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.。     

Allele-specific primers for diagnostic PCR authentication of Dendrobium officinale

Based on rDNA ITS sequences of D. officinale and the other 37 species of Dendrobium, a pair of allele-specific diagnostic primers, TP-JB01S and TP-JB01X, were designed to authenticate D. officinale from the other species. Before the diagnostic PCR, the primer pair, P1 and P2, for amplifying the whole ITS region was used to validate template DNA and to obtain the appropriate template DNA for the diagnostic PCR. Diagnostic PCRs were performed using the diagnostic primers with the total DNAs of the original plants as a template. When the annealing temperature was raised to 66 degrees C, only the template DNA of D. officinale could be amplified whereas the diagnostic PCRs of the other Dendrobium species were all negative. The diagnostic PCRs have been repeated many times and have played an important role in authenticating the stems of D. officinale in China. Compared with the authentication method by sequencing DNA fragments, the allele-specific diagnostic PCR is not only simpler and time-saving but also practical and effective.     

曲茎石斛及其近似种鉴别的形态和DNA分子证据

目的　探讨曲茎石斛 (南阳居群 )与同属近似种 :细茎石斛 (南阳居群 )、霍山石斛 (霍山居群 )、铁皮石斛(天台居群 )药材鉴别的形态及DNA分子证据。方法　对曲茎石斛 (南阳居群 )及其近似种的药材进行了外部形态和rDNAITS序列比较。结果　曲茎石斛及其近似种药材的外部形态虽无明显区别 ,但在rDNAITS序列上却存在着显著而稳定的差异。曲茎石斛 (南阳居群 )与铁皮石斛 (天台居群 )的rDNAITS序列的差异最小 ,绝对遗传距离为 7;但与细茎石斛 (南阳居群 )及霍山石斛 (霍山居群 )rDNAITS区的差异较大 ,绝对遗传距离分别为 4 0和 4 2。在rDNAITS区域中 ,作者共挑选了 7个碱基位点用作鉴别曲茎石斛 (南阳居群 )及其近似种的DNA证据。结论　根据药材的形态特征及rDNAITS区碱基序列差异 ,可准确鉴别曲茎石斛及其近似种药材。     

Differentiation of Dendrobium species used as "Huangcao Shihu" by rDNA ITS sequence analysis

The genus Dendrobium Sw. is composed of 74 species and two varieties in China, and 32 species carry the name "Huangcao Shihu" on the herbal medicine market, making the identification of the origin of "Huangcao Shihu" difficult for consumers. Here, the ITS regions were sequenced and evaluated to differentiate the 18 Dendrobium species used as "Huangcao Shihu". Diversity in DNA sequences among various species was found with the inter-specific sequence divergence ranging from 3.2% to 37.9% in ITS1 and 5.0% to 26.6% in ITS2. Moreover, the variations within species were very low, ranging in sequence divergence from 0 to 3.0% in ITS1 and 0 to 4.0% in ITS2. Therefore, these species could be easily distinguished at the DNA level. Furthermore, based on the divergent ITS regions, five pairs of species-specific primers were designed and used for the rapid PCR identification of five Dendrobium species listed in the Chinese Pharmacopoeia.     

Characters of nrDNA ITS region sequences of fruits of Alpinia galanga and their adulterants.

The fruits of Alpinia galanga (L.) Sw. are used as a traditional Chinese medicine; but the dry fruits of A. conchigera, A. suishaensis, A. maclurei and A. polyantha are also used as the medicine in local areas. Because dry fruits of these related plants are similar to those of Alpinia galanga (L.) Sw. in odor, morphological characters and chemical components, and even anatomical characters, it is difficult to identify the medicine. Nuclear ribosomal DNA internal transcribed spacer (ITS) regions of the five taxa were directly sequenced using an automated sequencer. Sequence analysis showed that the ITS 1 ranges from 177 to 178 base pairs (bp), and the ITS 2 from 225 to 234 bp. The size of the 5.8S coding region is 164 bp for all species. Also, the pairwise sequence divergence is higher and some molecular markers were determined. According to these molecular markers, Alpinia galanga (L.) Sw. and the related species can easily be distinguished from each other. Therefore, evidence from nrDNA ITS sequence variation can identify the medicine at the DNA level.     

中药黄草石斛rDNA ITS序列分析

目的　研究黄草石斛ITS片段遗传多样性,分析该片段在黄草药材DNA分子鉴别和石斛属植物系统学研究中的意义。方法　用一对引物进行PCR扩增,扩增产物纯化后用双脱氧终止法(Sangerdideoxy)测序。结果　获得核糖体DNA中ITS和5 8SrDNA完整序列,14个石斛类群的ITS 1与ITS 2序列的长度分别为228-233bp和242-247 bp。石斛种间ITS 1序列的差异百分率为11.79% - 31.58% ,ITS 2序列的差异百分率为10.29% - 25.30% ,金钗石斛种内ITS 1序列的差异百分率为0.87% ,ITS 2序列无差异。石斛各类群与外类群的差异百分率ITS 1序列为23.56% - 36.89% ,ITS 2序列为26.5.2 % - 33.31%。用NJ法根据ITS 1与ITS 2序列数据重建系统发生树。结论　两段序列在石斛种内保守,在种间有较大的差异,与外类群的差异最大,可作为中药黄草石斛分子鉴定的标记,而石斛属的系统发生关系尚须进一步研究     

Molecular analysis of the genus Mitragyna existing in Thailand based on rDNA ITS sequences and its application to identify a narcotic species: Mitragyna speciosa

In Thailand, there are four Mitragyna species; M. speciosa, M. hirsuta, M. diversifolia, and M. rotundifolia. One, M. speciosa, is a narcotic plant and has medicinal importance for its opium-like effect. Since the use of M. speciosa has been forbidden in Thailand, the leaves of M. diversifolia or others are frequently used as substitutes but are not considered as effective. Therefore, accurate authentication of M. speciosa is essential for both medicinal and forensic purposes. The nucleotide sequences of internal transcribed spacers (ITS) and the 5.8S coding region of nuclear ribosomal DNA (rDNA) of the Mitragyna species were analyzed. The whole length of ITS1-5.8S-ITS2 region was 608 bp in M. speciosa, 607 bp in the other species. Nineteen sites of nucleotide substitutions and 3 sites of 1-bp indels were observed, and M. speciosa showed specific sequence differed from the others. Based on the ITS sequences, a distinctive site recognized by a restriction enzyme XmaI in M. speciosa was found and then PCR-restriction fragment length polymorphism (RFLP) analysis was established to differentiate M. speciosa from the others. By the method, a 409-bp PCR fragment of ITS1-5.8S (partial) rDNA region from M. speciosa was cleaved into two fragments of 119 bp and 290 bp while the other species remained undigested. This method provides an effective and accurate identification of M. speciosa.     

DNA microarray for identification of the herb of dendrobium species from Chinese medicinal formulations

A DNA microarray for detecting processed medicinal Dendrobium species (Herba Dendrobii) was constructed by incorporating the ITS1-5.8S-ITS2 sequences of 16 Dendrobium species on a glass slide. Using fluorescence-labeled ITS2 sequences as probes, distinctive signals were obtained for the five medicinal Dendrobium species listed in the Chinese Pharmacopoeia. The established microarray was able to detect the presence of D. nobile in a Chinese medicinal formulation containing nine herbal components.     

Cloning and expression of a novel cDNA encoding a mannose-binding lectin from Dendrobium officinale.

Using RNA extracted from Dendrobium officinale young leaves and primers designed according to the conservative regions of orchidaceae lectins, the full-length cDNA of Dendrobium officinale agglutinin2 (DOA2) was cloned by rapid amplification of cDNA ends (RACE). The full-length cDNA of doa2 was 777 bp and contained a 513 bp open reading frame (ORF) encoding a lectin precursor of 170 amino acids. Through comparative analysis of doa2 gene and its deduced amino acid sequence with those of other orchidaceae species and Amaryllidaceae species, it was found that DOA2 had many common characters of mannose-binding lectin superfamily including three mannose-binding sites. Semi-Quantitative RT-PCR analysis revealed that doa2 mRNA expression was detected in all tested tissues including root, stem and leaf, however, the expression was higher in stem, and lower in leaf. As the doa2 mRNA was detected in all the tested plant tissues, the doa2 was considered to be a constitutively expressed gene. The recombinant protein was expressed in E. coli and purified. Anti-fungal assay showed that DOA2 has anti-fungal activity towards Gibberella zeae. To our knowledge, this is the first report on cDNA cloning of mannose binding lectin from Dendrobium officinale.     

枫斗类石斛rDNA ITS区的全序列数据库及其序列分析鉴别

目的建立枫斗类石斛的rDNA ITS区碱基全序列数据库,利用该数据库对枫斗类石斛待检种进行准确鉴别。方法对枫斗类石斛的rDNA ITS区进行了PCR扩增、测序,运用CLUSTRAL,MEGA等软件以及枫斗类石斛rDNA ITS区全序列数据库对待检种rDNA ITS区进行序列分析鉴别。结果建立了21种枫斗类石斛的rDNA ITS区全序列数据库, 枫斗类石斛在该区的种间差异显著而稳定,转换和颠换总数为11～122,变异位点数为341,信息位点数为195。与外类群植物云南石仙桃间的差异较大,转换和颠换总数为131～161。枫斗类石斛居群间的差异较小,转换和颠换总数为0～6。结论利用枫斗类石斛的全序列数据库及遗传分析软件,通过对待检种rDNA ITS区进行序列测定,可以成功鉴别属于数据库中枫斗类石斛的待检种。     

Authentication of an endangered herb <Emphasis Type="Italic">Changium smyrnioides</Emphasis> from different producing areas based on rDNA ITS sequences and allele-specific PCR

The rDNA ITS region of 18 samples of Changium smyrnioides from 7 areas and of 2 samples of Chuanminshen violaceum were sequenced and analyzed. The amplified ITS region of the samples, including a partial sequence of ITS1 and complete sequences of 5.8S and ITS2, had a total length of 555 bp. After complete alignment, there were 49 variable sites, of which 45 were informative, when gaps were treated as missing data. Samples of C. smyrnioides from different locations could be identified exactly based on the variable sites. The maximum parsimony (MP) and neighbor joining (NJ) tree constructed from the ITS sequences based on Kumar’s two-parameter model showed that the genetic distances of the C. smyrnioides samples from different locations were not always related to their geographical distances. A specific primer set for Allele-specific PCR authentication of C. violaceum from Jurong of Jiangsu was designed based on the SNP in the ITS sequence alignment. C. violaceum from the major genuine producing area in Jurong of Jiangsu could be identified exactly and quickly by Allele-specific PCR.     

花椒及其混淆品的rDNA ITS区序列分析与鉴别

目的研究不同居群的花椒及其混淆品的rDNA ITS区碱基序列的特征及其差异，为花椒的鉴别提供可靠的分子标记。方法运用PCR产物直接测序和克隆测序法对甘肃、陕西、四川、河北等7个花椒居群及3个混淆种的rDNA ITS区(包括ITS1，5.8S，ITS2)碱基序列进行序列测定。结果首次报道花椒ITS区的碱基序列，序列总长度为619-620 bp，长度变异较少，与混淆种长度仅相差4 bp。花椒各居群中，rDNA ITS区碱基序列有15个变异位点、12个信息位点、3个特异性识别位点。与混淆品间的碱基差异则较为显著，多达71个变异位点，有4个花椒特异性识别位点。结论依据花椒ITS区的序列特征可准确鉴别各居群的花椒及其混淆品；亲缘关系密切的花椒居群在地理位置上也非常靠近；rDNA ITS序列特征可作为花椒种内和种间鉴别的有效分子标记。     

Identification of dendrobium species used for herbal medicines based on ribosomal DNA internal transcribed spacer sequence

Stems of genus Dendrobium (Orchidaceae) have been traditionally used as an herbal medicine (Dendrobii Herba) in Eastern Asia. Although demand for Dendrobium is increasing rapidly, wild resources are decreasing due to over-collection. This study aimed to identify plant sources of Dendrobii Herba on the market based on sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. We constructed an ITS1-5.8S-ITS2 sequence database of 196 Dendrobium species, and the database was employed to identify 21 herbal samples. We found that 13 Dendrobium species (D. catenatum, D. cucullatum, D. denudans, D. devonianum, D. eriiflorum, D. hancockii, D. linawianum, D. lituiflorum, D. loddigesii, D. polyanthum, D. primulinum, D. regium, and D. transparens) were possibly used as plant sources of Dendrobii Herba, and unidentified species allied to D. denudans, D. eriiflorum, D. gregulus, or D. hemimelanoglossum were also used as sources. Furthermore, it is clear that D. catenatum is one of the most important sources of Dendrobii Herba (5 out of 21 samples).     

铁皮石斛内生真菌的鉴定及菌株205509的次级代谢产物研究

摘要：目的 鉴定铁皮石斛内生真菌及从中发现活性菌株,探究菌株205509产生的次级代谢产物。 方法 利用分子生物学方法并结合形态特征,对9株铁皮石斛内生真菌进行鉴定;采用琼脂扩散法和MTT法,筛选出次级代谢产物丰富,且具有抑制病原指示菌和人乳腺癌MCF-7细胞系的活性菌株;利用大米固体培养基对活性菌株进行发酵,乙酸乙酯萃取;采用硅胶、反相硅胶、葡聚糖凝胶Sephadex LH-20和HPLC色谱技术进行分离纯化,得到化合物;通过质谱(MS)和核磁共振(1H NMR和13C NMR)等波谱技术并结合文献比对,确定化合物结构。结果 9株铁皮石斛内生真菌分属3个科的3个属,初步判定其中1株为枝顶孢霉属(Acremonium)的一个新种,2株为树粉孢属(Oidiodendron)的一个新种,2株为Acremoniopsis属的未确定种;获得抗菌活性和细胞毒活性较好的菌株205509,并从中分离得到了4个化合物,其中化合物HXW-3浓度为3 μg/mL时对嗜水气单胞菌(Aeromonas hydrophila)、鼠伤寒沙门菌(Salmonella typhimurium)和蜡样芽胞杆菌(Bacillus cereus)表现出抑制活性。结论 铁皮石斛内生真菌物种较新颖,其次级代谢产物具有较好的生理活性,值得进一步研究。     

紫苏属药用植物的rDNA ITS区SNP分子标记与位点特异性PCR鉴别

目的分析单种属——紫苏属各变种间rDNA ITS区的序列以及存在的单核苷酸多态性(SNP)现象，设计出位点特异性PCR引物，用于紫苏属各变种间的分子标记鉴别。方法对紫苏属各变种多个体的rDNA ITS区全序列进行了准确测定，运用Clustral X 1.8，MEGA 3.0进行排序并进行SNP分析，从而设计出鉴别各变种的等位基因位点特异性PCR鉴别引物。结果紫苏属各变种(紫苏、白苏、鸡冠苏和耳齿紫苏等)的rDNA ITS区全序列共有615～618 bp的长度，ITS1为233～235 bp，5.8S为179 bp，ITS2为203～204 bp，GC含量为61.5%～61.9%。从rDNA ITS区碱基变异的整体情况来看，紫苏属各变种间不仅在非编码的转录间隔区ITS1和ITS2内存在非编码区单核苷酸多态性(ncSNP)，而且在保守的5.8S编码区内也存在3个位点的单核苷酸多态性，即编码区SNP(cSNP)，所有的SNP均只具2等位多态性。5.8S区cSNP的出现与产生该变异的变种出现的显著形态差异关联。本文还利用这些SNP位点设计出了鉴别紫苏属各变种的位点特异性PCR引物，无需测序即可对紫苏属的原植物及“苏子”、“苏叶”等药材进行有效准确的分子鉴别。结论紫苏属药用植物rDNA ITS区存在的SNP可用作紫苏属各变种鉴别的分子标记。     

曲茎石斛及其近似种鉴别的形态和DNA分子证据

目的　探讨曲茎石斛(南阳居群)与同属近似种:细茎石斛(南阳居群)、霍山石斛(霍山居群)、铁皮石斛(天台居群)药材鉴别的形态及DNA分子证据。方法　对曲茎石斛(南阳居群)及其近似种的药材进行了外部形态和rDNA ITS序列比较。结果　曲茎石斛及其近似种药材的外部形态虽无明显区别,但在rDNA ITS序列上却存在着显著而稳定的差异。曲茎石斛(南阳居群)与铁皮石斛(天台居群)的rDNA ITS序列的差异最小,绝对遗传距离为7;但与细茎石斛(南阳居群)及霍山石斛(霍山居群)rDNA ITS区的差异较大,绝对遗传距离分别为40和42。在rDNA ITS区域中,作者共挑选了7个碱基位点用作鉴别曲茎石斛(南阳居群)及其近似种的DNA证据。结论　根据药材的形态特征及rDNA ITS区碱基序列差异,可准确鉴别曲茎石斛及其近似种药材。     

中国不同地区蛇床的rDNA ITS序列分析

目的：探讨不同分布区的蛇床Cnidium monnieri的ITS序列变异与其地理分布和化学成分的相关性。方法：设计2对引物,Pf+Pb及P5.8S ITS1+P5.8S ITS2,PCR扩增产物纯化后用银染法或ABI 310测序。结果：得到核糖体DNA中的ITS及5.8S rDNA完全序列,18S和26S rDNA部分序列,共约700 bp。5个地点样品的ITS-1及ITS-2的序列大小分别为210～217 bp和219～224 bp。ITS-1碱基序列的遗传距离0.00～1.93%,ITS-2碱基序列的遗传距离0.46～2.34%,ITS-1较为保守。以NJ法根据ITS-2序列数据重建系统发生树。哈尔滨样品聚为一组,衡水与德州样品和郑州与高淳样品各自聚为一组。结论：ITS-2序列的变异与中国产蛇床的纬度分布相关,而其与蛇床化学型的关系尚需作进一步研究。     

Enzymatic fingerprints of polysaccharides of Dendrobium officinale and their application in identification of Dendrobium species

Enzymatic fingerprinting of polysaccharides from Dendrobium officinale was studied and applied to authenticate Dendrobium species. Results showed that Dendrobium officinale species from Anhui province, Fujian province, Yunnan province, Guangdong province and Guangxi province of China, could be identified by polysaccharide analysis using carbohydrate gel electrophoresis (PACE). However, the fingerprints of Dendrobium officinale from Jiangxi province, Hu'nan province and Wenzhou, Yandangshan and Fuyang in Zhejiang province were very similar. As far as the fingerprints of different Dendrobium species were concerned, the differences between Dendrobium officinale, Dendrobium huoshanense, Dendrobium moniliforme, Dendrobium devonianum, Dendrobium aphyllum, Dendrobium wilsonii and Dendrobium crystallinum were obvious. Moreover, the genetic relationships between different samples were analyzed by using principal component analysis and unweighted pair group method with arithmetic mean cluster analysis. Results suggested that polysaccharide fingerprint analysis by PACE has the potential to become a valuable new method for the identification and control of quality of herbal medicines in future.     

一种安徽产野生铁皮石斛内生真菌的分离鉴定及其组织分布

目的 分离鉴定安徽地区野生铁皮石斛内生真菌,旨在丰富其内生真菌资源种类。 方法 通过组织块法对内生真菌进行分离,运用形态学和分子生物学方法进行鉴定。结果 从中分离得到11株内生真菌,鉴定为5属11种。 结论 铁皮石斛内生真菌种类资源广泛分布,为研究其与宿主石斛共生关系提供理论依据。     

鼠尾草属药用植物及其近缘种的ITS序列分析

采用分子系统学方法分析鼠尾草属药用植物及其近缘种的遗传多样性，为准确进行基源鉴定、阐明本属内的种间关系及发现新的药用资源提供分子证据。本文从野外采集的27个鼠尾草属植物叶片样品中分离提取DNA，PCR扩增ITS区及5.8S rDNA完整序列并测序，采用Mega 3.1软件进行系统学分析。27个鼠尾草样品的ITS及5.8S rDNA区序列全长为612～617 bp，邻接法(neighbor-Joining)构建的系统发生树部分支持了形态学的属下划分，但对部分种的系统位置特别是三叶鼠尾草和黄花鼠尾草两个亚种的处理上与形态学划分存在明显的分歧。序列分析显示5.8S rDNA序列相当保守，而ITS区段则在亚属间差异明显，且原产我国的该属植物与欧美引进种明显具有不同起源。ITS系统树对于亚属和组的处理较为合理，但对组下的划分则表现出了信息量不足，需要其他相关证据的支持。ITS分析支持了丹参组内其他近缘种作为丹参类药材替代资源的合理性，同时也揭示了甘西鼠尾类高山丹参在遗传上与丹参类药材的显著不同。