / P.ussuriensis / THL1-14 / Inner Mongolia / – / – / A
055 / P.ussuriensis / THL1-15 / Inner Mongolia / – / – / A
056 / P.ussuriensis / THL1-16 / Inner Mongolia / – / – / A
057 / P.ussuriensis / THL1-17 / Inner Mongolia / – / – / A
058 / P.ussuriensis / THL1-18 / Inner Mongolia / – / – / A
059 / P.ussuriensis / THL1-19 / Inner Mongolia / – / – / A
060 / P.ussuriensis / THL1-20 / Inner Mongolia / – / – / A
061 / P.ussuriensis / THL2-1 / Inner Mongolia / – / – / A
062 / P.ussuriensis / THL2-2 / Inner Mongolia / – / – / A
063 / P.ussuriensis / THL2-3 / Inner Mongolia / – / – / A
064 / P.ussuriensis / THL2-4 / Inner Mongolia / – / – / A
065 / P.ussuriensis / THL2-5 / Inner Mongolia / – / – / A
066 / P.ussuriensis / THL2-6 / Inner Mongolia / – / – / A
067 / P.ussuriensis / THL2-7 / Inner Mongolia / – / – / A
068 / P.ussuriensis / THL2-8 / Inner Mongolia / – / – / A
069 / P.ussuriensis / THL2-9 / Inner Mongolia / – / – / A
070 / P.ussuriensis / THL2-10 / Inner Mongolia / – / – / A
071 / P.ussuriensis / THL2-11 / Inner Mongolia / – / – / A
072 / P.ussuriensis / THL2-12 / Inner Mongolia / – / – / A
073 / P.ussuriensis / THL2-13 / Inner Mongolia / – / – / A
074 / P.ussuriensis / THL2-14 / Inner Mongolia / – / – / A
075 / P.ussuriensis / RSL1-1 / Inner Mongolia / – / – / A
076 / P.ussuriensis / RSL1-2 / Inner Mongolia / – / – / A
077 / P.ussuriensis / RSL1-3 / Inner Mongolia / – / – / A
078 / P.ussuriensis / RSL1-4 / Inner Mongolia / – / – / A
079 / P.ussuriensis / RSL1-5 / Inner Mongolia / – / – / A
080 / P.ussuriensis / RSL1-6 / Inner Mongolia / – / – / A
081 / P.ussuriensis / RSL1-7 / Inner Mongolia / – / – / A
082 / P.ussuriensis / RSL1-8 / Inner Mongolia / – / – / A
083 / P.ussuriensis / RSL1-9 / Inner Mongolia / – / – / A
084 / P.ussuriensis / RSL1-10 / Inner Mongolia / – / – / A
085 / P.ussuriensis / RSL1-11 / Inner Mongolia / – / – / A
086 / P.ussuriensis / RSL1-12 / Inner Mongolia / – / – / A
087 / P.ussuriensis / RSL1-13 / Inner Mongolia / – / – / A
088 / P.ussuriensis / RSL1-14 / Inner Mongolia / – / – / A
089 / P.ussuriensis / RSL1-15 / Inner Mongolia / – / – / A
090 / P.ussuriensis / RSL1-16 / Inner Mongolia / – / – / A
091 / P.ussuriensis / RSL1-17 / Inner Mongolia / – / – / A
092 / P.ussuriensi / RSL1-18 / Inner Mongolia / – / – / A
093 / P.ussuriensis / RSL1-19 / Inner Mongolia / – / – / A
094 / P.ussuriensis / RSL1-20 / Inner Mongolia / – / – / A
095 / P.ussuriensis / RSL1-21 / Inner Mongolia / – / – / A
096 / P.ussuriensis / RSL1-22 / Inner Mongolia / – / – / A
097 / P.ussuriensis / RSL1-23 / Inner Mongolia / – / – / A
098 / P.ussuriensis / RSL1-24 / Inner Mongolia / – / – / A
099 / P.ussuriensis / RSL2-1 / Inner Mongolia / – / – / A
100 / P.ussuriensis / RSL2-2 / Inner Mongolia / – / – / A
101 / P.ussuriensis / RSL2-3 / Inner Mongolia / – / – / A
102 / P.ussuriensis / RSL2-4 / Inner Mongolia / – / – / A
103 / P.ussuriensis / RSL2-5 / Inner Mongolia / – / – / A
104 / P.ussuriensis / RSL2-6 / Inner Mongolia / – / – / A
105 / P.ussuriensis / RSL2-7 / Inner Mongolia / – / – / A
106 / P.ussuriensis / RSL2-8 / Inner Mongolia / – / – / A
107 / P.ussuriensis / RSL2-9 / Inner Mongolia / – / – / A
108 / P.ussuriensis / RSL2-10 / Inner Mongolia / – / – / A
109 / P.ussuriensis / RSL2-11 / Inner Mongolia / – / – / A
110 / P.ussuriensis / RSL2-12 / Inner Mongolia / – / – / A
111 / P.ussuriensis / RSL2-13 / Inner Mongolia / – / – / A
112 / P.ussuriensis / RSL2-14 / Inner Mongolia / – / – / A
113 / P.ussuriensis / RSL2-15 / Inner Mongolia / – / – / A
114 / P.ussuriensis / RSL2-16 / Inner Mongolia / – / – / A
115 / P.ussuriensis / RSL2-17 / Inner Mongolia / – / – / A
116 / P.ussuriensis / RSL2-18 / Inner Mongolia / – / – / A
117 / P.ussuriensis / RSL2-19 / Inner Mongolia / – / – / A
118 / P.ussuriensis / RSL2-20 / Inner Mongolia / – / – / A
119 / P.ussuriensis / RSL2-21 / Inner Mongolia / – / – / A
120 / P.ussuriensis / RSL2-22 / Inner Mongolia / – / – / A
121 / P.ussuriensis / RSL2-23 / Inner Mongolia / – / – / A
122 / P.ussuriensis / RSL2-24 / Inner Mongolia / – / – / A
123 / P.ussuriensis / RSL2-25 / Inner Mongolia / – / – / A
124 / P.ussuriensis / RSL2-26 / Inner Mongolia / – / – / A
125 / P.ussuriensis / RSL2-27 / Inner Mongolia / – / – / A
126 / P.ussuriensis / RSL2-28 / Inner Mongolia / – / – / A
127 / P.ussuriensis / SWX1-1 / Heilongjiang / – / – / A
128 / P.ussuriensis / SWX1-2 / Heilongjiang / – / – / A
129 / P.ussuriensis / SWX1-3 / Heilongjiang / – / – / A
130 / P.ussuriensis / SWX1-4 / Heilongjiang / – / – / A
131 / P.ussuriensis / SWX1-5 / Heilongjiang / – / – / A
132 / P.ussuriensis / SWX1-6 / Heilongjiang / – / – / A
133 / P.ussuriensis / SWX1-7 / Heilongjiang / – / – / A
134 / P.ussuriensis / SWX1-8 / Heilongjiang / – / – / A
135 / P.ussuriensis / SWX1-9 / Heilongjiang / – / – / A
136 / P.ussuriensis / SWX1-10 / Heilongjiang / – / – / A
137 / P.ussuriensis / SWX2-1 / Heilongjiang / – / – / A
138 / P.ussuriensis / SWX2-2 / Heilongjiang / – / – / A
139 / P.ussuriensis / SWX2-3 / Heilongjiang / – / – / Ap
140 / P.ussuriensis / SWX2-4 / Heilongjiang / – / – / A
141 / P.ussuriensis / SWX2-5 / Heilongjiang / – / – / A
142 / P.ussuriensis / SWX2-6 / Heilongjiang / – / – / A
143 / P.ussuriensis / SWX2-7 / Heilongjiang / – / – / A
144 / P.ussuriensis / SWX2-8 / Heilongjiang / – / – / A
145 / P.ussuriensis / SWX2-9 / Heilongjiang / – / – / A
146 / P.ussuriensis / SWX2-10 / Heilongjiang / – / – / A
147 / P.ussuriensis / YCS1-1 / Heilongjiang / – / – / A
148 / P.ussuriensis / YCS1-2 / Heilongjiang / – / – / A
149 / P.ussuriensis / YCS1-3 / Heilongjiang / – / – / A
150 / P.ussuriensis / YCS1-4 / Heilongjiang / – / + / C
151 / P.ussuriensis / YCS1-5 / Heilongjiang / – / – / A
152 / P.ussuriensis / YCS2-1 / Heilongjiang / – / – / A
153 / P.ussuriensis / YCS2-2 / Heilongjiang / – / – / A
154 / P.ussuriensis / YCS2-3 / Heilongjiang / – / – / A
155 / P.ussuriensis / YCS2-4 / Heilongjiang / – / – / A
156 / P.ussuriensis / YCS2-5 / Heilongjiang / – / – / A
157 / P.ussuriensis / YCS2-6 / Heilongjiang / – / – / A
158 / P.ussuriensis / YCS2-7 / Heilongjiang / – / – / A
159 / P.ussuriensis / YCS2-8 / Heilongjiang / – / + / C
160 / P.ussuriensis / YCS2-9 / Heilongjiang / – / – / A
161 / P.ussuriensis / YCS2-10 / Heilongjiang / – / – / A
162 / P.ussuriensis / FYX-1 / Heilongjiang / – / – / A
163 / P.ussuriensis / FYX-2 / Heilongjiang / – / – / As
164 / P.ussuriensis / FYX-3 / Heilongjiang / – / – / A
165 / P.ussuriensis / FYX-4 / Heilongjiang / – / – / A
166 / P.ussuriensis / FYX-5 / Heilongjiang / – / – / A
167 / P.ussuriensis / FYX-6 / Heilongjiang / – / – / A
168 / P.ussuriensis / FYX-7 / Heilongjiang / – / – / A
169 / P.ussuriensis / FYX-8 / Heilongjiang / – / – / A
170 / P.ussuriensis / FYX-9 / Heilongjiang / – / – / A
171 / P.ussuriensis / FYX-10 / Heilongjiang / – / – / A
172 / P.ussuriensis / JLGZL-1 / Jilin / – / – / Ap,s
173 / P.ussuriensis / JLGZL-2 / Jilin / – / – / A
174 / P.ussuriensis / JLGZL-3 / Jilin / + / – / B
175 / P.ussuriensis / JLGZL-4 / Jilin / – / – / A
176 / P.ussuriensis / JLGZL-5 / Jilin / – / – / A
177 / P.ussuriensis / JLGZL-6 / Jilin / – / – / A
178 / P.ussuriensis / JLGZL-7 / Jilin / – / – / A
179 / P.ussuriensis / JLGZL-8 / Jilin / – / – / A
180 / P.ussuriensis / JLGZL-9 / Jilin / – / – / A
181 / P.ussuriensis / JLGZL-10 / Jilin / – / – / A
182 / P.ussuriensis / JLGZL-11 / Jilin / – / – / A
183 / P.ussuriensis / JLGZL-12 / Jilin / – / – / A
184 / P.ussuriensis / JLGZL-13 / Jilin / – / – / A
185 / P.ussuriensis / JLGZL-14 / Jilin / – / – / A
186 / P.ussuriensis / JLGZL-15 / Jilin / – / – / A
187 / P.ussuriensis / ‘Qingoushageda’ / Liaoning / + / – / B
188 / P.ussuriensis / ‘Manyuanxiang’ / Liaoning / – / – / A
189 / P.ussuriensis / ‘Balixiang’ / Liaoning / – / – / A
190 / P.ussuriensis / ‘Nanguoli’ / Liaoning / – / – / A
191 / P.ussuriensis / ‘Miansuan’ / Gansu / – / – / A
192 / P.ussuriensis / ‘Jingbaili’ / Beijing / – / – / A
193 / P.ussuriensis / ‘Yaguangli’ / Beijing / – / – / A
194 / P.ussuriensis / ‘Ruanerli’ / Gansu / – / – / A
195 / P.ussuriensis / ‘Huagai’ / Liaoning / – / – / A
196 / P. pyrifolia. / ‘Xingihaizili’ / Guizhou / – / – / A
197 / P. pyrifolia. / ‘Wenshanhongxia’ / Yunnan / – / – / A
198 / P. pyrifolia. / ‘Baozhu’ / Yunnan / – / – / A
299 / P. pyrifolia. / ‘Chubixiang’ / Hubei / + / – / B
200 / P. pyrifolia. / ‘Zhimali’ / Yunnan / – / – / A
201 / P. pyrifolia. / ‘Lijiangxiang’ / Yunnan / – / – / A
202 / P. pyrifolia. / ‘Cangxixueli’ / Sichuan / – / – / A
203 / P. pyrifolia. / ‘Xinya’ / Zhejiang / + / – / B
204 / P. pyrifolia. / ‘Shuidonggua’ / Sichuan / – / – / B
205 / P. bretschneideri / ‘Maogong’ / Sichuan / + / – / B
206 / P. bretschneideri / ‘Xuehuali’ / Anhui / + / – / B
207 / P. bretschneideri / ‘Jinhua’ / Sichuan / – / – / A
208 / P. bretschneideri. / ‘Xixiadaxiangshui’ / Shandong / – / – / A
209 / P. bretschneideri / ‘Wanrongjinli’ / Shanxi / – / – / A
210 / P. bretschneideri / ‘Huahongli’ / Hunan / + / – / B
211 / P. bretschneideri / ‘Enli’ / Shandong / + / + / A
212 / P. bretschneideri. / ‘Huangxianchangba’ / Shandong / + / – / B
213 / P. bretschneideri. / ‘Boshanchi’ / Shandong / – / – / A
214 / P. bretschneideri / ‘Chonghuadali’ / Sichuan / + / – / B
215 / P. bretschneideri / ‘Huochengdonghuang’ / Sichuan / – / – / A
216 / P. bretschneideri / ‘Suanchengtuo’ / Xinjiang / – / – / A
217 / P. sinkiangensis / ‘Zhaixiamote’ / Xinjiang / – / – / A
2181 / P. sinkiangensis / ‘Lanzhouchangba’ / Xinjiang / – / + / C
219 / P. sinkiangensis / ‘Huangjuju(b)’ / Xinjiang / – / – / A
220 / P. sinkiangensis / ‘Huangsuanli’ / Xinjiang / – / – / A
221 / P. sinkiangensis / ‘Huangjuju(a)’ / Xinjiang / – / – / A
222 / P. sinkiangensis / ‘Heisuanli’ / Xinjiang / – / – / A
223 / P. sinkiangensis / ‘Donghuangli’ / Xinjiang / – / – / A
224 / P. sinkiangensis / ‘Yilihongjuju’ / Xinjiang / – / – / A
225 / P. sinkiangensis / ‘Huachangba’ / Xinjiang / – / + / C
226 / P. communis. / ‘La France’ / France / – / + / C
227 / P. communis. / ‘Ladana’ / from abroad / – / + / C
228 / P. communis. / ‘Red Clapp’s Favorite ’ / from abroad / – / + / C
229 / P. communis. / ‘OHF51’ / America / – / + / C
230 / P. communis. / ‘Kongdeli’ / America / + / – / B
231 / P. communis. / ‘Fujiali’ / France / – / + / C
232 / P. communis. / ‘Bartlett’ / UK / – / + / C
233 / P. communis. / ‘Alexandrine Douillard’ / France / – / + / C
234 / P. communis. / ‘Cascade’ / not in detail / – / + / C
235 / P. communis. / ‘Ailaite’ / not in detail / – / – / C
236 / P. communis. / ‘Abate Fetel’ / not in detail / – / + / C
237 / P. communis. / ‘Laolukujie’ / not in detail / – / + / C

+ and - means the presence or absence of large gaps (deletions) in two intergenic regions.

* Classification and nomenclature of these Pyrus followed Yu (1979), and Ohwi (1965) in this study.

Chinese pear cultivarswere maintainedfromthe Pyrus germplasm collection in the Research Institute of Pomology, Chinese Academy of Agricultural Science in Xingcheng, Liaoning province for P. ussuriensis and P. bretschneideriin the Institute of Fruit and Tea, Hubei Academy of Agricultural Science in Wuhan, Hubei province for P. pyrifolia, and in the Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences for P. communis.and P. sinkiangensis.