A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding.
Medicinal plants of the Panax genus belonging to Araliaceae family are well-known, rare plants used as tonics in traditional Chinese medicine and have been described in the Chinese Pharmacopoeia. Because of the high price and the huge human demand, these commercial products often contain adulterants. In this study, 377 sequences from four species were analyzed. Single nucleotide polymorphisms (SNPs) were detected and patterns of intragenomic variation in internal transcribed spacer 2 (ITS2) from the four Panax species were studied. Intraspecific variations were analyzed based on three typical DNA barcodings (ITS2, matK and psbA-trnH). Results from this study revealed that intraspecific genetic distances in Panax ginseng and Panax quinquefolius were quite low (0-0.002) and the multi-copy ITS2 could be considered a single locus in the genomes of these two species. Five stable SNPs were detected in ITS2 region to identify the Panax medicinal species. Considering the mixed powder of P. ginseng and P. quinquefolius, double peaks could be clearly examined at SNP positions and the height of the peaks could indicate the mixed ratio roughly. Our findings indicate that SNP-based molecular barcodes could be developed as a routine method for the identification of the Panax genus with closely related species and the mixed powder P. ginseng and P. quinquefolius.
Center for Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China.
Xiaochen
X
Chen
Baosheng
B
Liao
Jingyuan
J
Song
Xiaohui
X
Pang
Jianping
J
Han
Shilin
S
Chen
D058893:DNA Barcoding, Taxonomic; D018744:DNA, Plant / Q000235:genetics*; D006801:Humans; D008516:Medicine, Chinese Traditional; D005894:Panax / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D013045:Species Specificity
D018744:DNA, Plant
AFLP; Amplified fragment length polymorphism; HMM; Hidden Markov Model; ITS; ITS2; Intragenomic divergence; Intraspecific variation; K2P; Kimura-two-parameter; Panax; RAPD; RFLP; Random amplified polymorphic DNA; Restriction fragment length polymorphism; SNP; SNPs; Single nucleotide polymorphisms; internal transcribed spacer; internal transcribed spacer 2