DNA barcoding in herbal medicine: Retrospective and prospective.

DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.

The chloroplasts genomic analyses of four specific Caragana species.

BACKGROUND: Many species of the genus Caragana have been used as wind prevention and sand fixation plants. They are also important traditional Chinese medicine, and ethnic medicine resource plant. Thus, chloroplast genomes (cp-genome) of some of these important species must be studied. METHODS: In this study, we analyzed the chloroplast genomes of C. jubata, C. erinacea, C. opulens, and C. bicolor, including their structure, repeat sequences, mutation sites, and phylogeny. RESULTS: The size of the chloroplast genomes was between 127,862 and 132,780 bp, and such genomes contained 112 genes (30 tRNA, 4 rRNA, and 78 protein-coding genes), 43 of which were photosynthesis-related genes. The total guanine + cytosine (G+C) content of four Caragana species was between 34.49% and 35.15%. The four Caragana species all lacked inverted repeats and can be classified as inverted repeat-lacking clade (IRLC). Of the anticipated genes of the four chloroplast genomes, introns were discovered in 17 genes, most of which were inserted by one intron. A total of 50 interspersed repeated sequences (IRSs) were found among them, 58, 29, 61, and 74 simple sequences repeats were found in C. jubata, C. bicolor, C. opulens, and C. erinacea, respectively. Analyses of sequence divergence showed that some intergenic regions (between trnK-UUU and rbcl; trnF-GAA and ndhJ; trnL-CAA and trnT-UGU; rpoB and trnC-GCA; petA and psbL; psbE and pebL; and sequences of rpoC, ycf1, and ycf2) exhibited a high degree of variations. A phylogenetic tree of eight Caragana species and another 10 legume species was reconstructed using full sequences of the chloroplast genome. CONCLUSIONS: (1) Chloroplast genomes can be used for the identification and classification of Caragana species. (2) The four Caragana species have highly similar cpDNA G+C content. (3) IRS analysis of the chloroplast genomes showed that these four species, similar to the chloroplast genome of most legumes, lost IRLC regions. (4) Comparative cp-genomic analysis suggested that the cp genome structure of the Caragana genus was well conserved in highly variable regions, which can be used to exploit markers for the identification of Caragana species and further phylogenetic study. (5) Results of phylogenetic analyses were in accordance with the current taxonomic status of Caragana. The phylogenetic relationship of Caragana species was partially consistent with elevation and geographical distribution.

The chromosome-scale genome of Magnolia officinalis provides insight into the evolutionary position of magnoliids.

Magnolia officinalis, a representative tall aromatic tree of the Magnoliaceae family, is a medicinal plant that is widely used in diverse industries from medicine to cosmetics. We report a chromosome-scale draft genome of M. officinalis, in which ∼99.66% of the sequences were anchored onto 19 chromosomes with the scaffold N50 of 76.62 Mb. We found that a high proportion of repetitive sequences was a common feature of three Magnoliaceae with known genomic data. Magnoliids were a sister clade to eudicots-monocots, which provided more support for understanding the phylogenetic position among angiosperms. An ancient duplication event occurred in the genome of M. officinalis and was shared with Lauraceae. Based on RNA-seq analysis, we identified several key enzyme-coding gene families associated with the biosynthesis of lignans in the genome. The construction of the M. officinalis genome sequence will serve as a reference for further studies of Magnolia, as well as other Magnoliaceae.

The complete chloroplast genome of Aconitum scaposum.

Aconitum scaposum Franch 1894 belongs to the Genus Aconitum and Subgenus Lycoctonum (Ranunculaceae). It is widely distributed in China and adjacent areas, used as herbal medicine and had highy toxic components. This species has little reasearch information, especially its chloroplast (cp) genome information being unclear. Therefore, with the method of high salt and low pH to extract the cp of A. scaposum, we sequenced and assembled the complete cp genome of A. scaposum using Illumina high-throughput sequencing platform. The results showed the cp genome of A. scaposum was 157 688 bp in length, including a pair of inverted repeated regions (IRa 26 156 bp and IRb 26 232 bp, respectively), large single copy region (LSC 69 309 bp) and small single copy region (SSC 16 917 bp). And cp genome of A. scaposum consisted of 145 unique genes, 8 ribosomal RNA (rRNA) genes and 38 transfer RNA (tRNA) genes, with GC content was 38%. Meanwhile, based on the cp complete genome, we performed the phylogenetic tree of 66 species with maximum likelihood (ML) method, respectively. Among them, we selected one Delphinium species as the outgroup and the bootstrap of each braches were greater than 90%. The results indicated that the phylogenetic relationship of A. scaposum was relatively closely related to A. scaposum var. vaginatum compared to other Aconitum species.

Ginseng Omics for Ginsenoside Biosynthesis.

Ginseng, also known as the king of herbs, has been regarded as an important traditional medicine for several millennia. Ginsenosides, a group of triterpenoid saponins, have been characterized as bioactive compounds of ginseng. The complexity of ginsenosides hindered ginseng research and development both in cultivation and clinical research. Therefore, deciphering the ginsenoside biosynthesis pathway has been a focus of interest for researchers worldwide. The new emergence of biological research tools consisting of omics and bioinformatic tools or computational biology tools are the research trend in the new century. Ginseng is one of the main subjects analyzed using these new quantification tools, including tools of genomics, transcriptomics, and proteomics. Here, we review the current progress of ginseng omics research and provide results for the ginsenoside biosynthesis pathway. Organization and expression of the entire pathway, including the upstream MVA pathway, the cyclization of ginsenoside precursors, and the glycosylation process, are illustrated. Regulatory gene families such as transcriptional factors and transporters are also discussed in this review.

[Research on contents of anthraquinones,dianthrones and tannins in Rheum tanguticum on PCA and CA].

Anthraquinones,dianthrones and tannins are the main active ingredients of Rheum tanguticum. In this study the three components were determined by HPLC,and the results were analyzed by multiple comparisons,principal components analysis(PCA)and correspondence analysis(CA). The results showed that the contents of components in different growing areas and types(wild and cultivated) reached a significant level(P<0. 05). Baiyu county,Xiaojin county and Ruoergai county had obvious advantages in the accumulation of catechin hydrate,rhien and sensenoside A respectively. The principal component was different in two growing type and the wild environment was conducive to combined anthraquinones accumulation. For active components,normalized planting was better than retail cultivating. Therefore,the effect on the accumulation of chemical components in Rh. tangusticum,should be taken into full account in the selection of the cultural base of Rh. tanguticum. The standardized cultivating is superior to retail cultivating in terms of the accumulation of active ingredients,and standardized planting is inferior to the wild.