Background: Five DNA regions, namely, rbcL, matK, ITS, ITS2, and psbA-trnH, have been recommended as primary DNA barcodes for plants. Studies evaluating these regions for species identification in the large plant taxon, which includes a large number of closely related species, have rarely been reported. Results: The feasibility of using the five proposed DNA regions was tested for discriminating plant species within Asteraceae, the largest family of flowering plants. Among these markers, ITS2 was the most useful in terms of universality, sequence variation, and identification capability in the Asteraceae family. The species discriminating power of ITS2 was also explored in a large pool of 3,490 Asteraceae sequences that represent 2,315 species belonging to 494 different genera. The result shows that ITS2 correctly identified 76.4% and 97.4% of plant samples at the species and genus levels, respectively. In addition, ITS2 displayed a variable ability to discriminate related species within different genera. Conclusions: ITS2 is the best DNA barcode for the Asteraceae family. This approach significantly broadens the application of DNA barcoding to resolve classification problems in the family Asteraceae at the genera and species levels.

DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. Until today, a universal DNA barcode marker for plants remains elusive. The rbcL and matK regions have been proposed as the “core barcode” for plants and the ITS2 and psbA-trnH intergenic spacer (PTIGS) regions were later added as supplemental barcodes. The use of PTIGS region as a supplemental barcode has been limited by the lack of computational tools that can handle significant insertions and deletions in the PTIGS sequences. Here, we compared the most commonly used alignment-based and alignment-free methods and developed a web server to allow the biologists to carry out PTIGS-based DNA barcoding analyses.

Scutellaria baicalensis is a well-known medicinal plant that produces biologically active flavonoids, such as baicalin, baicalein, and wogonin. Pharmacological studies have shown that these compounds have anti-inflammatory, anti-bacterial, and anti-cancer activities. Therefore, it is of great significance to investigate the genetic information of S. baicalensis, particularly the genes related to the biosynthetic pathways of these compounds. Here, we constructed the full-length transcriptome of S. baicalensis using a hybrid sequencing strategy and acquired 338,136 full-length sequences, accounting for 93.3% of the total reads. After the removal of redundancy and correction with Illumina short reads, 75,785 nonredundant transcripts were generated, among which approximately 98% were annotated with significant hits in the protein databases, and 11,135 sequences were classified as lncRNAs. Differentially expressed gene (DEG) analysis showed that most of the genes related to flavonoid biosynthesis were highly expressed in the roots, consistent with previous reports that the flavonoids were mainly synthesized and accumulated in the roots of S. baicalensis. By constructing unique transcription models, a total of 44,071 alternative splicing (AS) events were identified, with intron retention (IR) accounting for the highest proportion (44.5%). A total of 94 AS events were present in five key genes related to flavonoid biosynthesis, suggesting that AS may play important roles in the regulation of flavonoid biosynthesis in S. baicalensis. This study provided a large number of highly accurate full-length transcripts, which represents a valuable genetic resource for further research of the molecular biology of S. baicalensis, such as the development, breeding, and biosynthesis of active ingredients.

Ephedrae Herba and Ephedrae Radix et Rhizoma (Mahuang) have been used as Chinese herbal medicines. Ephedra plants mainly live in deserts and have good governance of desertification. Despite their important medicinal and environmental protection value, dietary supplements containing ephedrine from Ephedra species may threaten the health of people. Morphological resemblance amongst species causes difficulty in identifying the original species of Ephedra herbs. Chloroplast (CP) genome shows good prospects in identification and phylogenetic analysis. This study introduced the structures of the CP genomes of three Ephedra species and analysed their phylogenetic relationships. Three complete CP genomes of Ephedra showed four-part annular structures, namely, two single-copy regions and two inverted repeat regions. The entire CP genomes of three Ephedra species in terms of size were 109,550 bp (E. sinica), 109,667 bp (E. intermedia), and 109,558 bp (E. equisetina). Each CP genome of the three Ephedra species encoded 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. Eleven high-variation regions were screened through mVISTA to be potential specific DNA barcodes for identifying Ephedra species. Maximum likelihood and maximum parsimony trees showed that CP genomes could be used to identify Ephedra species. The Ephedra species had a close phylogenetic relationship with Gnetum species and Welwitschia mirabilis. This research provided valuable information for the identification and phylogenetic analysis of gymnosperms and drug safety of Ephedra.

The radix of Glehnia littoralis Fr. Schmidt ex Miq. (Beishashen), is often misidentified and adultered in Chinese medicine. Its seven common adulterants include Chuanminshen violaceum Sheh et Shan (Chuanmingshen), Changium smyrnioides Wolff (Mingdangshen), Sphallerocarpus gracilis (Bess.) K.-Pol. (Miguoqin), Adenophora polyantha Nakai (Shishashen), Silene tatarinowii Regel (Shishengyingzicao), Adenophora tetraphylla (Thunb.) Fisch (Lunyeshashen) and Adenophora stricta Miq. (Shashen). This study aims to evaluate the feasibility of the second internal transcribed spacer (ITS2) DNA barcoding to discriminate between Glehniae Radix and its common adulterants. In this study, we collected 46 samples of G. littoralis and 59 samples of its seven common adulterants. Genomic DNA sequences were extracted from samples, including original plants and commercially processed crude drugs. The ITS2 of the ribosomal DNA sequences were amplified and sequenced bi-directionally. The sequences were assembled by CodonCode Aligner 3.5.7. The descriptive data analysis was conducted and neighbor-joining (NJ) phylogenetic tree was constructed by MEGA 5.0 in accordance with the kimura 2 -parameter (K2P) model. The identification efficiency was evaluated based on the BLAST1 methods. The ITS2 secondary structures were predicted and compared between Glehniae Radix and its adulterants by the ITS2 database. As the 46 ITS2 sequences of G. littoralis were identical to each other, the identification efficiency of the ITS2 region was 100 %. A NJ tree based on the ITS2 sequences, and the predicted secondary structures of ITS2, distinguished Glehniae Radix from its adulterants. DNA barcoding based on ITS2 distinguished commercial processed Glehniae Radix from common herbal adulterants.