Application of single-nucleotide polymorphism analysis of the trnK gene to the identification of Curcuma plants

We previously found that Curcuma plants and drugs derived from Curcuma longa, C. phaeocaulis, C. zedoaria, and C. aromatica could be identified by the nucleotide differences at two sites and the existence of a 4-base indel on trnK gene. In this paper, based on species-specific nucleotide sequences, the application of a new method, single-nucleotide polymorphism (SNP) analysis was investigated to identify Curcuma plants more conveniently. First, three types of reverse primer were synthesized in different lengths, 34 mer, 26 mer, and 30 mer, to anneal the template DNAs from each species at sites immediately upstream from substitution positions 177 and 645, and at the site including the 4-base insertion from 728 to 731, respectively. After single-base extension reaction of these primers using fluorescent-labeled ddNTPs and PCR products of the trnK gene region as template, the resulting products were detected using an ABI PRISM 310 Genetic Analyzer. The electrophoretogram showed three or two peaks at different positions depending on the 27 mer, 31 mer, and 35 mer product lengths. Each peak was derived from the incorporated fluorescent-labeled ddNMPs complementary to template nucleotides at positions 645, 724, and 177, respectively. C. phaeocaulis showed three peaks of ddCMP, ddAMP, and ddAMP. The other three species showed two peaks derived from 27 mer and 35 mer products: peaks of ddCMP and ddAMP in C. longa, those of ddCMP and ddTMP in C. zedoaria, and those of ddTMP and ddAMP in C. aromatica. Thus SNP analysis to identify four Curcuma plants was newly developed.     

中日产川芎的matK、ITS基因序列及其物种间的亲缘关系

目的分析中国产川芎Ligusticum chuanxiong Hort.及日本产川芎Cnidium officinale Makino的核基因组ITS和叶绿体基因组matK序列,为探讨中日产川芎物种间的亲缘关系提供分子依据。方法采用PCR直接测序技术测定川芎和日本川芎的ITS基因和matK基因核苷酸序列并作序列变异分析。结果川芎和日本川芎的matK序列长度均为1268 bp,编码422个氨基酸。ITS1-5.8S-ITS2序列长度均为699 bp,其中18S rRNA基因3′端序列54 bp,ITS1序列215 bp,5.8S rRNA基因序列162 bp,ITS2序列222 bp,26S rRNA基因5′端序列46 bp。根据排序比较,川芎原植物与其商品药材间的matK基因和ITS基因序列完全相同,而川芎与日本川芎间matK基因则仅有1个变异位点,即在上游959 nt处1个转换替代(T→C),反映在氨基酸序列则发生一个非同义取代V(GTG)→A(GCG);ITS基因也仅有1个变异位点,即在ITS1上游54 nt处1个转换替代(T→C)。结论通过进化速率较快的基因序列同源性分析,基本可以认为中日所产川芎基原一致,日本川芎学名似应改为Ligusticum chuanxiong Hort.。     

Sequence analysis of Chinese and Japanese Curcuma drugs on the 18S rRNA gene and trnK gene and the application of amplification-refractory mutation system analysis for their authentication

The botanical origins of Chinese and Japanese Curcuma drugs were determined to be Curcuma longa, C. phaeocaulis, the Japanese population of C. zedoaria, C. kwangsiensis, C. wenyujin, and C. aromatica based on a comparison of their 18S rRNA gene and trnK gene sequences with those of six Curcuma species reported previously. Moreover, to develop a more convenient identification method, amplification-refractory mutation system (ARMS) analysis of both gene regions was performed on plants. The ARMS method for the 18S rRNA gene was established using two types of forward primers designed based on the nucleotide difference at position 234. When DNAs of four Curcuma species were used as templates, PCR amplification with either of the two primers only generated a fragment of 912 base pairs (bp). However, when DNAs of the purple-cloud type of C. kwangsiensis and C. wenyujin were used, PCR amplifications with both primers unexpectedly generated the fragment, suggesting that these two were heterozygotes. The ARMS method for the trnK gene was also established using a mixture of four types of specific reverse primers designed on the basis of base substitutions and indels among six species, and common reverse and forward primers. C. phaeocaulis or the Chinese population of C. zedoaria, the Japanese population of C. zedoaria or the purple-cloud type of C. kwangsiensis, the pubescent type of C. kwangsiensis or C. wenyujin, and C. aromatica were found to show specific fragments of 730, 185, 527 or 528, and 641 or 642 bp, respectively. All species including C. longa also showed a common fragment of 897-904 bp. Using both ARMS methods, together with information on producing areas, the identification of Curcuma plants was achieved. Moreover, the ARMS method for the trnK gene was also useful for authentication of Curcuma drugs.     

川芎和引种日本川芎的RAPD分析与鉴定

目的从DNA分子水平上探讨川芎和引种日本川芎的亲缘关系及不同居群的遗传变异。方法提取35个样本的基因组DNA,并进行随机扩增多态性DNA(RAPD)分析和聚类分析。所选15个引物的RAPD,得出35个样本的聚类树状图。结果川芎和引种的日本川芎有明显的种间遗传差异,居群内遗传变异小,小生境对遗传性状有影响。结论所用方法可为川芎和日本川芎的鉴定及其道地性研究提供分子生物学依据。     

Molecular analysis of medicinally-used Chinese and Japanese Curcuma based on 18S rRNA gene and trnK gene sequences.

Curcuma drugs have been used discriminatingly for invigorating blood circulation, promoting digestion, and as a cholagogic in China. However, there is confusion about the drug's botanical origins and clinical uses because of morphological similarity of Curcuma plants and drugs. In order to develop an ultimate identification, molecular analysis based on 18S rRNA gene and trnK gene sequences were performed on 6 Curcuma species used medicinally in China and Japan. The 18S rRNA gene sequences were found to be of 1810 bps in length. In comparison with the common sequence of C. longa, C. phaeocaulis, C. wenyujin and C. aromatica, that of C. kwangsiensis had one base substitution, and the same base difference was observed between the Chinese and the Japanese populations of C. zedoaria. The trnK gene sequences were found to span 2698-2705 bps. There were base substitutions, small deletions or insertions at some sites between the trnK coding region and matK region among each species. Based on the base substitutions, C. zedoaria and C. kwangsiensis specimens were divided into two groups, respectively. An identical sequence was detected in C. phaeocaulis and in the Chinese population of C. zedoaria, as well as in the Japanese population of C. zedoaria and in one group of C. kwangsiensis with a purple-colored band in leaves. New taxonomic information to be used for authenticating Curcuma drugs was obtained.     

6种川产姜黄属药用植物叶绿体trnK基因序列变异分析及其分子鉴定

目的建立6种川产姜黄属（Curcuma）药用植物快速简单的分子鉴定方法。方法采用叶绿体赖氨酸tRNA基因（trnK）测序与序列变异分析方法。结果6种姜黄属药用植物（包括姜黄C. longa、莪术C. phaeocaulis、川郁金C. sichuanensis、川郁金C. chuanyujin、川黄姜C. chuanhuangjiang、川莪术C. chuanezhu）完整trnK基因长度在2699～2705 bp。序列可变区包括matK基因编码区和trnK外显子与matK内含子之间区域，共有6个单核苷酸多态性（SNPs）位点、1个9-bp的缺失重复序列和2个4-bp、14-bp插入重复序列。结论trnK基因序列可变位点可以作为6种川产姜黄属药用植物快速简单的分子鉴定标记，并为它们之间种的归并提供了分子依据。     

6种川产姜黄属药用植物叶绿体trnK基因序列变异分析及其分子鉴定

目的建立6种川产姜黄属(Curcuma)药用植物快速简单的分子鉴定方法.方法采用叶绿体赖氨酸tRNA基因(trnK)测序与序列变异分析方法.结果 6种姜黄属药用植物(包括姜黄C. longa、莪术C. phaeocaulis、川郁金C. sichuanensis、川郁金C. chuanyujin、川黄姜C. chuanhuangjiang、川莪术C. chuanezhu)完整trnK基因长度在2699～2705 bp.序列可变区包括matK基因编码区和trnK外显子与matK内含子之间区域,共有6个单核苷酸多态性(SNPs)位点、1个9-bp的缺失重复序列和2个4-bp、14-bp插入重复序列.结论 trnK基因序列可变位点可以作为6种川产姜黄属药用植物快速简单的分子鉴定标记,并为它们之间种的归并提供了分子依据.     

Rapid identification of Curcuma longa and C. aromatica by LAMP

We have developed a novel method for the identification of Curcuma longa and C. aromatica called "loop-mediated isothermal amplification (LAMP)," based on trnK gene sequences. LAMP employs four primers that recognize six regions on the target DNA. Cycling elongation was initiated when the four primers were annealed to the target DNA. Amplifications were detected by measuring turbidity due to the formation of magnesium pyrophosphate. We designed allele-specific primer sets for C. longa and C. aromatica, respectively. LAMP using a primer set for C. longa and total DNA extracted from C. longa rhizome (0.5-10.0 ng) as template was detected up to 70 min. On the other hand, in the reaction using a primer set for C. longa and total DNA from C. aromatica as template, no amplifications were detected. The same tendency could be seen in the reactions using a set of primers for C. aromatica. LAMP enabled not only identification but also detection with high specificity. This rapid, specific, sensitive, and convenient method is expected to be applicable to the identification of the botanical origin of commercially available herbal products.     

川芎化学成分的气相-质谱与指纹图谱研究(Ⅰ)

目的　对川芎药材进行气质联用成分分析与指纹图谱的研究。方法　采用气质联用分析技术对川芎不同溶剂提取物进行比较 ,并初步比较了川芎与当归的不同。结果　确定气质联用分析条件 ,分析川芎乙醚提取液的化学成分 ,建立了川芎的特征指纹图谱。结论　在此条件下 ,川芎图谱具有较好的特征性 ,可作为川芎专属性的指纹图谱     

Species identification from Ginseng drugs by multiplex amplification refractory mutation system (MARMS)

The multiplex amplification refractory mutation system (MARMS) was applied to the identification of 5 Panax species ( P. ginseng, P. japonicus, P. quinquefolius, P. notoginseng and P. vietnamensis). A set of specific primers, including 2-pair primers on chloroplast trnK gene and nuclear 18S rRNA gene regions, respectively, was designed and synthesized for each species on the basis of species-specific sequences of the 2 genes. By using 5 sets of specific primers, in turn, PCR amplifications were performed with total DNA extracted from 5 Panax species as template under appropriate condition, and each resulting product was detected by agarose gel electrophoresis. The results showed that two expected fragments, one from trnK gene and another from 18S rRNA gene regions, were observed simultaneously only when the set of species-specific primers encountered template DNA of the corresponding species. This assay could give more reliable results for identification of not only 5 Panax species but also corresponding Ginseng drugs by simultaneous detection of 4-site nucleotide differences on 2 completely different genes.     

SNP, ARMS and SSH authentication of medicinal Dendrobium officinale KIMURA et MIGO and application for identification of Fengdou drugs

Dried stems of Dendrobium officinale have been used as crude drugs in traditional Chinese medicine (TCM) with good tonic efficacy. Sequences of chloroplast, nuclear and mitochondria genes and the method of genomic DNA (gDNA) suppression subtraction hybridization (SSH) were used to authenticate different populations during the process of good agriculture practice (GAP) and crude drug quality control. Six populations could be authenticated successfully by nine single sucleotide polymorphism (SNP) sites and six pairs of diagnostic primers for amplification refractory mutation system (ARMS) were also designed to identify six populations on the basis of single nucleotide polymorphism (SNPs). The remainder two populations (JSR, GGL) with the same sequences could be authenticated by SSH. One population-specific fragment was obtained by SSH and a pair of specific primers (SSH-JB01, SSH-JB02) on the specific sequence was designed to authenticate GGL population from the other populations tested. As the resultants were population-specific, the botanic origins of fifty "Fengdou" drug samples from markets could be classified. It is evident that the combined methods provide a high throughput and reliable approach for identification of D. officinale plants and "Fengdou" drugs.     

Authentication of Curcuma species (Zingiberaceae) based on nuclear 18S rDNA and plastid trnK sequences

Curcuma drugs have been used discriminatingly for invigorating blood circulation, promoting digestion, and as a cholagogic in China. However, there is confusion about the drug's botanical origins and clinical uses because of morphological similarity of Curcuma plants and drugs. Comparative sequencing of the 18S rRNA gene in nuclear ribosomal DNA (rDNA) and trnK gene in chloroplast DNA (cpDNA) was carried out in order to examine interspecies phylogeny and to identify ultimately Curcuma species. A total of a hundred of accessions of eighteen species were analyzed. This resulted in an aligned matrix of 1810 bp for 18S rDNA and 2 800 bp for trnK. 18S rDNA sequence divergence within the ingroup ranged from 0-0.05%, trnK ranged from 0-0.19%. One base transversion-substituted site (from cytosine to thymine) was observed from the upstream of 18S rDNA at nucleotide position 234 in C. kwangsiensis and Japanese population of C. zedoaria which have separated genetic distance to other Curcuma taxa. Two noncoding regions embedded in trnK intron showed higher variability, including nucleotide substitutions, repeat insertion and deletions. Based on consensus of relationship, eighteen major lineages within Curcuma are recognized at the species level. The results suggest that Curcuma is monophyletic with 100% bootstrap support and sister to the genera Hedychium and Zingiber. The trnK sequences showed considerable variations between Curcuma species and thus were revealed as a promising candidate for barcoding of Curcuma species, which provide valuable characters for inferring relationship within species but are insufficient to resolve relationships among closely related taxa.     

川芎的适宜采收期和加工方法

目的研究不同采收期和不同加工方法对川芎有效成分含量的影响。方法按《中国药典》2000年版方法分别测定了不同产地、3个采收期和6种干燥加工方法川芎中水分、挥发油的含量,HPLC法测定了阿魏酸的含量,酸性染料比色法测定了总生物碱的含量。结果5月10日~30日,挥发油的含量随采收期的延迟而降低,阿魏酸含量则明显增加;总生物碱含量显著增加。挥发油的含量以水洗后晒干法损失最大,其他方法差异不明显;阿魏酸以微波干燥的含量最高,远红外干燥法的次之;总生物碱以远红外和农户烘干法的含量最高。结论川芎最适宜的采收期以每年5月20日(约农历小满)后10 d为宜;加工方法以产地农户烘干法为宜。     

Simultaneous quantification of 12 bioactive components of Ligusticum chuanxiong Hort. by high-performance liquid chromatography

A sensitive and specific HPLC-UV method has been developed, for the first time, to simultaneously quantify 12 bioactive ingredients in Ligusticum chuanxiong Hort. (Rhizoma Chuanxiong). This assay was fully validated in respect to precision, accuracy and sensitivity. This method was successfully applied to quantify twelve ingredients in six different Chuanxiong samples. The results demonstrated significant variations in the total content and quantity of each of the main bioactive compounds in different herbs, indicating that quality control of bioactive ingredients in Chuanxiong is critical to ensure its clinical benefits. This assay can be readily utilized as quality control method for Chuanxiong.     

川芎挥发油的GC-MS指纹图谱研究

目的:建立川芎挥发油的气相色谱-质谱(GC-MS)指纹图谱。方法:采用超临界CO2流体萃取法提取川芎挥发油,用GC-MS联用技术对其进行指纹图谱研究,色谱柱为SGE-30QC3/AC225弹性石英毛细管柱(30m×0.32mm×0.25μm),进样口温度为280℃,程序升温,载气为氦气,进样量为1μL,分流比为10:1;采用电子轰击离子源(EI),离子源温度为200℃,接口温度为250℃,检测电压为0.8kV,质量扫描范围为30～400amu;并采用"中药指纹图谱计算机辅助相似度评价软件"计算相似度。结果:本方法有较好的重复性、精密度和稳定性(RSD均<3%);川芎挥发油主要含有α-蒎烯、胡萝卜烯醇、川芎内酯、藁本内酯、棕榈酸,这5种成分构成了川芎挥发油GC-MS特征指纹图谱;10批川芎挥发油的相似度均>0.92。结论:本研究可为川芎的质量控制提供依据。     

川芎RP-HPLC指纹图谱的建立及其质量研究

目的:用高效液相色谱法建立川芎的指纹图谱分析方法,控制川芎药材的质量。方法:采用梯度洗脱的方法进行色谱分离,使用“计算机辅助相似度评价软件”进行数据处理,对不同批药材指纹图谱的相似度进行比较分析。结果:共有10个色谱峰(RSD小于3％,n=10),不同批的川芎药材的指纹图谱相似度较好。结论:采用HPLC方法控制药材的指纹图谱,方法重现性好,用于川芎的质量评价切实可行,可靠、简便,为提高川芎质量控制标准提供参考。不同批的川芎药材化学组成相似,其相对比例较稳定。     

Intersimple sequence repeats (ISSR) molecular fingerprinting markers for authenticating populations of Dendrobium officinale Kimura et Migo

Intersimple sequence repeats (ISSR) molecular fingerprinting markers have been employed to authenticate eight populations of Dendrobium officinale using 10 primers selected from 76 ISSR primers. A total of 127 DNA fragments were amplified, of which 115 were polymorphic (90.5% of all bands). Sixteen specific authentication markers have been found. To enhance the efficiency of authentication, ISSR fingerprinting codes have been constructed using six polymorphic bands for authenticating D. officinale populations. Eight wild populations of D. officinale have been authenticated accurately using ISSR.     

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.     

Rapid detection of Panax ginseng by loop-mediated isothermal amplification and its application to authentication of Ginseng

We have developed a novel method called loop-mediated isothermal amplification (LAMP) to detect Panax ginseng, the botanical source of Ginseng (Ginseng Radix), and to distinguish P. ginseng from Panax japonicus. Six allele-specific primers (two outer primers, two inner primers, and two loop primers) were designed based on the 18S ribosomal RNA gene sequence of P. ginseng, and LAMP was performed using those primers and total DNA extracted from P. ginseng as template. Amplifications were observed from approximately 30 min onwards at DNA concentrations of 0.5 to 10.0 ng. The presence of loop primers shortened the reaction time considerably. In contrast, in the reactions using total DNA from P. japonicus as template, no amplifications were observed. LAMP also enabled us to distinguish Ginseng from Japanese Ginseng (Panacis Japonici Rhizoma). LAMP was proven to be a rapid, highly sensitive, and specific method for the detection of P. ginseng and Ginseng.     

Phylogenetic relationship in the genus Panax: inferred from chloroplast trnK gene and nuclear 18S rRNA gene sequences

Chloroplast trnK gene and nuclear 18S rRNA gene sequences of 13 Panax taxa, collected mainly from Sino-Japanese floristic region, were investigated in order to construct phylogenetic relationship and to assist taxonomic delimitation within this genus. The length of trnK gene sequence varied from 2537 bp to 2573 bp according to the taxa, whereas matK gene sequences, embedded in the intron of trnK gene, were of 1512 bp in all taxa. Species-specific trnK/ matK sequence provided much insight into phylogeny and taxonomy of this genus. 18S rRNA gene sequences were of 1808 or 1809 bps in length, only 9 types of 18S rRNA sequences were observed among 13 taxa. Parsimony and neighbor-joining analyses of the combined data sets of trnK-18S rRNA gene sequences yielded a well-resolved phylogeny within genus Panax, where three main clades were indicated. P. pseudoginseng and P. stipuleanatus formed a sister group located at a basal position in the phylogenetic tree, which suggested the relatively primitive position of these two species. Monophyly of P. ginseng, P. japonicus (Japan) and P. quinquefolius, which are distributed in northern parts of Asia or America, was well supported (Northern Clade). The remaining taxa distributed in southern parts of Asia formed a relatively large clade (Southern Clade). The taxonomic debated taxa traditionally treated as subspecies or varieties of P. japonicus or P. pseudoginseng showed various nucleotide sequences, but all fell into one cluster. It might suggest these taxa are differentiated from a common ancestor and are in a period of high variation, which is revealed not only on morphological appearance, but also on molecular divergence. By comparing trnK and 18S rRNA gene sequences among 13 Panax taxa, a set of valuable molecular evidences for identification of Ginseng drugs was obtained.