Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes

Abstract

DNA barcodes have been increasingly used in authentication of medicinal plants, while their wide application in materia medica is limited in their accuracy due to incomplete sampling of species and absence of identification for materia medica. In this study, 95 leaf accessions of 23 species (including one variety) and materia medica of three Pharmacopoeia-recorded species of Angelica in China were collected to evaluate the effectiveness of four DNA barcodes (rbcL, matK, trnH-psbA and ITS). Our results showed that ITS provided the best discriminatory power by resolving 17 species as monophyletic lineages without shared alleles and exhibited the largest barcoding gap among the four single barcodes. The phylogenetic analysis of ITS showed that Levisticum officinale and Angelica sinensis were sister taxa, which indicates that L. officinale should be considered as a species of Angelica. The combination of ITS + rbcL + matK + trnH-psbA performed slight better discriminatory power than ITS, recovering 23 species without shared alleles and 19 species as monophyletic clades in ML tree. Authentication of materia medica using ITS revealed that the decoction pieces of A. sinensis and A. biserrata were partially adulterated with those of L. officinale, and the temperature around 80 °C processing A. dahurica decoction pieces obviously reduced the efficiency of PCR and sequencing. The examination of two cultivated varieties of A. dahurica from different localities indicated that the four DNA barcodes are inefficient for discriminating geographical authenticity of conspecific materia medica. This study provides an empirical paradigm in identification of medicinal plants and their materia medica using DNA barcodes.

DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae

“…The resolution level obtained in this study is equivalent to the average level (67.2%) observed in a large dataset of 5,583 samples representing 1,349 species in 141 genera . Compared with the species resolution obtained with ITS for other large genera, such as Rhododendron (12.2%, 15.3%), Angelica (73.9%), Pedicularis (86.2%), and Primula (88.2%) Yan et al, 2014;Yuan et al, 2015), that obtained in this study corresponds to a medium level of identification efficiency.…”

“…For the tree‐based methods, three different phylogenetic trees, namely, neighbor‐joining (NJ) tree, maximum parsimony (MP) tree, and maximum likelihood (ML) tree, were evaluated to select the most suitable tree. The three trees were constructed with MEGA6.06 according to published protocols for species‐level discrimination within closely related groups (Liu et al, ; Tamura, Dudley, Nei, & Kumar, ; Yuan et al, ). Species discrimination was considered successful if all conspecific individuals formed a single clade.…”

“…DNA barcoding, which uses one or several short standardized DNA regions for species identification (CBOL Plant Working Group, ; Hebert, Cywinska, Ball, & deWaard, ; Kress, Wurdack, Zimmer, Weigt, & Janzen, ), exhibits the outstanding advantage of not being affected by morphological characteristics. This technique has been widely applied for species identification (Barco, Raupach, Laakmann, Neumann, & Knebelsberger, ; Liu, Provan, Gao, & Li, ; Yan et al, ), the discovery of new or cryptic species (Huemer, Karsholt, & Mutanen, ; Liu, Möller, Gao, Zhang, & Li, ; Zemlak, Ward, Connell, Holmes, & Hebert, ), the assessment of biodiversity (Ji et al, ; Lahaye et al, ; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ), the characterization of genetic diversity (Sucher & Carles, ; Zhang, Niu, Guo, Wang, & Eaton, ), and the identification of species used in traditional Chinese medicine (Chen et al, ; Yuan et al, ). DNA barcoding has been shown to be an effective method for a variety of applications that involve species identification (Yan et al, ), but its performance in this taxonomically complicated genus has not been evaluated.…”

Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

“…DNA barcoding, using a standardized DNA fragment to identify taxon, has shown promise in providing a practical, standardized, species-level identification tool for biodiversity assessments, life history and ecological studies, and forensic analyses, and this technique has been widely applied since its first appearance in 2003 (Hebert et al 2003;Kress et al 2005;Valentini et al 2009;Liu et al 2014;Chen et al 2015;Xu et al 2015b;Yuan et al 2015). Ideally, the barcode locus would be the same for all kingdoms (Schoch et al 2012); nevertheless, finding a robust and effective barcode for kingdom Plantae has proved to be quite challenging.…”

DNA Barcoding for Differentiating the 11 Varieties of Musa Species

“…Musa acuminate Colla and M. balbisiana Impact Factor (JCC): 6.1964 NAAS Rating: 3.11 et al, 2016). ITS is widely used in plant molecular systematic studies at the generic and species levels as it has the potential to generate a high resolution of inter-and intraspecific relationships (Baldwin et al, 1995;Keller et al, 2010;Buchheim et al, 2011;Yuan et al, 2015). In spite of the merits of ITS, it has a major drawback of universality and specificity of PCR primers for the ITS region which causes difficulty in amplification and sequencing (Cheng et al, 2016).…”