Tingguo Kang

Background: Pulsatilla saxatilis, a new species of the genus Pulsatilla has been discovered. The morphological information of this species has been well described, but its chloroplast genome characteristics and comparison with species of the same genus remain to be reported. Results: Our results showed that the total length of chloroplast (cp.) genome of P. saxatilis is 162,659 bp, with a GC content of 37.5%. The cp. genome contains 134 genes, including 90 known protein-coding genes, 36 tRNA genes, and 8 rRNA genes. P. saxatilis demonstrated similar characteristics to other species of genus Pulsatilla. Herein, we compared cp. genomes of 10 species, including P. saxatilis, and found that the cp. genomes of the genus Pulsatilla are extremely similar, with a length of 162,322–163,851 bp. Furthermore, The SSRs of Pulsatilla ranged from 10 to 22 bp in length. Among the four structural regions of the cp. genome, most long repeats and SSRs were detected in the LSC region, followed by that in the SSC region, and least in IRA/ IRB regions. The most common types of long repeats were forward and palindromic repeats, followed by reverse repeats, and only a few complementary repeats were found in 10 cp. genomes. We also analyzed nucleotide diversity and identified ccsA_ndhD, rps16_trnK-UUU, ccsA, and rbcL, which could be used as potential molecular markers for identification of Pulsatilla species. The results of the phylogenetic tree constructed by connecting the sequences of high variation regions were consistent with those of the cp. gene phylogenetic tree, and the species more closely related to P. saxatilis was identified as the P. campanella. Conclusion: It was determined that the closest species to P. saxatilis is P. campanella, which is the same as the conclusion based on pollen grain characteristics, but different from the P. chinensis determined based on morphological characteristics. By revealing information on the chloroplast characteristics, development, and evolution of the cp. genome and the potential molecular markers, this study provides effective molecular data regarding the evolution, genetic diversity, and species identification of the genus Pulsatilla.

Background: Burdock is a biennial herb of Asteraceae found in Northern Europe, Eurasia, Siberia, and China. Its mature dry fruits, called Niu Bang Zi, are recorded in various traditional Chinese medicine books. With the development of sequencing technology, the mitochondrial, chloroplast, and nuclear genomes, transcriptome, and sequence-related amplified polymorphism (SRAP) fingerprints of burdock have all been reported. To make better use of this data for further research and analysis, a burdock database was constructed. Results: This burdock multi-omics database contains two burdock genome datasets, two transcriptome datasets, eight burdock chloroplast genomes, one burdock mitochondrial genome, one A. tomentosum chloroplast genome, one A. tomentosum mitochondrial genome, 26 phenotypes of burdock varieties, burdock rhizosphere-associated microorganisms, and chemical constituents of burdock fruit, pericarp, and kernel at different growth stages (using UPLC-Q-TOF–MS). The wild and cultivation distribution of burdock in China was summarized, and the main active components and pharmacological effects of burdock currently reported were concluded. The database contains ten central functional modules: Home, Genome, Transcriptome, Jbrowse, Search, Tools, SRAP fingerprints, Associated microorganisms, Chemical, and Publications. Among these, the “Tools” module can be used to perform sequence homology alignment (Blast), multiple sequence alignment analysis (Muscle), homologous protein prediction (Genewise), primer design (Primer), large-scale genome analysis (Lastz), and GO and KEGG enrichment analyses (GO Enrichment and KEGG Enrichment). Conclusions: The database URL is http://210.22.121.250:41352/. This burdock database integrates molecular and chemical data to provide a comprehensive information and analysis platform for interested researchers and can be of immense help to the cultivation, breeding, and molecular pharmacognosy research of burdock.

Dictamnus dasycarpus Turcz. 1842 is a medicinal plant of China. Its dry root bark is called BAIXIANPI, which is a common traditional Chinese medicine. Here, we report the complete chloroplast genome of D. dasycarpus. The length of the genome, large single-copy (LSC), small single-copy (SSC), inverted repeat (IR), and GC content was 157,056 bp, 84,497 bp, 18,487 bp, 27,036 bp, and 38.5%, respectively. A total of 132 genes were annotated, including 87 protein coding, eight rRNA, and 37 tRNA genes. Interestingly, 15 genes contained single intron while two others contained two introns. The phylogenetic tree showed the two D. dasycarpus (D. albus) clustered in a clade, which was sister to clade formed by the species of Melicope, Tetradium, Phellodendron, and Zanthoxylum.

Pulsatilla saxatilis (Ranunculaceae), a new species from Fengcheng in Liaoning province, north-east China, is described and illustrated. Gross-morphologically this species is closely similar to P. chinensis in having 3-foliolate leaves, solitary, erect flowers, and persistent, prolonged styles in fruiting period, but differs by having light blue, whitish-blue or white (vs. violet) sepals and persistent styles 2–2.5 cm (vs. 3.5–6.5 cm) long. Pollen morphology also lends strong support for the description of the new species, with P. saxatilis having pantoporate pollen grains while its putative closest ally, P. chinensis, having tricolpate ones.

Arctium lappa has a long medicinal and edible history with great economic importance. Here, the first high‐quality chromosome‐level draft genome of A. lappa was presented by the Illumina and PacBio sequencing data. The assembled genome was approximately 1.79 Gb with a N50 contig size of 6.88 Mb. Approximately 1.70 Gb (95.4%) of the contig sequences were anchored onto 18 chromosomes using Hi‐C data; the scaffold N50 was improved to be 91.64 Mb. Furthermore, we obtained 1.12 Gb (68.46%) of repetitive sequences and 32,771 protein‐coding genes; 616 positively selected candidate genes were identified. Among candidate genes related to lignan biosynthesis, the following were found to be highly correlated with the accumulation of arctiin: 4‐coumarate‐CoA ligase (4CL), dirigent protein (DIR), and hydroxycinnamoyl transferase (HCT). Additionally, we compared the transcriptomes of A. lappa roots at three different developmental stages and identified 8,943 differentially expressed genes (DEGs) in these tissues. These data can be utilized to identify genes related to A. lappa quality or provide a basis for molecular identification and comparative genomics among related species.

The complete mitochondrial genome of Aucklandia lappa was sequenced for the first time. The mitochondrial genome length was 320,439 bp, with 45.05% GC contents. There were 67 genes annotated, including 31 known protein-coding genes, 25 tRNAs, and six rRNAs. The maximum likelihood method was used to establish the phylogenetic tree of 37 species. Results have shown that A. lappa and Arctium lappa were sister groups. It reveals the genetic relationship between different species and provides a theoretical basis for the establishment of a classification system.

The complete mitochondrial genome of an important medicinal plant Glycyrrhiza uralensis Fisch. is reported for the first time. The mitochondrial genome sequence of G. uralensis was 463,869 bp in length and had a GC content of 45.19%. The genome contained 40 protein-coding genes (PCGs), 30 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). The phylogenetic tree was built based on 25 plants, using the maximum-likelihood method. These data will provide certain help to determine the taxonomic status of G. uralensis.

Background: Polygonum multiflorum and Achyranthes bidentate are traditional Chinese herbs, which show significant antiosteoporosis (OP) effect. These two herbs are commonly used as a combination in traditional Chinese medicine. Materials and Methods: In this study, the left humerus section of the mice were stained with hematoxylin and eosin staining to establish the spectrum-effect relationships between the high-performance liquid chromatography fingerprint of different solvent extracts and the anti-OP effect. Finally, we analyzed the correlation between the content of main compounds of different solvent extracts and the anti-OP effect. Results: The compatibility had obvious therapeutic effect on OP induced by retinoic acid. The results of pharmacodynamic analysis showed that the extract had a certain effect on the bone-specific alkaline phosphatase, the level of tartrate-resistant acid phosphatase-5b (TRACP-5b), and estrogen 2 and had a great influence on TRACP-5b especially. The results of spectrum-effect relationships and correlation analysis showed that the level of β-ecdysterone and tetrahydroxystilbene is negatively correlated with bone resorption index and TRACP-5b. The higher the content of the two compounds in the combination, the better the effect of treating mouse OP induced by retinoic acid. Conclusion: It is suggested that the compatibility of P. multiflorum and A. bidentata can be used to treat OP, and their mechanism of action is through reducing osteoclastic effect. β-ecdysterone and tetrahydroxystilbene may be the active components of combination of Polygoni multiflori-A. bidentate.