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Identifying Chinese species of Gammarus(Crustacea:Amphipoda) using dna barcoding

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Current Zoology 2009年第2期55卷 158-164页

作者： Zhong-e HOU Zhu LI Shu-qiang LI Institute of Zoology Chinese Academy of Sciences Beijing 100101 China Beijing Museum of Natural History Beijing 100050 China

Using a standard cytochrome c oxidase I sequence,dna barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of dna barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species,Gammarus lacustris,was 3.5%,and mean interspecific divergence reached 21.9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values,and likely indicated the presence of cryptic species. Although dna barcoding is effective,future identification of species of Gammarus should incorporate dna barcoding and morphological detection.

关键词： Gammarus Cytochrome c oxidase I dna barcoding Cryptic species Taxonomy

Phylogenetic Analysis of Brine Shrimp (Artemia) in China Using dna barcoding

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Genomics, Proteomics & Bioinformatics 2008年第3期6卷 155-162页

作者： Weiwei Wang Qibin Luo Haiyan Guo Peter Bossier Gilbert Van Stappen Patrick Sorgeloos Naihong Xin Qishi Sun Songnian Hu Jun Yu Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310008 China School of Traditional Chinese Materia Medica Shenyang Pharmaceutical University Shenyang 110016 China Laboratory of Aquaculture ＆ Artemia Reference Center Ghent University B-9000 Ghent Belgium Salt Research Institute Tianjin 300450 China.

dna barcoding is a powerful approach for characterizing species of organisms, especially those with almost identical morphological features, thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study, we chose a 648-bp segment of the mitochondrial gene, cytochrome c oxidase subunit 1 （COI）, as a standard barcode region to establish phylogenetic relationships among brine shrimp （Artemia） species from major habitats around the world and further focused on the biodiversity of Artemia species in China, especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000 m showed clear differences from other Artemia populations in China. We also observed two consistent amino acid changes, 153A/V and 183L/F, in the COI gene between the high and low altitude species in China. Moreover, indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau, demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations.

关键词： Artemia dna barcoding molecular phylogeny Tibetan Plateau

Identification of Common Edible and Medicinal Mushrooms by dna barcoding

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World Journal of Traditional Chinese Medicine 2016年第3期2卷 10-16页

作者： Yan-Yan Su Huan Tang Xi-Wen Li Wei Sun Zeng-Hua Chen Li Xiang Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Huaibei Normal University Beijing Qianjunfang Academy of Sciences

Objective:To identify common edible and medicinal mushrooms using the internal transcribed spacer(ITS) ***:A total of eighty-five samples belonging to forty-three species were used in this *** regions were amplified and *** ITS regions were analyzed using BLAST and MEGA 5.10 ***:Forty species were identified correctly via BLAST method whereas forty-one species were distinguished via Neighbor joining(NJ)*** the species could be distinguished by BLAST combined with NJ tree and ITS sequence ***:Forty-three common species of edible and medicinal mushrooms were effectively identified using dna barcoding technology based on ITS region.

关键词： Edible mushroom Medicinal mushroom ITS dna barcoding

Identification of Kalidium species(Chenopodiaceae)by dna barcoding

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Research in Cold and Arid Regions 2017年第1期9卷 89-96页

作者： XiaoHui Liang YuXia Wu State Key Laboratory of Grassland Agro-Ecosystem School of Life SciencesLanzhou UniversityLanzhouGansu 730000China

dna barcoding is an increasingly prevalent molecular biological technology which uses a short and conserved dna fragment to facilitate rapid and accurate species identification. Kalidium species are distributed in saline soil habitat throughout Southeast Europe and Northwest Asia, and used mainly as forage grass in China. The discrimination of Ka-lidium species was based only on morphology-based identification systems and limited to recognized species. Here, we tested four dna candidate loci, one nuclear locus （ITS, internal transcribed spacer） and three plastid loci （rbcL9 matK and ycflb）, to select potential dna barcodes for identifying different Kalidium species. Results showed that the best dna barcode was ITS locus, which displayed the highest species discrimination rate （100%）, followed by matK （33.3%）,ycflb （16.7%）, and rbcL （16.7%）. Meanwhile, four loci clearly identified the variant species, Kalidium cuspidatum （Ung.-Stemb.） ***.A. J. Li,as a single species in Kalidium.

关键词： dna barcoding Kalidium species identification

Phylogenetic Analysis of Brine Shrimp (Artemia) in China Using dna barcoding

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Genomics,Proteomics & Bioinformatics 2008年第Z1期 155-162页

作者： Peter Bossier Gilbert Van Stappen Patrick Sorgeloos Laboratory of Aquaculture & Artemia Reference Center Ghent University

dna barcoding is a powerful approach for characterizing species of organisms,especially those with almost identical morphological features,thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study,we chose a 648-bp segment of the mitochondrial gene,cytochrome c oxidase subunit 1 (COI),as a standard barcode region to establish phylogenetic relation-ships among brine shrimp (Artemia) species from major habitats around the world and further focused on the biodiversity of Artemia species in China,especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000 m showed clear differences from other Artemia pop-ulations in China. We also observed two consistent amino acid changes,153A/V and 183L/F,in the COI gene between the high and low altitude species in China. Moreover,indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau,demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations.

关键词： Artemia dna barcoding molecular phylogeny Tibetan Plateau

dna barcoding database for Chinese Pharmacopoeia

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DNA barcoding database for Chinese Pharmacopoeia

dna barcoding the Polygonaceae in Chinese pharmacopoeia

第一届《药学学报》药学前沿论坛暨2015年中国药学会中药与天然药物专业委员会会议

作者：姚辉 SONG Jing-yuan SHI Lin-chun HAN Jian-ping SUN Wei CHEN Shi-lin Institute of Medicinal Plant Development Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences

In recent years,traditional identification methods(botanical source and morphological identification,microscopic identification,and physiochemical identification) have been unable to meet the demands of rapid development in China’s pharmaceutical *** barcoding technology emerged in 2003 and revolutionized the available identification *** team proposed and verified that nuclear ITS2 is suitable to identify traditional Chinese medicines(TCMs).A novel identification system for Chinese herbal medicines in Chinese Pharmacopoeia(ChP),which employs dna barcodes,was set up and has been adopted in the latest ChP(2015edition).However,systematic research on identification of TCMs in ChP by using dna barcoding remains *** this study,we established a dna barcoding database for medicinal species in ChP(http://***/en/).One sample of original species and three samples of medicinal materials were available for each Chinese Materia *** of the samples were collected from China,whereas some of them were collected from other countries,such as Japan,Korea,Canada,and the United *** date,six different modules have been implemented in the web server,***,Protocol,Database,News,Documents,and *** the Identification module,nr ITS2 was the core dna barcode for identifying medicinal plants,whereas the psbA-trnH region was a complementary *** was used to identify medicinal *** database provides standard sequences for each medicinal species in ChP,thereby contributing great practical significance to clinical safety in utilization of ***,this system can help prevent illegal drug trade in circulation.

关键词： Chinese Materia Medica dna barcoding ITS2 identification Chinese Pharmacopoeia

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DNA barcoding the Polygonaceae in Chinese pharmacopoeia

dna barcoding Of Coleoidea(Mollusca:Cephalopoda) From Chinese Waters

中华中医药学会第九届中药鉴定学术会议

作者： Jingyuan Song,Shilin Chen*,Hui Yao,Yulin Lin,Ying Li,Xiwen Li,Qiong Wu,Xiaocheng Jia,Jianping Han,Fengmei Suo,Linchun Shi,Xinye Ma (Institute of Medicinal Plant Development,Chinese Academy of Medical Sciences,Beijing 100193,PR China)

dna barcoding is a short fragment of the genome and species identification is completed by using dna barcoding, particularly when diagnostic morphological characteristics are *** Polygonaceae offers medicinal products(e.g. Rheum officinale Baillon and Fallopia multiflora(Thunberg) Haraldson),grain(Fagopyrum esculentum Moench,buckwheat), and edible vegetables(*** acetosa *** Rheum raponticum L.).The present study identifies,for the first time,ten species of Polygonaceae in Chinese Pharmacopoeia and eight other species of Polygonaceae by dna barcoding technique. We compared eight dna barcoding candidate sequences in Polygonaceae through PCR amplification with universal primers and reaction *** results indicated that the chloroplast trnH-psbA intergenic spacer can distinguish eighteen species of Polygonaceae,while the chloroplast rbcL gene combined with the chloroplast rpoCl gene or with the nuclear ribosomal internal transcribed spacer can also distinguish *** demonstrate dna barcoding is an efficient and universal identification method for the Polygonaceae in Chinese Pharmacopoeia.

关键词： dna barcoding Polygonaceae identification

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DNA Barcoding Of Coleoidea(Mollusca:Cephalopoda) From Chines...

Identification and quality analysis of Panax notoginseng and Panax vietnamensis *** through integrated dna barcoding and HPLC

中国动物学会·中国海洋湖沼学会贝类学分会第九次会员代表大会暨第十五次学术讨论会

作者： Lina Dai Xiaodong Zheng Lingfeng Kong Qi Li~* Fisheries College,Ocean University of China,Qingdao 266003

Cephalopoda is the third largest molluscan class and comprises more than 800 identified species,of which about 125 species have been recorded in Chinese *** extant cephalopods can be subdivided into two subclasses:Nautiloidea and Coleoidea. Members of Coleoidea are economically trawled fisheries targets and are common in fisher *** species identification and knowledge about distribution of this subclass help provide better informed conservation *** morphometry has been successfully employed to identify differences between subspecies or species in most coleoids,some coleoids are difficult to distinguish with traditional morphological identification owing to the existence of closely related *** a useful tool for rapid species assignment,dna barcoding can offer significant potential for coleoid identification.

关键词： Coleoidea dna barcoding cryptic diversity COI 16S rRNA

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Chinese Herbal Medicines 2018年第2期10卷 177-183页

作者： Juan Yang Lin-lin Dong Guang-fei Wei Hao-yu Hu Guang-wei Zhu Jie Zhang Shi-lin then Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine Institute of Chinese Materia MedicaChina Academy of ChineseMedical SciencesNo.16 NanxiaojieDongzhimennei Ave.Beijing 100700China

Objective：Root or rhizome of Panax notoginseng（Sanqi）is known for its eutherapeutic *** vietnamensis ***,called Yesanqi or Yuenan sanqi by local residents,is also commercially *** are similar in morphology,leading to serious safety problems in clinical *** is necessary to find the rapid and efficient methods to identify ***：*** and *** *** were identified by dna barcoding based on the ITS2 *** R1 and ginsenosides（Rb1,Rg1,Re,Rd,Rc,and Rb2）were analyzed in the roots,fibrils,stems,leaves,and flowers of *** and *** *** using high-performance liquid chromatography（HPLC）.Results：*** and *** *** were separated into branches of divergent clusters,and *** *** and Panax vietnamensis were clustered into a clade with 98%similarity according to dna barcoding *** chemical compositions of *** and *** *** were similar in roots;while their compositions and contents of notoginsenoside R1 and ginsenosides in flowers,leaves,stems,and fibrils were ***：ITS2 is a rapid and efficient method to identify *** and *** *** analysis indicated that pharmacological action might be different between *** and *** ***.

关键词： dna barcoding HPLC identification Panax notoginseng(Burk.)F. H. Chen