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Evaluation of four commonly used DNA barcoding Loci for chinese medicinal plants of the family schisandraceae.

Zhang J, Chen M, Dong X, Lin R, Fan J, Chen Z - PLoS ONE (2015)

Bottom Line: Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level.The feasibility of DNA barcodes for identification of geographical authenticity was also verified here.The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China.

ABSTRACT
Many species of Schisandraceae are used in traditional Chinese medicine and are faced with contamination and substitution risks due to inaccurate identification. Here, we investigated the discriminatory power of four commonly used DNA barcoding loci (ITS, trnH-psbA, matK, and rbcL) and corresponding multi-locus combinations for 135 individuals from 33 species of Schisandraceae, using distance-, tree-, similarity-, and character-based methods, at both the family level and the genus level. Our results showed that the two spacer regions (ITS and trnH-psbA) possess higher species-resolving power than the two coding regions (matK and rbcL). The degree of species resolution increased with most of the multi-locus combinations. Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level. Here we propose the combination of ITS+trnH-psbA+matK+rbcL as the most ideal DNA barcode for discriminating the medicinal plants of Schisandra and Kadsura, and the combination of ITS+trnH-psbA as the most suitable barcode for Illicium species. In addition, the closely related species Schisandra rubriflora Rehder & E. H. Wilson and Schisandra grandiflora Hook.f. & Thomson, were paraphyletic with each other on phylogenetic trees, suggesting that they should not be distinct species. Furthermore, the samples of these two species from the southern Hengduan Mountains region formed a distinct cluster that was separated from the samples of other regions, implying the presence of cryptic diversity. The feasibility of DNA barcodes for identification of geographical authenticity was also verified here. The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.

No MeSH data available.


Plots of maximum intraspecific vs. minimum interspecific p-distances for single regions of Schisandraceae.Each dot represents a species for which two or more individuals were sampled. Dots above the diagonal line indicate the presence of a barcoding gap.
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pone.0125574.g001: Plots of maximum intraspecific vs. minimum interspecific p-distances for single regions of Schisandraceae.Each dot represents a species for which two or more individuals were sampled. Dots above the diagonal line indicate the presence of a barcoding gap.

Mentions: We calculated genetic distances for each DNA region using MEGA v5.05 [78] based on the uncorrected p-distance model, which has been shown to perform as well as or better than the broadly used Kimura-2-parameter model [79–81]. The pairwise distances, intra- and interspecific distances were calculated for each species that were represented by more than one individual. Additionally, the differences of intra- and interspecific divergences between each pair of four commonly used barcoding loci were tested by Wilcoxon signed-ranks tests [7,15] in PASW Statistics 18.0 (IBM, Armonk, New York, USA). To assess the differences between intra- and interspecific divergences within each commonly used barcoding locus, Wilcoxon two-sample tests were performed. For each species, the minimum interspecific distances were compared with maximum intraspecific distances in order to detect the presence of a barcoding gap [82,83]. In Figs 1 and 2, the dot above the 1:1 slope indicates the presence of a barcoding gap for the species, whereas the dot below the 1:1 slope implies no barcoding gap [81,84].


Evaluation of four commonly used DNA barcoding Loci for chinese medicinal plants of the family schisandraceae.

Zhang J, Chen M, Dong X, Lin R, Fan J, Chen Z - PLoS ONE (2015)

Plots of maximum intraspecific vs. minimum interspecific p-distances for single regions of Schisandraceae.Each dot represents a species for which two or more individuals were sampled. Dots above the diagonal line indicate the presence of a barcoding gap.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4418597&req=5

pone.0125574.g001: Plots of maximum intraspecific vs. minimum interspecific p-distances for single regions of Schisandraceae.Each dot represents a species for which two or more individuals were sampled. Dots above the diagonal line indicate the presence of a barcoding gap.
Mentions: We calculated genetic distances for each DNA region using MEGA v5.05 [78] based on the uncorrected p-distance model, which has been shown to perform as well as or better than the broadly used Kimura-2-parameter model [79–81]. The pairwise distances, intra- and interspecific distances were calculated for each species that were represented by more than one individual. Additionally, the differences of intra- and interspecific divergences between each pair of four commonly used barcoding loci were tested by Wilcoxon signed-ranks tests [7,15] in PASW Statistics 18.0 (IBM, Armonk, New York, USA). To assess the differences between intra- and interspecific divergences within each commonly used barcoding locus, Wilcoxon two-sample tests were performed. For each species, the minimum interspecific distances were compared with maximum intraspecific distances in order to detect the presence of a barcoding gap [82,83]. In Figs 1 and 2, the dot above the 1:1 slope indicates the presence of a barcoding gap for the species, whereas the dot below the 1:1 slope implies no barcoding gap [81,84].

Bottom Line: Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level.The feasibility of DNA barcodes for identification of geographical authenticity was also verified here.The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China.

ABSTRACT
Many species of Schisandraceae are used in traditional Chinese medicine and are faced with contamination and substitution risks due to inaccurate identification. Here, we investigated the discriminatory power of four commonly used DNA barcoding loci (ITS, trnH-psbA, matK, and rbcL) and corresponding multi-locus combinations for 135 individuals from 33 species of Schisandraceae, using distance-, tree-, similarity-, and character-based methods, at both the family level and the genus level. Our results showed that the two spacer regions (ITS and trnH-psbA) possess higher species-resolving power than the two coding regions (matK and rbcL). The degree of species resolution increased with most of the multi-locus combinations. Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level. Here we propose the combination of ITS+trnH-psbA+matK+rbcL as the most ideal DNA barcode for discriminating the medicinal plants of Schisandra and Kadsura, and the combination of ITS+trnH-psbA as the most suitable barcode for Illicium species. In addition, the closely related species Schisandra rubriflora Rehder & E. H. Wilson and Schisandra grandiflora Hook.f. & Thomson, were paraphyletic with each other on phylogenetic trees, suggesting that they should not be distinct species. Furthermore, the samples of these two species from the southern Hengduan Mountains region formed a distinct cluster that was separated from the samples of other regions, implying the presence of cryptic diversity. The feasibility of DNA barcodes for identification of geographical authenticity was also verified here. The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.

No MeSH data available.