Volume 8, Issue 11, Pages 1612-1622 (November 2015) Genetic and Epigenetic Diversities Shed Light on Domestication of Cultivated Ginseng (Panax ginseng)  Ming-Rui Li, Feng-Xue Shi, Yu-Xin Zhou, Ya-Ling Li, Xin-Feng Wang, Cui Zhang, Xu-Tong Wang, Bao Liu, Hong-Xing Xiao, Lin-Feng Li  Molecular Plant  Volume 8, Issue 11, Pages 1612-1622 (November 2015) DOI: 10.1016/j.molp.2015.07.011 Copyright © 2015 The Author Terms and Conditions

Figure 1 Cultivated Ginseng in the Field and the Root Morphologies of Wild and Cultivated Ginseng. (A) We can judge the age of cultivated ginseng based on the number of compound leaves. The sample shown in (A) is a 6-year-old cultivated ginseng because it has five compound leaves. (B and C) Wild ginseng collected from southern population KD and northern population EL, respectively. (D) Landrace COMMON ginseng from population FS. (E) Landrace BIANTIAO ginseng from population BT. (F and G) Landrace SHIZHU ginseng from population SZ. Molecular Plant 2015 8, 1612-1622DOI: (10.1016/j.molp.2015.07.011) Copyright © 2015 The Author Terms and Conditions

Figure 2 Population-Based UPGMA Tree of Cultivated Ginseng and the Wild Relatives Based on the Six Microsatellites. Blue, cultivar accessions; red, wild accessions; black, other Panax species. LN includes the wild accessions from southern populations CY, HR, and KD. The population names of the remaining wild and cultivated ginseng are the same as in Supplemental Table 4. PN, Panax notoginseng; PQ, Panax quinquefolius; PS, Panax stipuleanatus; PZ, Panax zingiberensis. Molecular Plant 2015 8, 1612-1622DOI: (10.1016/j.molp.2015.07.011) Copyright © 2015 The Author Terms and Conditions

Figure 3 Bayesian Population Assignment Test for the Cultivated and Wild Ginseng and Four Other Congeneric Species Inferred by STRUCTURE Based on Microsatellites. The bars on the top indicate that these individuals were retrieved from the same species. Bar plots on the left y-axis showing Bayesian assignment probabilities. Each vertical bar corresponds to one individual. Populations are separated by black bars and identified at the bottom. LN, wild accessions from southern populations CY, HR, and KD; the population names of the remaining wild and cultivated ginseng are the same as in Supplemental Table 4. PN, Panax notoginseng; PQ, Panax quinquefolius; PS, Panax stipuleanatus; PZ, Panax zingiberensis. Molecular Plant 2015 8, 1612-1622DOI: (10.1016/j.molp.2015.07.011) Copyright © 2015 The Author Terms and Conditions

Figure 4 Genetic Clusters and Neighbor-Joining Tree of the 20 Wild and Cultivated Ginseng Accessions Based on SNPs from the Whole-Genome Data. (A) Cultivated and wild ginseng accessions are shown in blue and red, respectively. ∗ indicates the two GAOLI accessions distributed in the southern Korean peninsula. Branch lengths of the two accessions are not shown. (B) The bars on the top indicate these accessions are cultivated (blue) and wild (red) ginseng. Bar plots on the left y-axis showing Bayesian assignment probabilities. GL, landrace GAOLI; BT, landrace BIANTIAO; SZ, landrace SHIZHU; FS, CB, WH, and TQ are landrace COMMON from different populations; XL, SJ, DP, HR, CY, KD, and EL are wild accessions from different populations. The population names and locations of the 20 accessions are shown in Supplemental Table 4 and Supplemental Figure 4. Molecular Plant 2015 8, 1612-1622DOI: (10.1016/j.molp.2015.07.011) Copyright © 2015 The Author Terms and Conditions

Figure 5 Nucleotide Diversity and Demographic History of Cultivated and Wild Ginseng Based on 49 Nuclear Genes. (A) The numbers on the left and right y-axes are the nucleotide diversity and the number of synonymous and nonsynonymous mutations, respectively. BT, landrace BIANTIAO; CN, northern population of COMMON ginseng; CS, southern population of COMMON ginseng; GL, landrace GAOLI; SZ, landrace SHIZHU; WC, domestication center population of wild ginseng; WN, northern populations of wild ginseng; WS, southern populations of wild ginseng. (B) The cultivated ginseng includes the five libraries GL, BT, SZ, CS, and CN. The wild ginseng contains the three libraries WC, WN, and WS. The details for each parameter are shown in Supplemental Table 2. Molecular Plant 2015 8, 1612-1622DOI: (10.1016/j.molp.2015.07.011) Copyright © 2015 The Author Terms and Conditions

Figure 6 Levels of CG and CHG Methylation in Cultivated and Wild Ginseng. The numbers on the left y-axis are the percentage of methylation loci. Molecular Plant 2015 8, 1612-1622DOI: (10.1016/j.molp.2015.07.011) Copyright © 2015 The Author Terms and Conditions