DNA barcodes for discriminating the medicinal plant Scutellaria baicalensis (Lamiaceae) and its adulterants

Scutellaria baicalensis GEORGI (Lamiaceae) is the botanical origin of the well-known traditional Chinese medicine "Huang Qin" (Radix Scutellariae). Due to overexploitation that had induced a decline in natural sources, the dried roots of its congeners, S. amoena, S. rehderiana, and S. viscidula, have been used to adulterate it in recent years. This practice may cause a series of inconsistent therapeutic effects and quality control problems in the herbal medicine industry. Hence, we sequenced and analyzed three candidate DNA barcodes, the ribosomal RNA maturase gene (matK), the ribulose-1,4-bisphosphate carboxylase large subunit gene (rbcL), and the psbA-trnH intergenic spacer (psbA-trnH), to discriminate S. baicalensis and its adulterants. All candidate DNA barcodes had been successfully amplified from leaf samples. Comparatively, only psbA-trnH had been yielded from commercially prepared crude drug samples. Based on the sequence divergence, rbcL can assign S. baicalensis and its adulterants into the correct family and genus, whereas, either matK or psbA-trnH can accurately discriminate S. baicalensis and its adulterants. We proposed the multilocus barcodes rbcL+psbA-trnH for the species identification of S. baicalensis and its adulterants, and the unique barcode psbA-trnH for the authentication of commercial Radix Scutellariae. The DNA barcoding technique could be applied to the quality control of "Huang Qin"-based medicinal preparations and to the management of medicinal herb trade in the markets.     

Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region

Medicinal pteridophytes are an important group used in traditional Chinese medicine; however, there is no simple and universal way to differentiate various species of this group by morphological traits. A novel technology termed "DNA barcoding" could discriminate species by a standard DNA sequence with universal primers and sufficient variation. To determine whether DNA barcoding would be effective for differentiating pteridophyte species, we first analyzed five DNA sequence markers (psbA-trnH intergenic region, rbcL, rpoB, rpoC1, and matK) using six chloroplast genomic sequences from GeneBank and found psbA-trnH intergenic region the best candidate for availability of universal primers. Next, we amplified the psbA-trnH region from 79 samples of medicinal pteridophyte plants. These samples represented 51 species from 24 families, including all the authentic pteridophyte species listed in the Chinese pharmacopoeia (2005 version) and some commonly used adulterants. We found that the sequence of the psbA-trnH intergenic region can be determined with both high polymerase chain reaction (PCR) amplification efficiency (94.1%) and high direct sequencing success rate (81.3%). Combined with GeneBank data (54 species cross 12 pteridophyte families), species discriminative power analysis showed that 90.2% of species could be separated/identified successfully by the TaxonGap method in conjunction with the Basic Local Alignment Search Tool 1 (BLAST1) method. The TaxonGap method results further showed that, for 37 out of 39 separable species with at least two samples each, between-species variation was higher than the relevant within-species variation. Thus, the psbA-trnH intergenic region is a suitable DNA marker for species identification in medicinal pteridophytes.     

基于ITS序列鉴别特色民族药材土牛膝及其混伪品的研究

目的:利用DNA条形码对特色民族药材土牛膝(粗毛牛膝、野生牛膝和柳叶牛膝)及其混伪品进行分子鉴定.方法:利用DNA条形码方法,分别对土牛膝及其混伪品的ITS和MatK基因片段进行扩增并双向测序,使用Codon?Code?Aligner软件对扩增序列进行拼接,用MEGA软件对数据比对分析,并基于K2P模型进行遗传距离分析...     

基于matK和ITS2及二级结构对药材香薷及其混伪品的鉴别研究

目的 快速、准确鉴别药材香薷及其混伪品，保障香薷的药材质量和用药安全。方法 收集石香薷、江香薷和香薷植物材料分别进行matK和ITS2序列的扩增与测序，测序结果经Codon Code Aligner软件校对，同时从GenBank下载石香薷、江香斋及其易混品种海州香薷、香薷、密花香薷、牛至等物种的matK和ITS序列。其中，ITS序列经隐马尔可夫模型去除两端的5.8S和28S序列，共得到16个物种的ITS2序列50条；经Clustal软件校对共获得9个物种的matK序列28条。通过Mega7.0软件分析matK和ITS2序列，计算所有物种种内和种间遗传距离，构建邻接法(neighbor joining，NJ)聚类树，通过ITS2 Database预测ITS2二级结构，采用4Sale软件比对二级结构，通过ProfDistS软件构建基于联合ITS2一级序列及其二级结构的剖面邻接(profile neighbor-joining，PNJ)系统发育树。结果 基于matK和ITS2序列的遗传距离均表明香薷正品与其各种混伪品之间存在明显barcoding gap。NJ和PNJ进化树的拓扑关系一致，可以区分药材香薷及其混伪品。香薷的ITS2二级结构与其各混伪品具有显著差异。结论 建议matK和ITS2序列均可以作为鉴别香薷与其混伪品的DNA条形码，ITS2二级结构信息的加入可丰富鉴定结果，为香薷药材的准确鉴别、香薷属与石荠苎属植物的科学分类提供参考。     

安罗替尼联合AP方案治疗晚期非小细胞肺癌的临床研究

目的 基于线粒体cytochrome coxidase I（CO I）和16 S rRNA基因开发DNA双重条形码鉴定方法,由此验证并补充形态鉴定,以期建立一种准确、有效地鉴定地龙及混淆品原动物的方法。方法 对收集到的66份样品依据形态特征进行初步鉴定,使用优化后的引物同时扩增CO I和16 S rRNA序列。优化一步法双重PCR实验条件。用MEGA 5.1计算地龙及其混淆品的种内、种间遗传距离,基于K2P模型构建NJ树。结果 CO I和16 S rRNA双重DNA条形码鉴定与形态鉴定结合,可准确鉴别地龙及混淆品原动物。结论 形态鉴定是分子鉴定的基础,分子鉴定是形态鉴定的有力补充。二者结合可最大程度地实现地龙及其混淆品原动物的准确鉴定。DNA双重条形码鉴定方法也可为地龙药材鉴定以及其他动物药材的分子鉴定提供参考。     

中药材龟甲的分子鉴定研究

用PCR产物直接测序法对中药材龟甲(板)进行鉴别。从乌龟 Chinemys revesii 和其他20种产地为中国或东南亚国家的龟类的组织材料中提取DNA,扩增约110bp的线粒体12SrRNA,基因片段并进行序列分析,构建了21种龟类的12SrRNA基因片段序列数据库。序列比较的结果表明乌龟与其它20种龟类的这段序列均有差别,序列差异在3.7～15.7%之间。从江苏省药品检验所提供的19块龟甲检品上各取样0.1～0.5g提取 DNA,扩增与上述相同的基因片段,与构建的数据库进行比较,结果表明19块龟甲中只有3块的原动物为乌龟,其余的龟甲均为混淆品。本文的结果为药材龟甲的鉴定找到了有效、可靠的分子遗传标记方法。     

广藿香的基因序列与挥发油化学型的相关性分析

目的探讨“南药”广藿香Pogostemon cablin (Blanco) Benth.不同产地间的叶绿体和核基因组的基因型与挥发油化学型的关系，为广藿香道地性品质评价、规范化种植提供分子依据。方法用PCR直接测序技术对广藿香6个产地样本的叶绿体matK基因和核18S rRNA基因核苷酸序列进行测序分析研究。结果广藿香6个样本的matK基因序列长均为1 245 bp，编码415个氨基酸成熟酶。18S rRNA基因序列长为1 803～1 805 bp。根据排序比较，广藿香6个样本间的matK基因序列存在47个变异位点，18S rRNA基因存在17个变异位点，非加权组平均法构建的系统分支树表明广藿香基因序列分化与其产地、所含挥发油化学变异类型呈良好的相关性。结论结合挥发油分析数据，基因测序分析技术可作为广藿香道地性品质评价方法这一以及规范化种植过程关键技术“物种鉴定”的强有力工具。     

Molecular authentication of the animal crude drug Sailonggu (bone of Myospalax baileyi)

Two pairs of allele-specific diagnostic primers (SL1L/SL1H and SL2L/SL2H) for distinguishing the Chinese crude drug Sailonggu (bone of plateau zokor, Myospalax baileyi) from its substitutes were designed based on complete sequences of mitochondrial 12S rRNA and cytochrome b genes of the original animals of Myospalacinae, bamboo rat Rhizomys sinensis and black lipped pika Ochotona curzoniae. Total DNA was extracted from crude drug samples and original animals. Allele-specific diagnostic PCRs were performed using these primers with the total DNA as a template annealing at 65 degrees C. Positive amplifications were obtained from all DNA templates of Sailonggu and M. baileyi, whereas negative amplifications resulted from those of other zokors, the bamboo rat and black lipped pika. These results indicate that Sailonggu samples can be definitely distinguished from their substitutes by diagnostic PCR, and no incorrect discrimination was found under the same reaction conditions. Each of the two diagnostic primer pairs can be used to distinguish crude drug Sailonggu from its substitutes or adulterants. The three Sailonggu samples studied were diagnosed as genuine Sailonggu. In addition, the results of sequence alignment and phylogenetic analysis are congruent with that of the allele-specific diagnostic PCR.     

Genetic characterization and authentication of Embelia ribes using RAPD-PCR and SCAR marker

Embelia ribes Burm. f. (Myrsinaceae) is one of the important plants used in Indian traditional medicine. RAPD-PCR analysis was performed to obtain species-specific DNA fragments. A band of 906 bp that was specific to Embelia ribes irrespective of the geographical source was obtained using the random decamer primer OPF 05. SCAR primers ER 1 (27 mer) and ER 2 (26 mer) were designed from the sequence of the RAPD marker which yielded an expected amplicon of 594 bp with the Embelia ribes DNA only. This methodology can be used for species identification of genuine Embelia ribes and to distinguish it from common substitutes and adulterants. BLAST: basic local alignment search tool ER 1: Embelia ribes forward primer ER 2: Embelia ribes reverse primer RAPD-PCR: random amplification of polymorphic DNA polymerase chain reaction SCAR: sequence characterized amplified region.     

通关藤及其常见混伪品的ITS2条形码鉴别研究

目的:采用ITS2序列分析,对通关藤及其混淆品进行鉴别,确保用药安全。方法:从GenBank下载通关藤序列,使用MEGA5.0软件对测序序列及下载序列进行对比分析,统计变异位点、计算遗传距离、构建样品NJ树,运用NCBI Blast进行物种鉴定,并与性状鉴别结果进行核对。结果:ITS2序列分析与遗传距离计算结果显示各通关藤样品间有明显差异,NJ树聚类结果能明显区分通关藤正品与伪品。结论:ITS2可准确鉴别通关藤及其伪品,可用于中药材真伪的快速鉴别,应用前景广阔。     

三七的18S rRNA,matK基因序列和HPLC化学指纹图谱分析研究

目的分析中药三七Panaxnotoginseng的18SrRNA和matK基因的分子特征和三七的化学指纹特征,为三七的正品药材基原鉴定提供分子和化学依据。方法采用PCR直接测序技术测定三七及其7种伪品的18SrRNA和matK基因部分核苷酸序列以及不同产地三七的DNA分子特征。利用HPLC的化学分析技术,明确产地对三七化学成分的影响,以及三七不同部位的化学指纹特征。结果(1)三七及其7种常见伪品的核糖体18SrRNA基因序列存在很大的差异。(2)不同产地的三七的核糖体18SrRNA和叶绿体matK基因序列特征完全一致,分别与GenBank上已报道的R1型(D85171)和M1型(AB027526)序列吻合。(3)不同产地的三七HPLC指纹图谱相似。(4)三七不同部位均具有其相对稳定的HPLC指纹特征,其中花、叶具有特有的指纹区,根、须根、剪口、筋条等不同商品规格的HPLC指纹图谱比较相似。结论基因序列标记能从分子水平定性分辨三七及其伪品的遗传背景差异,为中药品种标准化提供了先进可行、稳定可靠的分子标准;HPLC指纹图谱分析可以直观地为三七的化学成分定性,三七不同商品规格的特征性指纹有望成为以其为原材料的各种产品的质控标准,而三七不同部位(尤其是花和叶)的HPLC指纹图谱将有望成为制定三七花、三七叶新药用资源质控标准的依据。     

Species identification of licorice using nrDNA and cpDNA genetic markers

For the accurate identification of medicinal licorice species, nucleotide sequences of four types of DNA regions were researched for 205 specimens, including three species used as licorice: Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata. The four DNA regions were the internal transcribed spacer (ITS) on nuclear ribosomal DNA, the rbcL gene, the matK gene, and the trnH-psbA intergenic region on chloroplast DNA (cpDNA). Ten genotypes were consequently recognized as combinations of the sequence data obtained from the four DNA regions. Species-specific genotypes were defined from the frequency of the appearance of species in each genotype and from the phylogenetic relationships of the 10 genotypes. This revealed the possibility of identifying licorice species based on the 10 genotypes. Next, comparison of species identifications by each DNA region suggested that efficient identification of licorice species is possible using the genetic information obtained from the ITS and trnH-psbA intergenic region. Additionally, concerning the phylogenetic relationships of the Glycyrrhiza species used as licorice, it is suggested from the genetic information of the four types of DNA regions that G. glabra is more closely related to G. inflata than to G. uralensis. In the G. uralensis examined, four genotypes were recognized as intra specific variations. The appearance frequency of each genotype in G. uralensis differed according to the area in China. G. uralensis may have expanded its distribution areas from western to eastern China because many licorices with the phylogenetic ancestral genotype were observed in western areas, while many with the derivative genotype were observed in eastern areas.     

广藿香与土藿香的DNA序列分析及其分子鉴别

目前市场上藿香类商品药材有两种 ,一种为唇形科刺蕊草属 (Ｐｏｇｏｓｔｅｍｏｎ)植物广藿香Ｐｏｇｏｓｔｅｍｏｎｃａｂｌｉｎ (Ｂｌａｎｃｏ)Ｂｅｎｔｈ.的干燥地上部分 ,主产广东、海南 ,习称“广藿香”,均为栽培品 ,有芳香化浊、开胃止呕、发表解暑的功效 ,是中成药“藿香正气水”的主要原料。据我们分析广州市郊黄村产“石牌广藿香”药材茎枝挥发油成分 ,其中 71 %为广藿香酮(ｐｏｇｏｓｔｏｎｅ) [1 ] ;另一种来源于同科另一属 ,即藿香属(Ａｇａｓｔａｃｈｅ)植物藿香Ａｇａｓｔａｃｈｅｒｕｇｏｓａ (Ｆｉｓｃｈ.ｅｔＭｅｙ.)Ｏ .Ｋ…     

用随机扩增多态DNA（RAPD）技术鉴别中药材天花粉及其类似品

目的：对来源于１３个种３个变种的天花粉及基类似品进行鉴别研究,并进行方法学的探讨。方法：应用随机扩增多态ＤＮＡ（ＲＡＰＤ）技术进行鉴别,采用聚类分析方法分析并对药材贮存时间及产地对实验结果的影响进行探讨。结果：反天花粉正品与类似品有效地分成三大类。结论：认为在实验采取设对照组,对结果采用聚类分析等方法,ＲＡＰＤ技术鉴别药材具有一定的可靠性和实用价值,这为解决粉未及破碎药材的鉴别提供了新的方法。     

3种清风藤属植物低极性部位GC-MS分析及抗炎活性

目的探究鄂西清风藤、灰背清风藤和小花清风藤低极性部位成分特点及其抗炎活性。方法运用气相色谱-质谱技术对鄂西清风藤、灰背清风藤和小花清风藤干燥茎叶石油醚萃取液中经石油醚洗脱所得的低极性部位进行成分分析,采用NIST 17和Wiley 275数据库对色谱峰进行检索,人工比对鉴定各化合物的结构,并采用峰面积归一化法计算各成分的相对百分含量。以吲哚美辛为阳性对照,以一氧化氮(NO)生成抑制率为指标,比较上述3种清风藤属植物低极性部位对脂多糖诱导人类风湿性关节炎成纤维样滑膜细胞RA-FLS、小鼠单核巨噬细胞RAW264.7生成NO的影响,并计算半数抑制浓度(IC₅₀)。结果从鄂西清风藤、灰背清风藤和小花清风藤低极性部位中分别确认了70、40、33种成分,均包含长链脂肪烃、长链醇/醛/酯、单萜等成分,但三者共有成分仅有正十二烷、正二十二烷等5种。鄂西清风藤中萜类成分丰富(40.89%),灰背清风藤中三萜成分的相对百分含量较高(30.29%),小花清风藤中长链脂肪烃成分的相对百分含量较高(87.70%)。上述3种清风藤属植物低极性部位对RA-FLS细胞NO生成的IC₅₀分别为2.22、1.69、4.15μg/mL,对RAW264.7细胞NO生成的IC₅₀分别为1.23、4.02、3.05μg/mL,均低于吲哚美辛(12.97、10.66μg/mL)。结论上述3种清风藤属植物低极性部位均含有长链脂肪烃、单萜、长链醇/醛/酯等成分,且三者均具有一定的抗炎活性。     

Authentication of stems of Dendrobium officinale by rDNA ITS region sequences

The rDNA ITS regions of five Dendrobium species were sequenced. Each Dendrobium species was found to have a unique sequence in the ITS region, so that they could be easily distinguished at the DNA level. The aligned 644 bp of the ITS region includes 235 bp ITS1, 163 bp 5.8S, and 246 bp ITS2. One hundred and eighty-nine sites are variable. The sequences of D. officinale could be easily distinguished from the other four adulterant species according to the sequence variation at 11 sites, 7 in ITS1, 1 in 5.8S, and 3 in ITS2. These could be used as molecular characters to distinguish the stems of D. officinale from the adulterants.     

重楼属药用植物DNA条形码鉴定研究

为评价DNA条形码候选序列对重楼属药用植物的鉴定作用, 探讨重楼属药用植物鉴定新方法, 本研究对重楼属11个物种17份样品的psbA-trnH、rpoB、rpoC1、rbcL、matK和核ITS2序列进行PCR扩增和测序, 比较各序列扩增和测序效率、种内和种间变异, 进行barcoding gap分析, 采用BLAST1和Nearest Distance方法评价不同序列的鉴定能力。结果显示, ITS2序列在所研究的重楼属药用植物中的扩增和测序效率均为100%, 其种内种间变异、barcoding gap与其他DNA条形码候选序列相比具有明显的优势, ITS2序列在重楼属中的鉴定成功率达到100%, 而生物条形码协会 (CBOL) 植物工作组推荐的matK和rbcL序列的鉴定成功率分别为52.9% 和5.9%, 二者联合鉴定能力没有提高, 对于ITS2序列扩大至29个物种67份样品依然具有100%的鉴定成功率。实验结果表明, ITS2序列能够准确鉴定重楼属药用植物, 可以作为潜在的药用植物通用条形码序列。     

Genome-based approaches to the authentication of medicinal plants

Medicinal plants are the source of a large number of essential drugs in Western medicine and are the basis of herbal medicine, which is not only the primary source of health care for most of the world's population living in developing countries but also enjoys growing popularity in developed countries. The increased demand for botanical products is met by an expanding industry and accompanied by calls for assurance of quality, efficacy and safety. Plants used as drugs, dietary supplements and herbal medicines are identified at the species level. Unequivocal identification is a critical step at the beginning of an extensive process of quality assurance and is of importance for the characterization of the genetic diversity, phylogeny and phylogeography as well as the protection of endangered species. DNA-based methods have been developed for the identification of medicinal plants. Nuclear and chloroplast DNA is amplified by the polymerase chain reaction and the reaction products are analyzed by gel electrophoresis, sequencing, or hybridization with species-specific probes. Genomic fingerprinting can differentiate between individuals, species and populations and is useful for the detection of the homogeneity of the samples and presence of adulterants. Although sequences from single chloroplast or nuclear genes have been useful for differentiation of species, phylogenetic studies often require consideration of DNA sequence data from more than one gene or genomic region. Phytochemical and genetic data are correlated but only the latter normally allow for differentiation at the species level. The generation of molecular "barcodes" of medicinal plants will be worth the concerted effort of the medicinal plant research community and contribute to the ongoing effort of defining barcodes for every species on earth.     

Commercialized non-Camellia tea: traditional function and molecular identification

Non-Camellia tea is a part of the colorful Chinese tea culture, and is also widely used as beverage and medicine in folk for disease prevention and treatment. In this study, 37 samples were collected, including 33 kinds of non-Camellia teas and 4 kinds of teas (Camellia). Traditional functions of non-Camellia teas were investigated. Furthermore, non-Camellia teas of original plants were characterized and identified by molecular methods. Four candidate regions (rbcL, matK, ITS2, psbA-trnH) were amplified by polymerase chain reaction. In addition, DNA barcodes were used for the first time to discriminate the commercial non-Camellia tea and their adulterants, and to evaluate their safety. This study showed that BLASTN and the relevant phylogenetic tree are efficient tools for identification of the commercial non-Camellia tea and their adulterants. However, some sequences from original plants have not been found and there is a limitation of sequence number of original plants in GenBank. Submitting more original plant sequences to the GenBank will be helpful for evaluating the safety of non-Camellia teas.KEY WORDS: Non-Camellia tea, Traditional function, Molecular identification, BLASTN, Phylogenetic tree     

Molecular analysis of Rheum species used as Rhei Rhizoma based on the chloroplast matK gene sequence and its application for identification

Rhei Rhizoma (Dahuang in Chinese) is widely known as a purgative and antiinflammatory agent. In the Japanese Pharmacopoeia, Rhei Rhizoma is prescribed for four Rheum species, Rheum palmatum, R. tanguticum, R. officinale, and R. coreanum, while the first three species are prescribed for Dahuang in the Chinese Pharmacopoeia. Due to the morphologic similarity of the aerial parts and frequent occurrence of intermediate forms, the taxonomy of this genus and the correct identification of Rheum species and their derivative drugs are very difficult. To resolve taxonomic problems of the genus Rheum and develop an ultimate identification method for plants and drugs, molecular analysis of the chloroplast matK gene and nuclear 18S ribosomal RNA gene were performed on nine species. The sequence comparison of the matK gene revealed that most species had variable sequences not only inter- but also intraspecies. However, the specimens of the same species belonged to the same subclade in the phylogenetic tree constructed based on matK gene sequences, except for R. palmatum, in which specimens belonged to three subclades related to their production areas. The nucleotide differences at positions 587, 707, and 838 distinguished official species from others, while specific nucleotides at positions 367 and 937 became identification markers for R. palmatum, R. tanguticum, and R. officinale (or R. coreanum). Moreover, three groups of R. palmatum, each belonging to three subclades, were characterized by the nucleotides at positions 619, 769, 883, and 1061. By detecting marker nucleotides, the botanical origins of Rhei Rhizoma were determined.