Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome se- quences...Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome se- quences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16- epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.展开更多
The aim of this study was to establish a method for discriminating Dendrobium officinale from four of its close relatives Den- drobium chrysanthum, Dendrobium erystallinum, Dendrobium aphyllum and Dendrobium devonianu...The aim of this study was to establish a method for discriminating Dendrobium officinale from four of its close relatives Den- drobium chrysanthum, Dendrobium erystallinum, Dendrobium aphyllum and Dendrobium devonianum based on chemical composition analysis. We analyzed 62 samples of 24 Dendrobium species. High performance liquid chromatography analysis confirmed that the four low molecular weight compounds 4＇,5,7-trihydroxyflavanone （naringenin）, 3,4-dihydroxy-4＇,5-dime- tboxybibenzyl （DDB^2）, 3＇,4-dihydroxy-3,5＇-dimethoxybibenzyl （gigantol）, and 4,4＇-dihydroxy-3,3＇,5-trimethoxybibenzyl （moscatilin）, were common in the genus. The phenol-sulfuric acid method was used to quantify polysaccharides, and the mon- osaccharide composition of the polysaccharides was determined by gas chromatography. Stepwise discriminant analysis was used to differentiate among the five closely related species based on the chemical composition analysis. This proved to be a simple and accurate approach for discriminating among these species. The results also showed that the polysaccharide content, the amounts of the four low molecular weight compounds, and the mannose to glucose ratio, were important factors for species discriminaut. Therefore, we propose that a chemical analysis based on quantification of naringenin, bibenzyl, and polysaccha- rides is effective for identifying D. officinale.展开更多
采集湖南省新宁县崀山世界自然遗产风景名胜区和广西省乐业县雅长兰科植物自然保护区这两个生境中处于生长期的铁皮石斛(Dendrobium of ficinale)的营养根,并进行分离培养。通过对分离所得的41个菌株进行形态观察和ITS序列测定相结合的...采集湖南省新宁县崀山世界自然遗产风景名胜区和广西省乐业县雅长兰科植物自然保护区这两个生境中处于生长期的铁皮石斛(Dendrobium of ficinale)的营养根,并进行分离培养。通过对分离所得的41个菌株进行形态观察和ITS序列测定相结合的鉴定,共获得内生真菌34种。对担子菌和子囊菌分别进行了系统发育树构建结果显示,子囊菌为优势种类(31种),以炭角菌目(Xylariales)和肉座菌目(Hypocreales)的种类为主,担子菌则以胶膜菌科(Tulasnellaceae)为主。Simpson多样性指数分析结果表明,不同生境下野生铁皮石斛内生真菌的多样性都很高,且雅长的高于崀山的。展开更多
Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and m...Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and mat Ktrbc L is unable to distinguish D. officinale from 5 closely related species of it(D. tosaense, D.shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes.Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species.By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species,indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).展开更多
Objective:To evaluate the antibacterial properties ot Allium sativum(garlic) cloves and Zingiber officinale(ginger) rhizomes against multi-drug resistant clinical pathogens causing nosocomial infection.Methods:The clo...Objective:To evaluate the antibacterial properties ot Allium sativum(garlic) cloves and Zingiber officinale(ginger) rhizomes against multi-drug resistant clinical pathogens causing nosocomial infection.Methods:The cloves of garlic and rhizomes of ginger were extracted with 95%(v/v) ethanol.The ethanolic extracts were subjected to antibacterial sensitivity test against clinical pathogens.Results:Anti-bacterial potentials of the extracts of two crude garlic cloves and ginger rhizomes were tested against five gram negative and two gram positive multi-drug resistant bacteria isolates.All the bacterial isolates were susceptible to crude extracts of both plants extracts.Except Enterobacter sp.and Klebsiella sp.,all other isolates were susceptible when subjected to ethanolic extracts of garlic and ginger.The highest inhibition zone was observed with garlic(19.4S mm) against Pseudomonas aeruginosa(P.aeruginosa).The minimal inhibitory concentration was as low as 67.00 μg/mL against P.aeruginosa.Conclusions:Natural spices of garlic and ginger possess effective anti-bacterial activity against multi-drug clinical pathogens and can be used for prevention of drug resistant microbial diseases and further evaluation is necessary.展开更多
With the internationally growing popularity of traditional Chinese medicine(TCM), TCM-induced nephropathy has attracted public attention. Minimizing this toxicity is an important issue for future research. Typical nep...With the internationally growing popularity of traditional Chinese medicine(TCM), TCM-induced nephropathy has attracted public attention. Minimizing this toxicity is an important issue for future research. Typical nephrotoxic TCM drugs such as Aristolochic acid, Tripterygium wilfordii Hook. f, Rheum officinale Baill, and cinnabar mainly damage renal proximal tubules or cause interstitial nephritis. Transporters in renal proximal tubule are believed to be critical in the disposition of xenobiotics. In this review, we provide information on the alteration of renal transporters by nephrotoxic TCMs, which may be helpful for understanding the nephrotoxic mechanism of TCMs and reducing adverse effects. Studies have proven that when administering nephrotoxic TCMs, the expression or function of renal transporters is altered, especially organic anion transporter 1 and 3. The alteration of these transporters may enhance the accumulation of toxic drugs or the dysfunction of endogenous toxins and subsequently sensitize the kidney to injury.Transporters-related drug combination and clinical biomarkers supervision to avoid the risk of future toxicity are proposed.展开更多
Dendrobium officinale,an important medicinal plant of the genus Dendrobium in Orchidaceae family,has been used as traditional Chinese medicine(TCM)for nearly thousands of years.Here,we report the first chromosome-leve...Dendrobium officinale,an important medicinal plant of the genus Dendrobium in Orchidaceae family,has been used as traditional Chinese medicine(TCM)for nearly thousands of years.Here,we report the first chromosome-level reference genome of D.officinale,based on Pac Bio long-reads,Illumina short-reads and HiC data.The high-quality assembled genome is 1.23 Gb long,with contig N50 of 1.44 Mb.A total of 93.53%genome sequences were assembled into 19 pseudochromosomes with a super scaffold N50 of 63.07 Mb.Through comparative genomic analysis,we explored the expanded gene families of D.officinale,and also their impact on environmental adaptation and biosynthesis of secondary metabolites.We further performed detailed transcriptional analysis of D.officinale,and identified the candidate genes involved in the biosynthesis of three main active ingredients,including polysaccharides,alkaloids and flavonoids.In addition,the MODIFYING WALL LIGNIN-1(MWL1)gene,which inferred from Genome-Wide Association Studies(GWAS)based on the resequencing date from D.officinale and five related species and their morphologic features,may contribute to the plant production(yield of stems)of D.officinale.Therefore,the high-quality reference genome reported in this study could benefits functional genomics research and molecular breeding of D.officinale.展开更多
文摘Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome se- quences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16- epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.
基金supported by the National Natural Science Foundation of China (Grant Nos. 30830117 and 31170016) the Major Scientific and Technological Special Project for Significant New Drugs Creation (Grant No. 2012ZX09301002-001-031)
文摘The aim of this study was to establish a method for discriminating Dendrobium officinale from four of its close relatives Den- drobium chrysanthum, Dendrobium erystallinum, Dendrobium aphyllum and Dendrobium devonianum based on chemical composition analysis. We analyzed 62 samples of 24 Dendrobium species. High performance liquid chromatography analysis confirmed that the four low molecular weight compounds 4＇,5,7-trihydroxyflavanone （naringenin）, 3,4-dihydroxy-4＇,5-dime- tboxybibenzyl （DDB^2）, 3＇,4-dihydroxy-3,5＇-dimethoxybibenzyl （gigantol）, and 4,4＇-dihydroxy-3,3＇,5-trimethoxybibenzyl （moscatilin）, were common in the genus. The phenol-sulfuric acid method was used to quantify polysaccharides, and the mon- osaccharide composition of the polysaccharides was determined by gas chromatography. Stepwise discriminant analysis was used to differentiate among the five closely related species based on the chemical composition analysis. This proved to be a simple and accurate approach for discriminating among these species. The results also showed that the polysaccharide content, the amounts of the four low molecular weight compounds, and the mannose to glucose ratio, were important factors for species discriminaut. Therefore, we propose that a chemical analysis based on quantification of naringenin, bibenzyl, and polysaccha- rides is effective for identifying D. officinale.
文摘采集湖南省新宁县崀山世界自然遗产风景名胜区和广西省乐业县雅长兰科植物自然保护区这两个生境中处于生长期的铁皮石斛(Dendrobium of ficinale)的营养根,并进行分离培养。通过对分离所得的41个菌株进行形态观察和ITS序列测定相结合的鉴定,共获得内生真菌34种。对担子菌和子囊菌分别进行了系统发育树构建结果显示,子囊菌为优势种类(31种),以炭角菌目(Xylariales)和肉座菌目(Hypocreales)的种类为主,担子菌则以胶膜菌科(Tulasnellaceae)为主。Simpson多样性指数分析结果表明,不同生境下野生铁皮石斛内生真菌的多样性都很高,且雅长的高于崀山的。
基金supported by the National Natural Science Foundation of China (Grant Nos. 31170300 and 31670330)the Priority Academic Program Development of Jiangsu Higher Education Institutions to Xiaoyu Ding (Grant No. 2015-SWYY-014)
文摘Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and mat Ktrbc L is unable to distinguish D. officinale from 5 closely related species of it(D. tosaense, D.shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes.Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species.By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species,indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).
基金financrally supported by K.S.Rangasamy College of Arts and Science.Kuchipalayam,Tiruchengodr.Tamil Nadu,India(grant No.KSRCAS/PG/MB/0010 dt.10.11.2010)
文摘Objective:To evaluate the antibacterial properties ot Allium sativum(garlic) cloves and Zingiber officinale(ginger) rhizomes against multi-drug resistant clinical pathogens causing nosocomial infection.Methods:The cloves of garlic and rhizomes of ginger were extracted with 95%(v/v) ethanol.The ethanolic extracts were subjected to antibacterial sensitivity test against clinical pathogens.Results:Anti-bacterial potentials of the extracts of two crude garlic cloves and ginger rhizomes were tested against five gram negative and two gram positive multi-drug resistant bacteria isolates.All the bacterial isolates were susceptible to crude extracts of both plants extracts.Except Enterobacter sp.and Klebsiella sp.,all other isolates were susceptible when subjected to ethanolic extracts of garlic and ginger.The highest inhibition zone was observed with garlic(19.4S mm) against Pseudomonas aeruginosa(P.aeruginosa).The minimal inhibitory concentration was as low as 67.00 μg/mL against P.aeruginosa.Conclusions:Natural spices of garlic and ginger possess effective anti-bacterial activity against multi-drug clinical pathogens and can be used for prevention of drug resistant microbial diseases and further evaluation is necessary.
基金National Natural Science Foundation of China(Nos.81673684,81703626,81573690)Double First-Class University projects(No.CPU2018GY33)。
文摘With the internationally growing popularity of traditional Chinese medicine(TCM), TCM-induced nephropathy has attracted public attention. Minimizing this toxicity is an important issue for future research. Typical nephrotoxic TCM drugs such as Aristolochic acid, Tripterygium wilfordii Hook. f, Rheum officinale Baill, and cinnabar mainly damage renal proximal tubules or cause interstitial nephritis. Transporters in renal proximal tubule are believed to be critical in the disposition of xenobiotics. In this review, we provide information on the alteration of renal transporters by nephrotoxic TCMs, which may be helpful for understanding the nephrotoxic mechanism of TCMs and reducing adverse effects. Studies have proven that when administering nephrotoxic TCMs, the expression or function of renal transporters is altered, especially organic anion transporter 1 and 3. The alteration of these transporters may enhance the accumulation of toxic drugs or the dysfunction of endogenous toxins and subsequently sensitize the kidney to injury.Transporters-related drug combination and clinical biomarkers supervision to avoid the risk of future toxicity are proposed.
基金supported by grants from the National Natural Science Foundation of China(Grant No.31900268,31670330 and 32070353)Natural Science Foundation of Jiangsu Province,China(BK20190699)Natural science fund for colleges and universities in Jiangsu Province,China(19KJB180005)
文摘Dendrobium officinale,an important medicinal plant of the genus Dendrobium in Orchidaceae family,has been used as traditional Chinese medicine(TCM)for nearly thousands of years.Here,we report the first chromosome-level reference genome of D.officinale,based on Pac Bio long-reads,Illumina short-reads and HiC data.The high-quality assembled genome is 1.23 Gb long,with contig N50 of 1.44 Mb.A total of 93.53%genome sequences were assembled into 19 pseudochromosomes with a super scaffold N50 of 63.07 Mb.Through comparative genomic analysis,we explored the expanded gene families of D.officinale,and also their impact on environmental adaptation and biosynthesis of secondary metabolites.We further performed detailed transcriptional analysis of D.officinale,and identified the candidate genes involved in the biosynthesis of three main active ingredients,including polysaccharides,alkaloids and flavonoids.In addition,the MODIFYING WALL LIGNIN-1(MWL1)gene,which inferred from Genome-Wide Association Studies(GWAS)based on the resequencing date from D.officinale and five related species and their morphologic features,may contribute to the plant production(yield of stems)of D.officinale.Therefore,the high-quality reference genome reported in this study could benefits functional genomics research and molecular breeding of D.officinale.
