DNA barcoding of populations of Fallopia multiflora, an indigenous herb in China

The exploration of neuraminidase inhibitory activity on Fallopia denticulata, an ethnic herb in China

This study was designed to explore the bioactive ingredients in the extracts of Fallopia denticulata (C.C. Huang) Holub, a medicinal plant grown in China, which exhibits the best neuraminidase (NA) inhibition activity. Three fractions of ethyl acetate, ethanol, and water were tested on NA inhibition assay, and the best one was conducted by ultra-performance liquid chromatography-time-of-flight mass spectrometry in the negative and positive modes to analyze the metabolic components. The results revealed the identification of the following 21 compounds: 3 organic acids, 11 flavonoids, 1 coumarin, and 6 others, such as β-daucosterol, gallic acid, and syringic acid, of which 12 compounds were discovered for the first time in F. denticulata. In addition, we used the molecular docking technique to support the anti-NA activity of each compound in the best extract. The results confirmed that the two better bioactive compounds were (-)-epicatechin gallate and (+)-catechin. Therefore, F. denticulata could be used as a potential material for new anti-influenza drugs.

Determination of the species status of Fallopia multiflora, Fallopia multiflora var. angulata and Fallopia multiflora var. ciliinervis based on morphology, molecular phylogeny, and chemical analysis

Relationships among Fallopia multiflora (Thunb.) Haraldson., F. multiflora var. angulata (S. Y. Liu) H. J. Yan, Z. J. Fang & Shi Xiao Yu., and F. multiflora var. ciliinervis (Nakai) Yonekura & H. Ohashi. were determined based on macroscopic and microscopic morphology, molecular phylogeny, and chemical analysis. The macroscopic and microscopic morphologies of root tubers or rhizomes, stems, and leaves were compared among the three taxa. The content of 11 chemical components (catechin, polydatin, stilbene glucoside, emodin, emodin-8-O-β-D-glucopyranoside, rhein, chrysophanol, aloe-emodin, quercetin, physcion, and resveratrol) in the three taxa was determined by HPLC, and the chemical diversity was further evaluated by principal component and hierarchical cluster analyses. Molecular phylogenies were mapped using two chloroplast markers (matK and the psbA-trnH intergenic region) and a nuclear ribosomal marker [internal transcribed spacer 2 (ITS2) region]. Analyses of macroscopic and microscopic morphological characteristics revealed that the subterranean organs of F. multiflora and F. multiflora var. angulata are root tubers, whereas those of F. multiflora var. ciliinervis are rhizomes. In the phylogenetic trees, F. multiflora and F. multiflora var. angulata were clustered into a clade based on the combine matK + psbA-trnH sequence, with neighbour-joining, maximum likelihood, and Bayesian inference bootstrap support values of 99, 85, and 0.99, respectively. In addition, there were obvious differences in the chemical compositions of F. multiflora, F. multiflora var. angulata and F. multiflora var. ciliinervis. The root tubers of F. multiflora contain higher levels of stilbene glucoside and catechin, but lower levels of polydatin and anthraquinone compounds. In contrast to F. multiflora, the rhizomes of F. multiflora var. ciliinervis contain higher levels of polydatin and anthraquinone compounds, but lack stilbene glucoside. The content of all 11 assessed components was lower in F. multiflora var. angulata than in F. multiflora and F. multiflora var. cillinervis. Principal component and hierarchical cluster analyses revealed that F. multiflora and F. multiflora var. angulata individuals were clustered into a single clade, whereas F. multiflora var. ciliinervis individuals were clustered into a single clade separate from that containing F. multiflora and F. multiflora var. angulata individuals. On the basis of the results of our morphological, molecular phylogeny, and chemical analyses, we tentatively conclude that F. multiflora var. ciliinervis is an independent species, whereas F. multiflora var. angulata should be considered as a variety of F. multiflora.

Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae)

This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.

Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species

Background

Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range.

Results

All possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture.

Conclusions

Our results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64 % success and Salix, 86 % failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0678-0) contains supplementary material, which is available to authorized users.