Comparative analysis of chloroplast genomes of Pulsatilla species reveals evolutionary and taxonomic status of newly discovered endangered species Pulsatilla saxatilis.

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.

The burdock database: a multi-omic database for Arctium lappa, a food and medicinal plant.

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.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.

Oroxin B Induces Apoptosis by Down-Regulating MicroRNA-221 Resulting in the Inactivation of the PTEN/PI3K/AKT Pathway in Liver Cancer.

This study aims to investigate the anticancer effect of Oroxin B (OB) both in vitro and in vivo, and the molecular mechanism involved in microRNA-221 and the PI3K/Akt/PTEN pathway through modulation of apoptosis in Hepatocellular carcinoma (HCC). DEN-induced rats and HepG2 cells based on the microfluidic chip were employed, while the mRNA and protein expression of microRNA-221, PI3K, p-Akt and PTEN were evaluated by RT-PCR and Western blot analysis. Based on Microfluidic Chip and DEN-induced rat model, OB effectively exerts anti-liver cancer effect both in vitro and in vivo, and the expression of miR-221 in OB treated groups was significantly lower than that in the control group (** p < 0.01). The RT-PCR and Western blot results suggested the PI3K mRNA and protein in OB treated groups were both lower than those in control group and indicated the overexpression of PTEN. Therefore, OB effectively exerts anticancer effects by positively regulating the PTEN gene and then inactivating the PI3K/Akt signaling pathway through down-regulating the expression of the microRNA-221, thereby inducing apoptosis of liver cancer cells. This study offers a theoretical evidence for further development and clinical guidance of OB as an anti-tumor agent.

The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis.

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

Exploring the diversity and potential functional characteristics of microbiota associated with different compartments of Schisandra chinensis.

Introduction: Symbiotic microbial have a significant impact on the growth and metabolism of medicinal plants. Schisandra chinensis is a very functionally rich medicinal herb; however, its microbial composition and diversity have been poorly studied. Methods: In the present study, the core microbiomes associated with the rhizospheric soil, roots, stems, leaves, and fruits of S. chinensis from six geographic locations were analyzed by a macro-genomics approach. Results: Alpha and beta diversity analyses showed that the diversity of microbial composition of S. chinensis fruits did not differ significantly among the geographic locations as compared to that in different plant compartments. Principal coordinate analysis showed that the microbial communities of S. chinensis fruits from the different ecological locations were both similar and independent. In all S. chinensis samples, Proteobacteria was the most dominant bacterial phylum, and Ascomycota and Basidiomycota were the most dominant fungal phyla. Nitrospira, Bradyrhizobium, Sphingomonas, and Pseudomonas were the marker bacterial populations in rhizospheric soils, roots, stems and leaves, and fruits, respectively, and Penicillium, Golubevia, and Cladosporium were the marker fungal populations in the rhizospheric soil and roots, stems and leaves, and fruits, respectively. Functional analyses showed a high abundance of the microbiota mainly in biosynthesis. Discussion: The present study determined the fungal structure of the symbiotic microbiome of S. chinensis, which is crucial for improving the yield and quality of S. chinensis.

The complete chloroplast genome of Blechnopsis orientalis (Linnaeus) C. Presl 1753 (Blechnaceae).

Blechnopsis orientalis (Linnaeus) C. Presl (1753) is a fern used both as food and medicine. It is found primarily in southern China and Southeast Asia, thriving in warm, humid shrublands or sparse forest. The total length of the chloroplast genome is 155,211 bp, including a large single-copy region (LSC, 81,877 bp), a small single-copy region (SSC, 21,500 bp), and two inverted repeat regions (IRs, 25,917 bp). The GC content is 41.3%. A total of 131 genes were annotated, including 88 protein-coding genes, eight rRNA genes, and 35 tRNA genes. The phylogenetic analysis using the maximum-likelihood method showed that B. orientalis and Oceaniopteris gibba were closely related. This study provides genomic resources for phylogenetic genetics and resource exploitation of B. orientalis.

The complete chloroplast genome of Leonurus sibiricus Linnaeus (Labiatae, Leonurus Miller).

Leonurus sibiricus Linnaeus 1753, an annual or biennial herb found in northern China, Mongolia, and Russia, typically grows in stony, sandy grasslands, and pine forests. This study sequenced and reported the complete chloroplast genome of L. sibiricus for the first time. The entire circular genome measures 151,689 bp in length, with a GC content of 38.4%. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNAs, and eight rRNAs. The genome exhibits a typical quadripartite structure, comprising a large single-copy (LSC 82,820 bp) region, a small single-copy (SSC 17,619 bp) region, and a pair of inverted repeat (IR 25,625 bp each) regions. Phylogenetic analysis using the maximum-likelihood method indicates that L. sibiricus is most closely related to L. japonicus Houttuyn. This study provides valuable genomic resources for further research on the phylogenetics and biodiversity of the genus Leonurus.

The complete chloroplast genome sequence of Syringa oblata Lindl. var. alba Hort. ex Rehd. 1763 (Oleaceae).

Syringa oblata var. alba is a shrub or a small tree from China with high ornamental, medicinal, and edible value. Here, we present its first complete chloroplast genome. The entire circular genome is 155,648 bp in length, with large single-copy (LSC) length of 86,247, small single-copy (SSC) length of 17,937, inverted repeat (IR) length of 25,732, and GC content of 37.9%. One hundred and thirty-two genes, including 88 protein-coding, 36 tRNA, and eight rRNA genes were predicted. A phylogenetic tree of 25 plant species was constructed based on the maximum-likelihood method, indicating that S. oblata var. alba, S. vulgaris, and S. oblata form a sister group. This study will provide valuable basic information for phylogeny, species identification, and varieties breeding of this species.

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae).

Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (1933), a shrub or small tree, is native to northern and southern China. It is an excellent relief and medicinal plant. The complete chloroplast genome is 158,043 bp in length, with a large single-copy region of 86,957 bp, a small single-copy region of 20,138 bp, two inverted repeat regions of 25,474 bp each, and a GC content of 37.4%. There were 129 genes annotated, including 84 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic trees are constructed using plastome data from 38 species and the maximum-likelihood method. The results of the chloroplast genome-wide analysis and the phylogenetic tree show the taxonomic phylogeny of the G. biloba var. parviflora in relation to other species, increasing the accuracy of the phylogenetic classification of the plant.

The complete chloroplast genome of Dictamnus dasycarpus Turcz. (Rutaceae).

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.

The complete chloroplast genome sequence of Veratrum nigrum L.

The complete chloroplast genome of an important medicinal plant, Veratrum nigrum Linnaeus, was sequenced. The entire circular genome is 151,580 bp in length, with 37.7% GC contents. The genome has a large single-copy (LSC) region with a length of 81,806 bp, a small single-copy (SSC) region with a length of 17,472 bp, and two inverted repeat regions (IRs) with a length of 26,151 bp. It harbored 131 genes, including 85 protein coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis suggested V. nigrum formed a monophyletic clade with relatively short genetic distance to Veratrum oxysepalum and Veratrum taliense. This study will provide theoretical basis for further study on plant genetics phylogenetic research.

The complete chloroplast genome sequence of Convallaria majalis L.

The complete chloroplast genome of an important medicinal plant, Convallaria majalis Linnaeus, was sequenced for the first time. The entire circular genome is 162,218 bp in length, with 37.9% GC contents. The genome has consisted of a large single-copy region (LSC) with a length of 85,417 bp, a small single-copy region (SSC) with a length of 18,495 bp, and two inverted repeat regions (IRs) with a length of 29,153 bp each. The genome harbored 133 genes, including 87 protein coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic tree of 24 plant species was constructed based on the maximum-likelihood method. This study will provide theoretical basis for further study on plant genetics phylogenetic research.

Total Flavonoids from Oroxylum indicum Induce Apoptosis via PI3K/Akt/PTEN Signaling Pathway in Liver Cancer.

Total flavonoids (TF), derived from the seeds of Oroxylum indicum (L.) Vent., possess many pharmacological functions. In the present study, H22-bearing mice and SMMC-7721 models were employed to evaluate the antitumor activity of TF and to and investigate its possible mechanisms both in vitro and in vivo. Cell viability was evaluated by MTT assay; cell apoptosis rate was analyzed via Annexin V-FITC/PI double staining by flow cytometer. Meanwhile, the expressions of apoptosis-related mRNA and proteins were evaluated by RT-PCR and Western blot analysis. The results revealed that TF could significantly inhibit the tumor growth, and the possible mechanism was related to the effect of inducing tumor cells apoptosis through PI3K/Akt/PTEN signaling pathway. This study has provided a theoretical basis for the further development and application of TF as antitumor drugs.