[Objectives] To identify ITS2 barcode of Lablab Semen Album and its adulterants,and provide a new method for the identification of Lablab Semen Album. [Methods] The ITS2 sequence was amplified by PCR and sequenced bi-...[Objectives] To identify ITS2 barcode of Lablab Semen Album and its adulterants,and provide a new method for the identification of Lablab Semen Album. [Methods] The ITS2 sequence was amplified by PCR and sequenced bi-directionally. After splicing by Codon Code Aligner,the data were processed with the aid MEGA software to construct the cluster dendrogram( neighbor-joining,NJ tree). [Results]The ITS2 sequence of Lablab Semen Album had length of 218 bp; the constructed cluster dendrogram indicated that all species were monophyletic and could be distinguished from other species. [Conclusions] The ITS2 barcode can be used for rapid identification of Lablab Semen Album and its adulterants and this experiment further verified that DNA barcode technology is effective in identification of traditional Chinese medicines.展开更多
Objective To select a more suitable DNA barcode to identify the species in Artemisia L. Methods ITS, ITS2, and three other major universal barcode candidates（mat K, rbc L, and psb A-trn H） were evaluated in the iden...Objective To select a more suitable DNA barcode to identify the species in Artemisia L. Methods ITS, ITS2, and three other major universal barcode candidates（mat K, rbc L, and psb A-trn H） were evaluated in the identification efficiency using a total of 1433 sequences downloaded from Gen Bank representing 343 species in Artemisia L. ITS and ITS2 were evaluated in the PCR and sequencing rate, sequencing peak quality（Q value）, and misread rate. One hundred and twelve A. annua samples were collected from 11 populations across over China, which were amplified with universal primers on the ITS and ITS2 regions. Results ITS and ITS2 shared a higher identification efficiency and exhibited 71.43% and 64.11% detectability at the species level, respectively. The Q values of ITS and ITS2 showed that the direct PCR sequencing data were reliable for the ITS2 region and ITS exhibited poor sequencing trace quality. In certain sites, the ITS sequences exhibited reading ambiguities and errors, indicating that the misread and deletion sites in the ITS region would incorrectly inflate the identification ratio. Conclusion ITS2 is a suitable barcode for identification of species in Artemisia L., which enlarges the optimal range of divergence levels for taxonomic inferences using ITS2 sequences.展开更多
To ensure the safety of medications,it is vital to accurately authenticate species of the Apocynaceae family,which is rich in poisonous medicinal plants.We identified Apocynaceae species by using nuclear internal tran...To ensure the safety of medications,it is vital to accurately authenticate species of the Apocynaceae family,which is rich in poisonous medicinal plants.We identified Apocynaceae species by using nuclear internal transcribed spacer 2(ITS2)and psb Atrn H based on experimental data.The identification ability of ITS2 and psb A-trn H was assessed using specific genetic divergence,BLAST1,and neighbor-joining trees.For DNA barcoding,ITS2 and psb A-trn H regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified.The PCR amplification for ITS2 and psb A-trn H sequences was 100%.The sequencing success rates for ITS2 and psb A-trn H sequences were 81%and 61%,respectively.Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psb A-trn H region were downloaded from Gen Bank.Moreover,the analysis showed that the interspecific divergence of Apocynaceae species was greater than its intra-specific variations.The results indicated that,using the BLAST1 method,ITS2 showed a high identification efficiency of 97%and 100%of the samples at the species and genus levels,respectively,via BLAST1,and psb A-trn H successfully identified 95%and 100%of the samples at the species and genus levels,respectively.The barcode combination of ITS2/psb A-trn H successfully identified 98%and 100%of samples at the species and genus levels,respectively.Subsequently,the neighbor joining tree method also showed that barcode ITS2 and psb A-trn H could distinguish among the species within the Apocynaceae family.ITS2 is a core barcode and psb A-trn H is a supplementary barcode for identifying species in the Apocynaceae family.These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.展开更多
本研究通过对拟澳洲赤眼蜂 Trichogramma confusum、甘蓝夜蛾赤眼蜂 T. brassicae、广赤眼蜂 T.evanescens、食胚赤眼蜂 T. embryophagum,及松毛虫赤眼蜂 T. dendrolimi的 6个地理种群的 r DNA- ITS2进行克隆测序 ,又运用软件 DNAStar的...本研究通过对拟澳洲赤眼蜂 Trichogramma confusum、甘蓝夜蛾赤眼蜂 T. brassicae、广赤眼蜂 T.evanescens、食胚赤眼蜂 T. embryophagum,及松毛虫赤眼蜂 T. dendrolimi的 6个地理种群的 r DNA- ITS2进行克隆测序 ,又运用软件 DNAStar的 Meg Align程序对不同赤眼蜂属间、赤眼蜂属种间、同种不同地理种群之间以及同一赤眼蜂个体不同拷贝之间的 ITS2序列的遗传分歧及相似性进行了分析。结果表明 :赤眼蜂属与外群 ITS2序列的遗传相似性很低、赤眼蜂属内不同种之间 ITS2序列保守性适中、种内或不同地理种群之间以及同一个体不同 ITS2拷贝间非常保守。说明展开更多
柳树具观赏、生物修复、生物能源等多种功能,对其开展DNA条形码评估在种质资源保护和利用方面具有非常重要的应用价值。通过对柳树样品进行ITS、ITS2、matK、rbcL和rpoC1片段扩增和测序,结合GenBank数据,共获得柳树22个种,63份样品共计...柳树具观赏、生物修复、生物能源等多种功能,对其开展DNA条形码评估在种质资源保护和利用方面具有非常重要的应用价值。通过对柳树样品进行ITS、ITS2、matK、rbcL和rpoC1片段扩增和测序,结合GenBank数据,共获得柳树22个种,63份样品共计396条序列。比较了5个DNA片段的通用性、序列特征、种内和种间变异,并基于Best Match(BM)、Best Close Match(BCM)、BLAST及Neighbor Joining(NJ)4种方法评估DNA条形码在柳树中的鉴定能力。结果表明,5个DNA条形码中,ITS在柳树种扩增效率和测序成功率高,种内和种间遗传变异明显,鉴定效率最高,建议作为首选的单位点DNA条形码;3个条形码组合中,ITS+ITS2+rbcL鉴定成功率最高,为78.16%,4个DNA条形码组合中,ITS+ITS2+matK+rbcL物种鉴别成功率最高,为88.28%,建议ITS+ITS2+matK+rbcL作为柳树分子鉴定最优条形码组合。展开更多
DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for the...DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.展开更多
基金Supported by Key Program for Sci-tech Plan of Hunan Province Science and Technology Department(2014SK2001)Sci-tech Project for Food and Drug Safety of Hunan Food and Drug Administration(Xiang Shi Yao Ke R201612)
文摘[Objectives] To identify ITS2 barcode of Lablab Semen Album and its adulterants,and provide a new method for the identification of Lablab Semen Album. [Methods] The ITS2 sequence was amplified by PCR and sequenced bi-directionally. After splicing by Codon Code Aligner,the data were processed with the aid MEGA software to construct the cluster dendrogram( neighbor-joining,NJ tree). [Results]The ITS2 sequence of Lablab Semen Album had length of 218 bp; the constructed cluster dendrogram indicated that all species were monophyletic and could be distinguished from other species. [Conclusions] The ITS2 barcode can be used for rapid identification of Lablab Semen Album and its adulterants and this experiment further verified that DNA barcode technology is effective in identification of traditional Chinese medicines.
基金National Natural Science Foundation of China(No.81473303)Major Scientific and Technological Special Project for "Significant New Drugs Creation"(No.2014ZX09304307001)
文摘Objective To select a more suitable DNA barcode to identify the species in Artemisia L. Methods ITS, ITS2, and three other major universal barcode candidates（mat K, rbc L, and psb A-trn H） were evaluated in the identification efficiency using a total of 1433 sequences downloaded from Gen Bank representing 343 species in Artemisia L. ITS and ITS2 were evaluated in the PCR and sequencing rate, sequencing peak quality（Q value）, and misread rate. One hundred and twelve A. annua samples were collected from 11 populations across over China, which were amplified with universal primers on the ITS and ITS2 regions. Results ITS and ITS2 shared a higher identification efficiency and exhibited 71.43% and 64.11% detectability at the species level, respectively. The Q values of ITS and ITS2 showed that the direct PCR sequencing data were reliable for the ITS2 region and ITS exhibited poor sequencing trace quality. In certain sites, the ITS sequences exhibited reading ambiguities and errors, indicating that the misread and deletion sites in the ITS region would incorrectly inflate the identification ratio. Conclusion ITS2 is a suitable barcode for identification of species in Artemisia L., which enlarges the optimal range of divergence levels for taxonomic inferences using ITS2 sequences.
基金supported by the CAMS Initiative for Innovative Medicine(No.2016-12M-2-003)the Special Subsidies for Public Health Services of TCM("The National Survey of TCM Resources",DSS,MOF,No.66/2017)。
文摘To ensure the safety of medications,it is vital to accurately authenticate species of the Apocynaceae family,which is rich in poisonous medicinal plants.We identified Apocynaceae species by using nuclear internal transcribed spacer 2(ITS2)and psb Atrn H based on experimental data.The identification ability of ITS2 and psb A-trn H was assessed using specific genetic divergence,BLAST1,and neighbor-joining trees.For DNA barcoding,ITS2 and psb A-trn H regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified.The PCR amplification for ITS2 and psb A-trn H sequences was 100%.The sequencing success rates for ITS2 and psb A-trn H sequences were 81%and 61%,respectively.Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psb A-trn H region were downloaded from Gen Bank.Moreover,the analysis showed that the interspecific divergence of Apocynaceae species was greater than its intra-specific variations.The results indicated that,using the BLAST1 method,ITS2 showed a high identification efficiency of 97%and 100%of the samples at the species and genus levels,respectively,via BLAST1,and psb A-trn H successfully identified 95%and 100%of the samples at the species and genus levels,respectively.The barcode combination of ITS2/psb A-trn H successfully identified 98%and 100%of samples at the species and genus levels,respectively.Subsequently,the neighbor joining tree method also showed that barcode ITS2 and psb A-trn H could distinguish among the species within the Apocynaceae family.ITS2 is a core barcode and psb A-trn H is a supplementary barcode for identifying species in the Apocynaceae family.These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.
文摘本研究通过对拟澳洲赤眼蜂 Trichogramma confusum、甘蓝夜蛾赤眼蜂 T. brassicae、广赤眼蜂 T.evanescens、食胚赤眼蜂 T. embryophagum,及松毛虫赤眼蜂 T. dendrolimi的 6个地理种群的 r DNA- ITS2进行克隆测序 ,又运用软件 DNAStar的 Meg Align程序对不同赤眼蜂属间、赤眼蜂属种间、同种不同地理种群之间以及同一赤眼蜂个体不同拷贝之间的 ITS2序列的遗传分歧及相似性进行了分析。结果表明 :赤眼蜂属与外群 ITS2序列的遗传相似性很低、赤眼蜂属内不同种之间 ITS2序列保守性适中、种内或不同地理种群之间以及同一个体不同 ITS2拷贝间非常保守。说明
文摘柳树具观赏、生物修复、生物能源等多种功能,对其开展DNA条形码评估在种质资源保护和利用方面具有非常重要的应用价值。通过对柳树样品进行ITS、ITS2、matK、rbcL和rpoC1片段扩增和测序,结合GenBank数据,共获得柳树22个种,63份样品共计396条序列。比较了5个DNA片段的通用性、序列特征、种内和种间变异,并基于Best Match(BM)、Best Close Match(BCM)、BLAST及Neighbor Joining(NJ)4种方法评估DNA条形码在柳树中的鉴定能力。结果表明,5个DNA条形码中,ITS在柳树种扩增效率和测序成功率高,种内和种间遗传变异明显,鉴定效率最高,建议作为首选的单位点DNA条形码;3个条形码组合中,ITS+ITS2+rbcL鉴定成功率最高,为78.16%,4个DNA条形码组合中,ITS+ITS2+matK+rbcL物种鉴别成功率最高,为88.28%,建议ITS+ITS2+matK+rbcL作为柳树分子鉴定最优条形码组合。
基金supported by the National International Cooperation Program (Grant No. 2007DFA30990)Special Scientific Research Project of Health Profession (Grant No. 200802043)
文摘DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.
