Scientometric Analysis of Medicinal and Edible Plant Coptis.
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ABSTRACT: Objective: A scientometric analysis to obtain knowledge mapping of Coptis revealed the current research situation, knowledge base and research hotspots in Coptis research. Methods:Coptis-related documents published from 1987 to 2020 were selected through the Web of Science Core Collection. CiteSpace, VOSviewer and Microsoft Excel were used to construct knowledge maps of the Coptis research field. Results: A total of 367 documents and their references were analyzed. These papers were primarily published in mainland China (214), followed by Japan (57) and South Korea (52), and they each formed respective cooperation networks. The document co-citation analysis suggested that the identification of Coptis Salisb. species, the production of alkaloids, and the mechanisms of action of these alkaloids formed the knowledge bases in this field. A keyword analysis further revealed that the research hotspots were primarily concentrated in three fields of research involving berberine, Coptis chinensis Franch, and Coptis japonica (Thunb) Makino. Oxidative stress, rat plasma (for the determination of plasma alkaloid contents), and Alzheimer's disease are recent research hotspots associated with Coptis. Conclusion:Coptis research was mainly distributed in three countries: China, Japan, and South Korea. Researchers were concerned with the identification of Coptis species, the production of Coptis alkaloids, and the efficacy and pharmacological mechanism of the constituent alkaloids. In addition, the anti-oxidative stress, pharmacokinetics, and Alzheimer's disease treatment of Coptis are new hotspots in this field. This study provides a reference for Coptis researchers.
Project description:Endophytic microorganisms absorb nutrients and prevent pathogen damage, supporting healthy plant growth. However, the relationship between endophytic bacteria and berberine synthesis in the medicinal plant Coptis teeta Wall. remains unclear. Herein, we explored the community composition of endophytic bacteria related to berberine in roots, stems, and leaves of wild-type and cultivated C. teeta. Endophytic bacterial communities were analyzed by 16S rRNA sequencing, and berberine content in roots was analyzed by high-performance liquid chromatography. Proteobacteria, Actinobacteria, and Bacteroidetes were the major phyla, and Mycobacterium, Salmonella, Nocardioides, Burkholderia-Paraburkholderia, and Rhizobium were the dominant genera in root, stem, and leaf tissues. Root berberine content was positively correlated with total N, total P, total K, and available K in rhizosphere soil. In addition, root berberine content was positively correlated with Microbacterium and norank_f_7B-8, whereas soil total K was positively correlated with Microbacterium and Burkholderia-Paraburkholderia in roots. Our results demonstrated a clear correlation between dominant endophytic bacteria and berberine synthesis in C. teeta. The findings are useful for the promotion of berberine production in C. teeta via manipulation of endophytic bacteria.
Project description:Mesona chinensis Benth (MCB) (or Platostoma palustre or Platostoma chinense) is an important edible and medicinal plant in China. However, the mitochondrial genome (mitogenome, or mtDNA) of MCB has not been characterized or reported yet. In this study, we first sequenced and characterized the complete mitogenome of MCB. The MCB mitogenome was 494,599 bp in length and encoded 59 genes containing 37 protein-coding genes (PCGs), 19 tRNAs, and 3 rRNAs. Gene transfer analysis revealed that a total of 12 transfer segments with more than 93% identity (total length of 25,427 bp) were detected in the MCB mitogenome. Simple sequence repeats (SSR) analysis showed that 212 simple sequence repeats (SSR) were identified. Repeat sequence analysis revealed 305 repeat sequences (158 forward and 147 palindromic repeats) ranging from 30 bp to 48,383 bp and the 30-39 bp repeats were the majority type. Relative synonymous codon usage (RSCU) analysis uncovered that in total, 9,947 codons were encoding the protein-coding genes (PCGs). Serine (909, 9.1%) and leucine (879, 8.8%) were the two most abundant amino acids, while terminator (32, .3%) was the least abundant amino acid. Ka/Ks analysis indicated that almost all genes were subject to purification selection, except ccmB. Analysis of Lamiaceae mitogenomes constitution revealed that atpB and atpE were unique to the Rotheca serrata and Salvia miltiorrhiza mitogenomes. mttB gene loss was unique to the Boea hygrometrica mitogenome. The core fragments of the Lamiaceae mitogenomes harbored a higher GC content than the specific and variable fragments. In addition, phylogenetic analysis revealed that MCB was closely related to Salvia miltiorrhiza based on the mitogenomes. The current study provided valuable genomic resources for understanding and utilizing this important medicinal plant in the future.
Project description:Coptis quinquesecta, serving as a valuable medicinal plant, is a critically endangered and national key protected species of China. In the past, researches regarding this species mainly focused on its medicinal ingredients, whereas little effort has been made on its genetic information. Here we determined the first complete chloroplast genome of C. quinquesecta using genome skimming approach. The cp genome was 154,549?bp long, with a large single-copy region (LSC) of 84,409?bp and a small single-copy region (SSC) of 17,256?bp separated by a pair of inverted repeats (IRs) of 26,442?bp. It encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Besides, we reconstructed the phylogeny of Ranunculaceae based on the previously reported cp genomes of related taxa. A maximum likelihood (ML) phylogenetic analysis strongly supported the monophyly of Hydrastidoideae, Coptidoideae, and Thalictroideae, while Ranunculoideae was found to be paraphyletic.
Project description:The complete plastome of Houttuynia cordata, an important medicinal and edible plant, was identified and sequenced in this study. The circular plastome is 160,217?bp in length and consists of a pair of inverted repeats (IRs 26,854?bp each), which is separated by a large single-copy region (LSC, 88,189?bp) and a small single-copy region (SSC, 18,320?bp). It encodes 132 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). The phylogenetic analysis strongly reveals the sister group between H. cordata and the clade including Piper kadsura, Piper cenocladum, Saruma henryi, and Asarum sieboldii.
Project description:Houttuynia cordata (Saururaceae), an ancient and relic species, has been used as an important medicinal and edible plant in most parts of Asia. However, because of the lack of genome information and reliable molecular markers, studies on its population structure, or phylogenetic relationships with other related species are still rare. Here, we de novo assembled the complete chloroplast (cp) genome of H. cordata using the integration of the long PacBio and short Illumina reads. The cp genome of H. cordata showed a typical quadripartite cycle of 160,226 bp. This included a pair of inverted repeats (IRa and IRb) of 26,853 bp, separated by a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 18,340 bp. A total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes, were identified in this cp genome. Eighty-one genes were located on the LSC region, 13 genes were located on the SSC region, and 17 two-copy genes were located on the IR region. Additionally, 48 repeat sequences and 86 SSR loci, which can be used as genomic markers for population structure analysis, were also detected. Phylogenetic analysis using 21 cp genomes of the Piperales family demonstrated that H. cordata had a close relationship with the species within the Aristolochia genus. Moreover, the results of mVISTA analysis and comparisons of IR regions demonstrated that the cp genome of H. cordata was conserved with that of the Aristolochia species. Our results provide valuable information for analyzing the genetic diversity and population structure of H. cordata, which can contribute to further its genetic improvement and breeding.
Project description:Plant-based diets could be a key source of microRNAs in animals. Plant microRNAs are cross-kingdom gene expression regulators that could modulate mammalian gene expression, influencing their physiology. Therefore, it is important to identify the microRNA expression profile of plant foods in order to identify potential target genes and biological functions in the mammalian host. Next-generation sequencing was applied to identify microRNAs in RNA samples derived from nuts (walnut and almond), vegetables (spinach) and fruits (orange, apple, olive, pear, and tomato). Our data revealed that edible plant contain a large number and diverse type of microRNAs.
Project description:Hedychium flavum Roxb. 1820 is a perennial herb mainly distributed in China, India, Myanmar and Thailand with ornamental, edible and medicinal value. It is extensively cultivated as a source of aromatic essential oils, ornamental plant, food flavorings and vegetables, and folk medicine. In this study, we sequence the complete chloroplast genome of H. flavum by de novo assembly. The assembled genome has a typical quadripartite circular structure with 163,909 bp in length, containing a large single-copy region (LSC, 88,589 bp), a small single-copy region (SSC, 15,762 bp), and two inverted repeat regions (IRs, 29,779 bp). The cp genome contains 133 genes, including 87 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on the complete cp genome shows a close affinity of H. flavum and H. neocarneum with 100% bootstrap support. This study will provide useful genetic resource for further phylogenetic analysis of the genus Hedychium and Zingiberaceae.
Project description:Honeysuckle (the dried flower bud or opening flower of Lonicera japonica Thunb.), a medicinal and edible substance, has is greatly popular among consumers for its remarkable health effects, such as antioxidant, antibacterial, and anti-inflammatory effects. However, due to the influences of processing methods, storage conditions, and other factors, honeysuckles show different colors which can directly reflect the quality and the price on the market. In order to comprehensively compare the quality of different colors, 55 batches of honeysuckle samples were collected and analyzed. Their color parameters, chlorophyll content (chl), total phenol content (TPC), total flavonoid content (TFC), antioxidant activity (AA), main active compounds, and metabolites were measured. As a result, the initial green-white (GW) samples, a kind of highest-quality honeysuckle, had the smallest a* value, largest h*, chl, TPC, TFC, and AA values, and highest content of chlorogenic acid and cynaroside. There was a significant difference between GW samples and a series of discolored samples. As the color darkened or lightened, the quality gradually decreased. The yellow-brown (YB) samples were of the worst quality and were no longer available for clinical and health purposes. A series of differential metabolites, such as quercetin-7-O-glucoside and secologanoside, could be used as important references to evaluate the quality of differently colored samples. The metabolic profile of honeysuckle provided new insights into the process of color change and laid a foundation for further honeysuckle quality control. The correlation results showed that the a* and h* values significantly affect the abovementioned quality indicators and the 10 main active compounds. In other words, the color difference could directly reflect the quality and clinical efficacy. Multiple regression analysis was carried out using combined L*, a*, and b* values to predict the quality of honeysuckle. This is the first time the quality of different color honeysuckle samples on the post-harvest link has been systematically compared and a demonstration of medicinal and edible substances with different colors has been provided.
Project description:Rubus setchuenensis Bureau et Franch. is important in phylogeny and evolution amongst genus Rubus L. (Rosaceae) plants. The chloroplast genome of R. setchuenensis reported in this study is 156,231 bp in size, with an average GC content of 37.19%. The complete chloroplast genome has a typical quadripartite structure, including a large single copy (LSC) region (85,829 bp) and a small single copy (SSC) region (18,860 bp), which are separated by a pair of inverted repeats (IRs, 25,771 bp). This plastome contains 129 different genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis of 20 chloroplast genomes from genera Fragaria, Rosa and Rubus of the family Rosaceae suggested that R. setchuenensis clustered into one clade with the other three species of section Malachobatus Focke, and then grouped with four species of section Idaeobatus Focke, while species from Fragaria and Rosa were classified into a group, separately.
Project description:Crataegus hupehensis Sarg. is well-known for its medicinal and nutritive value. In this study, the complete chloroplast genome sequence of C. hupehensis was determined by using Illumina high-throughput sequencing approach. The complete chloroplast genome is 159,766 bp with 36.6% GC content. It contained a pair of inverted repeat regions of 26,385 bp, a large single-copy region of 87,852 bp, and a small single-copy region of 19,144 bp. It contained 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on chloroplast genomes indicated that C. hupehensisis was closely related to C. kansuensis and C. marshallii in the subfamily Maloideae. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Crataegus species.