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Identification of herbal medicinal materials using DNA barcodes 认领 引用 被引量：53
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作者 Ming LI Hui CAO +1 位作者 Paul Pui-Hay BUT Pang-Chui SHAW 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期271-283,共13页
Herbal medicinal materials have been used worldwide for centuries to maintain health and to treat disease. However, adulteration of herbal medicines remains a major concern of users and industry for reasons of safety ... Herbal medicinal materials have been used worldwide for centuries to maintain health and to treat disease. However, adulteration of herbal medicines remains a major concern of users and industry for reasons of safety and efficacy. Identification of herbal medicinal materials by DNA technology has been widely applied, started from the mid-1990s. In recent years, DNA barcoding of global plant species using four standard barcodes （rbcL, matK, trnH-psbA and ITS） has been a major focus in the fields of biodiversity and conservation. These DNA barcodes can also be used as reliable tools to facilitate the identification of herbal medicinal materials for the safe use of herbs, quality control, and forensic investigation. Many studies have applied these DNA barcodes for the identification of herbal medicinal species and their adulterants. The present article reviews efforts in the identification of herbal medicinal materials using the standard DNA barcodes and other DNA sequence-based markers. 展开更多
关键词 DNA barcode herbal medicinal materials internal transcribed spacer （ITS） marK molecular identification rbcL trnH-psbA.
Efficiency of DNA barcodes for species delimitation:A case in Pterygiella Oliv.(Orobanchaceae) 认领 引用 被引量：4
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作者 Li-Na DONG Alexandra H. WORTLEY +2 位作者 Hong WANG De-Zhu LI Lu LU 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期189-202,共14页
DNA barcoding is becoming an increasingly popular means to identify species. The obscure discrimination in the genus Pterygiella calls into question the re-assessment of the criterion for species delimitation. We coll... DNA barcoding is becoming an increasingly popular means to identify species. The obscure discrimination in the genus Pterygiella calls into question the re-assessment of the criterion for species delimitation. We collected 20 individuals, representing all five described species of this genus in its distributional range. The aim was to use three proposed barcode DNA regions （rbcL, matK, and ITS） to diagnose Pterygiella species, and ex- amine which barcode is more suitable for discerning the congeneric and related species. The results showed that the core barcodes matK and rbcL were comparatively less effective. However, the ITS region, especially ITS-1 and ITS-2, successfully identified all species in the genus. Furthermore, the secondary structure of ITS-2 RNA, especially compensatory base changes, appears complementary to classical primary sequence analysis for DNA barcoding. 展开更多
关键词 compensatory base changes （CBCs） DNA barcode ITS-2 non-monophyletic species Pterygiella Oliv. secondary structure.
Plant DNA barcodes: Applications today and in the future 认领 引用 被引量：17
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作者 W. John Kress 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2017年第4期291-307,共17页
DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, marK, trnH- psbA, and ITS2, h... DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, marK, trnH- psbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection. Forensic investigators have also applied these plant DNA barcodes in the regulatory areas of traffic in endangered species and monitoring commercial products, such as foods and herbal supplements. Major challenges ahead will focus on building the global plant DNA barcode library and adopting genomic sequencing technologies for a more efficient and cost- effective workflow in applying these genetic identification markers to additional fields of biological and commercial endeavors. 展开更多
关键词 conservation DNA barcode library forensics forest dynamics plots functional traits genomics identification,metabarcoding next-generation sequencing phylogeny.
Application of DNA Barcode Technology to the Identification of Exotic Mosquitoes at Ningbo Port 认领 引用 被引量：1
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作者 吴薇 王刚 +2 位作者 徐翮飞 赵彤言 夏才军 《Agricultural Science & Technology》 CAS 2017年第12期2454-2457,共4页
[Objective] The study aimed to solve the problem of morphological identi- fication difficulties and propose solutions for the identification of foreign mosquitoes that are difficult to identify. [Method] Based on the ... [Objective] The study aimed to solve the problem of morphological identi- fication difficulties and propose solutions for the identification of foreign mosquitoes that are difficult to identify. [Method] Based on the sequencing, alignment and anal- ysis of COl gene fragment, DNA barcode technology was used to identify 7 exotic mosquitoes, and the phylogenetic analysis was performed using MEGA6.0 and DNASTAR software. Then the morphological characteristics of the mosquitoes were reviewed. [Result[ These mosquitoes were Armigeres subalbatus, Culex gefidus, Anopheles gambiae, and Culiseta incidens. [Conclusion] DNA barcode technology is a useful supplement to the morphological classification method of mosquitoes. 展开更多
关键词 Mosquito： DNA barcode Entry
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Crane flies(Diptera: Tipuloidea: Tipulidae) from Dayaoshan National Nature Reserve, China and analysis of DNA barcodes, with description of one new species in the genus Indotipula 认领 引用
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作者 门秋雷 薛国喜 +1 位作者 孙梦溦 孙卓 《Entomotaxonomia》 CSCD 2017年第4期251-264,共14页
This paper reports six species of crane flies from Dayaoshan National Nature Reserve, Guangxi Zhuang Autonomous Region, China, including one new species, Indotipula jinxiuensis sp. nov. The males of Pselliophora guang... This paper reports six species of crane flies from Dayaoshan National Nature Reserve, Guangxi Zhuang Autonomous Region, China, including one new species, Indotipula jinxiuensis sp. nov. The males of Pselliophora guangxiensis Yang Yang, 1988 and Holorusia basiflava Yang Yang, 1993 and female of Pselliophora xanthopimplina Enderlein, 1921 are redescribed and illustrated with new morphological characters. The females of P. guangxiensis and H. basiflava are described and illustrated for the first time. A key for separating known species of Indotipula Edwards, 1931 from China is provided. DNA barcodes of all species in this study are provided and analyzed. 展开更多
关键词 Nematocera DNA barcodes redescription taxonomy key
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Three newly recorded species of Acerentomata(Hexapoda:Protura) from China,with analysis of DNA barcodes 认领 引用
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作者 卜云 钱昌元 栾云霞 《Entomotaxonomia》 CSCD 2017年第1期1-14,共14页
Three newly recorded species in the order Acerentomata in Protura from China are described:Filientomon duodecimsetosum Nakamura,2004,Verrucoentomon anatoli Shrubovych & Bernard,2012 and Verrucoentomon louisanne Sh... Three newly recorded species in the order Acerentomata in Protura from China are described:Filientomon duodecimsetosum Nakamura,2004,Verrucoentomon anatoli Shrubovych & Bernard,2012 and Verrucoentomon louisanne Shrubovych & Bernard,2012.The important morphological characters of Chinese specimens are described in detail.An updated key to Chinese Verrucoentomon species is provided.In addition,their DNA barcodes are sequenced and analyzed. 展开更多
关键词 proturans key DNA barcodes maxillary gland taxonomy
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Application of DNA barcodes in Hedyotis L.(Spermacoceae,Rubiaceae) 认领 引用 被引量：5
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作者 Xing GUO Mark R SIMMONS +2 位作者 Paul Pui-Hay BUT Pang-Chui SHAW Rui-Jiang WANG 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期203-212,共10页
The potential application of DNA barcodes of plastid （matK, trnH-psbA, petD, and rbcL） and nuclear （internal transcribed spacer （ITS） of rDNA） DNA regions was investigated for 25 Hedyotis taxa. The ITS showed th... The potential application of DNA barcodes of plastid （matK, trnH-psbA, petD, and rbcL） and nuclear （internal transcribed spacer （ITS） of rDNA） DNA regions was investigated for 25 Hedyotis taxa. The ITS showed the best species discrimination by resolving 23 of the species as exclusive lineages with no shared alleles between any of the 24 distinct species （H. assimilis and/-/, mellii are not supported as distinct species based on our molecular and morphological data）. Conversely, rbcL performed the worst and only resolved 10 of the species as exclusive lineages, and 10 species with shared alleles. Using ITS has the advantage of high PCR amplification success and it provides good intra- and interspecific variation distribution patterns. The most powerful plastid markers were petD and trnH-psbA, but we could amplify and sequence trnH-psbA for only 83% of the accessions sampled. Combination of ITS and petD performed extremely well, with all 24 of the distinct species resolved as exclusive lineages and no shared alleles between any of the distinct species. We therefore recommend ITS, or a combination of ITS andpetD, as the standard DNA barcode in Hedyotis, but acknowledge that there are no shared alleles between distinct species for matK and rbcL combined. 展开更多
关键词 DNA barcode Hedyotis molecular identification Rubiaceae taxonomy.
Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes 认领 引用 被引量：9
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作者 XIE Lei WANG Ying Wei +3 位作者 GUAN Shan Yue XIE Li Jing LONG Xin SUN Cheng Ye 《Biomedical and Environmental Sciences》 SCIE CAS CSCD 2014年第10期794-806,共13页
Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the perfo... Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes （motK, rbcL, and ITS） were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment （PWG） distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method. 展开更多
关键词 Poisonous plants DNA barcoding metK rbcL iTS
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Applications of Three DNA Barcodes in Assorting Intertidal Red Macroalgal Flora in Qingdao, China 认领 引用 被引量：10
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作者 ZHAO Xiaobo PANG Shaojun +1 位作者 SHAN Tifeng LIU Feng 《Journal of Ocean University of China》 SCIE CAS 2013年第1期139-145,共7页
This study is part of the endeavor to construct a comprehensive DNA barcoding database for common seaweeds in China. Identifications of red seaweeds, which have simple morphology and anatomy, are sometimes difficult s... This study is part of the endeavor to construct a comprehensive DNA barcoding database for common seaweeds in China. Identifications of red seaweeds, which have simple morphology and anatomy, are sometimes difficult solely depending on morphological characteristics. In recent years, DNA barcode technique has become a more and more effective tool to help solve some of the taxonomic difficulties. Some DNA markers such as COI（cytochrome oxidase subunit I） are proposed as standardized DNA barcodes for all seaweed species. In this study, COI, UPA （universal plastid amplicon, domain V of 23S rRNA）, and ITS （nuclear internal transcribed spacer） were employed to analyze common species of intertidal red seaweeds in Qingdao （119.3°-121°E, 35.35°-37.09°N）. The applicability of using one or a few combined barcodes to identify red seaweed species was tested. The results indicated that COI is a sensitive marker at species level. However, not all the tested species gave PCR amplification products due to lack of the universal primers. The second barcode UPA had effective universal primers but needed to be tested for the effectiveness of resolving closely related species. More than one ITS sequence types were found in some species in this investigation, which might lead to confusion in further analysis. Therefore ITS sequence is not recommended as a universal barcode for seaweeds identification. 展开更多
关键词 red seaweeds DNA barcoding COI ITS UPA
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Testing the potential of proposed DNA barcodes for species identification of Zingiberaceae 认领 引用 被引量：8
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作者 Lin-Chun SHI Jin ZHANG +10 位作者 Jian-Ping HAN Jing-Yuan SONG Hui YAO Ying-Jie ZHU Jia-Chun LI Zhen-Zhong WANG Wei XIAO Yu-Lin LIN Cai-Xiang XIE Zhong-Zhi QIAN Shi-Lin CHEN 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期261-266,共6页
In 2009, the Consortium for the Barcode of Life （CBOL） recommended the combination of rbcL and matK as the plant barcode based on assessments of recoverability, sequencing quality, and levels of species discriminati... In 2009, the Consortium for the Barcode of Life （CBOL） recommended the combination of rbcL and matK as the plant barcode based on assessments of recoverability, sequencing quality, and levels of species discrimination. Subsequently, based on a study of more than 6600 samples belonging to 193 families from seven phyla, the internal transcribed spacer （ITS） 2 locus was proposed as a universal barcode sequence for all major plant taxa used in traditional herbal medicine. Neither of these two studies was based on a detailed analysis of a particular family. Here, Zingiberaceae plants, including many closely related species, were used to compare the genetic divergence and species identification efficiency of ITS2, rbcL, marK, psbK-psbI, trnH-psbA, and rpoB. The results indicate that ITS2 has the highest interspecific divergence and significant differences between inter- and intraspecific divergence, whereas matK and rbcL have much lower divergence values. Among 260 species belonging to 30 genera in Zingiberaceae, the discrimination ability of the ITS2 locus was 99.5% at the genus level and 73.1% at the species level. Thus, we propose that ITS2 is the preferred DNA barcode sequence for identifying Zingiberaceae plants. 展开更多
关键词 DNA barcoding identification efficiency ITS2 Zingiberaceae.
Comparison of four DNA barcodes in identifying certain medicinal plants of Lamiaceae 认领 引用 被引量：10
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作者 Jian-Ping HAN Lin-Chun SHI +1 位作者 Xiao-Chen CHEN Yu-Lin LIN 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2012年第3期227-234,共8页
Many species in the family Lamiaceae have been widely used for the treatment of coronary heart disease, stroke, and other conditions, and authenticating each of these species has become an important topic of research.... Many species in the family Lamiaceae have been widely used for the treatment of coronary heart disease, stroke, and other conditions, and authenticating each of these species has become an important topic of research. Due to the lack of distinct phenotypic differences between the species, morphological identification is often inaccurate. In the third Consortium for the Barcode of Life, the combination ofmatK and rbcL was recommended as the universal barcode for plants, but this combination resolved only 70% of the species; the psbA-trnH intergenic region and internal transcribed spacer （ITS）/ITS2 were required for further study. In this study, we compared the sequences of the four candidate barcodes （matK, rbcL, ITS2, and psbA-trnH）, among different species of Lamiaceae medicinal plants based on three selection criteria： intraspecific and interspecific genetic divergences; Wilcoxon signed-rank tests; and species identification ability. The results showed that ITS2 was the most variable region of the four tested barcodes. Of 672 samples collected from 314 species, ITS2 successfully identified 78.3% at the species level and 100% at the genus level. This strategy could widen the optimal range of divergence levels for the identification of Lamiaceae medicinal plants. 展开更多
关键词 DNA barcoding identification ITS2 region Lamiaceae.
DNA barcodes identify Chinese medicinal plants and detect geographical patterns of Sinosenecio (Asteraceae) 认领 引用 被引量：4
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作者 Wei Gong Ying Liu +2 位作者 Jing Chen Yu Hong Hang-Hui Kong 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2016年第1期83-91,共9页
DNA barcodes have proved to be efficient for plants species discrimination and identification using short and standardized genomic regions. The genus Sinosenecio （Asteraceae） is used for traditional medicinal purpos... DNA barcodes have proved to be efficient for plants species discrimination and identification using short and standardized genomic regions. The genus Sinosenecio （Asteraceae） is used for traditional medicinal purposes in China. Most species of the genus occur in restricted geographical regions and exhibit a wide range of morphological variations within species, making them difficult to differentiate in the field. Previously, taxonomic revisions have been made based on morphological and cytological evidence. In the present study, barcoding analysis was performed on lo7 individuals representing 38 species in this genus to evaluate the performance of four candidate barcoding loci （matK, rbcL, trnH-psbA and internal transcribed spacer FITS]） and detect geographical patterns. Three different methods based on genetic distance, sequence similarity, and the phylogenetic tree were used. Comparably high species discrimination power was detected in species-level taxonomic process by the ITS dataset alone or combined with other loci, which was suggested to be the most suitable barcode for Sinosenecio. Our results are congruent with previous taxonomic studies concerning the monophyly of the S. oldhamianus group. The present study provides an empirical paradigm for the identification of medicinal plant species and their geographical patterns, ascertaining the congruence between taxonomical studies and barcoding analysis in Sinosenecio. 展开更多
关键词 DNA barcoding geographical patterns Sinosenecio species identification.
Developing DNA barcodes for species identification in Podophylloideae (Berberidaceae) 认领 引用 被引量：4
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作者 Yun-Rui MAO Yong-Hua ZHANG +2 位作者 Koh NAKAMURA Bi-Cai GUAN Ying-Xiong QIU 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2014年第4期487-499,共13页
Species of Podophyllum, Dysosma, Sinopodophyllum, and Diphylleia, genera from Podophylloideae of Berberidaceae, have long been used in traditional herbal medicine in East Asia and/or North America. Accurate identifica... Species of Podophyllum, Dysosma, Sinopodophyllum, and Diphylleia, genera from Podophylloideae of Berberidaceae, have long been used in traditional herbal medicine in East Asia and/or North America. Accurate identification of the species of these four genera is crucial to their medicinal uses. In this study, we tested the utility of nine barcodes (matK, rbcL, atpH-atpI, rpl32-trnL(UAG), rps18-clpp, trnL-trnF, trnL-ndhJ, trnS-trnfM, and internal transcribed spacer (ITS)) to discriminate different species of Podophylloideae. Thirty-six individuals representing 12 species of Podophylloideae were collected from different locations in China, Japan, and North America. We assessed the feasibility of amplification and sequencing of all markers, examined the levels of the barcoding gap based onDNA sequence divergence between ranges of intra-and interspecific variation using pairwise distances, and further evaluated successful identifications using each barcode by similarity-based and tree-based methods. Results showed that nine barcodes, except rps18-clpp, have a high level of primer universality and sequencing success. As a single barcode, ITS has the most variable sites, greater intra-and interspecific divergences, and the highest species discrimination rate (83%), followed by matK which has moderate variation and also high species discrimination rates. However, these species can also be discriminated by ITS alone, except Dysosma versipellis (Hance) M. Cheng ex T. S. Ying and D. pleiantha (Hance) Woodson. The combination of ITS+matK did not improve species resolution over ITS alone. Thus, we propose that ITS may be used as a sole region for identification of most species in Podophylloideae. The failure of ITS to distinguish D. versipellis and D. pleiantha is likely attributed to incomplete lineage sorting due to recent divergence of the two species. 展开更多
关键词 DNA barcoding Podophylloideae species identification traditional Chinese medicine
DNA barcode assessment of Ceramiales(Rhodophyta) in the intertidal zone of the northwestern Yellow Sea 认领 引用 被引量：2
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作者 杜国英 吴菲菲 +2 位作者 郭皓 薛红凡 茅云翔 《Chinese Journal of Oceanology and Limnology》 CSCD 2015年第3期685-695,共11页
A total of 142 specimens of Ceramiales （Rhodophyta） were collected each month from October 2011 to November 2012 in the intertidal zone of the northwestern Yellow Sea. These specimens covered 21 species, 14 genera, ... A total of 142 specimens of Ceramiales （Rhodophyta） were collected each month from October 2011 to November 2012 in the intertidal zone of the northwestern Yellow Sea. These specimens covered 21 species, 14 genera, and four families. Cluster analyses show that the specimens had a high diversity for the three DNA markers, namely, partial large subunit rRNA gene （LSU）, universal plastid amplicon （UPA）, and partial mitochondrial cytochrome c oxidase subunit I gene （COl）. No intraspecific divergence was found in our collection for these markers, except for a 1-3 bp divergence in the COI of Ceramium kondoi, Syrnphyocladia latiuscula, and Neosiphoniajaponica. Because short DNA markers were used, the phylogenetic relationships of higher taxonomic levels were hard to evaluate with poor branch support. More than half species of our collection failed to find their matched sequences owing to shortage information of DNA barcodes for macroalgae in GenBank or BOLD （Barcode of Life Data） Systems. Three specimens were presumed as Heterosiphonia crispella by cluster analyses on DNA barcodes assisted by morphological identification, which was the first record in the investigated area, implying that it might he a cryptic or invasive species in the coastal area of northwestern Yellow Sea. In the neighbor-joining trees of all three DNA markers, Heterosiphonia japonica converged with Dasya spp. and was distant from the other Heterosiphonia spp., implying that H.japonica had affinities to the genus Dasya. The LSU and UPA markers amplified and sequenced easier than the COI marker across the Ceramiales species, but the COI had a higher ability to discriminate between species. 展开更多
关键词 DNA barcoding Ceramiales red algae large subunit rRNA gene （LSU） universal plastid amplicon （UPA） cytochrome c oxidase subunit I gene （COI）
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DNA Barcode Screening and Preliminary Study on Phylogeny of Sea Snake Based on Genes COI and cytb 认领 引用 被引量：2
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作者 Xiangjun WANG Wen CHEN Haiying SU 《Agricultural Biotechnology》 2021年第6期35-45,共11页
[Objectives]The most common gene fragment used in animal DNA barcode technology is COI,but it is not necessarily suitable for all species.This study was conducted to screen genes suitable for the DNA barcode of sea sn... [Objectives]The most common gene fragment used in animal DNA barcode technology is COI,but it is not necessarily suitable for all species.This study was conducted to screen genes suitable for the DNA barcode of sea snakes.[Methods]All COI and cytb gene sequences on GenBank were searched and downloaded.After the comparison with Mega software,clustering trees of MrBayes system were established.[Results]Interspecies distances were greater than intraspecies distances for the two genes.The topological structures of their molecular hierarchical clustering trees were clear,and the support rates were high.[Conclusions]Therefore,it is concluded that not the DNA barcode of each species must be gene COI.Cytb is more suitable in terms of the mitochondrial gene of sea snakes. 展开更多
关键词 Sea snake DNA barcode Clustering tree COI gene cytb gene
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Most soil and litter arthropods are unidentifable based on current DNA barcode reference libraries 认领 引用
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作者 Ernesto Recuero Frank E.Etzler Michael S.Caterino 《Current Zoology》 SCIE CAS CSCD 2024年第5期637-646,共10页
We are far from knowing all species living on the planet.Understanding biodiversity is demanding and requires time and expertise.Most groups are understudied given problems of identifying and delimiting species.DNA ba... We are far from knowing all species living on the planet.Understanding biodiversity is demanding and requires time and expertise.Most groups are understudied given problems of identifying and delimiting species.DNA barcoding emerged to overcome some of the difficulties in identi-fying species.Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups.Here,we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the south-ern Appalachian Mountains(USA).We used 3 reference databases and several automated classification methods on a data set including several arthropod groups.Acari,Araneae,Collembola,Coleoptera,Diptera,and Hymenoptera were well represented,showing different performances across methods and databases.Spiders performed the best,with correct identification rates to species and genus levels of~50%across data-bases.Springtails performed poorly,no barcodes were identified to species or genus.Other groups showed poor to mediocre performance,from around 3%(mites)to 20%(beetles)correctly identified barcodes to species,but also with some false identifications.In general,BOLD-based identification offered the best identification results but,in all cases except spiders,performance is poor,with less than a fifth of specimens correctly identified to genus or species.Our results indicate that the soil arthropod fauna is still insufficiently documented,with many species unrepresented in DNA barcode libraries.More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNAbarcoding as a universally applicable identification method. 展开更多
关键词 Arthropoda automated identification DNA barcoding databases taxonomy taxonomic impediment
DNA barcodes and microsatellites: How they complement for species identification in the complex genus Tamarix (Tamaricaceae) 认领 引用 被引量：1
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作者 Alejandro Terrones Michelle van der Bank +1 位作者 Joaquin Moreno Ana Juan 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2022年第5期1140-1157,共18页
DNA barcoding allows the identification of an organism by comparing the sequence of selected DNA regions(barcodes)with a previously compiled database,and it can be useful for taxonomic identification of species in com... DNA barcoding allows the identification of an organism by comparing the sequence of selected DNA regions(barcodes)with a previously compiled database,and it can be useful for taxonomic identification of species in complex genera,such as Tamarix.Many species of this genus show convergent morphology,which leads to frequent errors in their identification.Highly variable genetic markers,such as microsatellites or short sequence repeats(SSR),could be used to dfferentiate species where DNA barcodes fail.Here,we tested the ability of both,5 different marker regions(rbcL,matK,ITS,trnH-psbA,and ycf),and 14 microsatellites,to properly identify Tamarix species,especially those from the Mediterranean Basin,and compared the pros and cons of the diferent analytical methods for species identification.DNA barcoding allows the genetic identification of certain species in Tamarix.The two-locus barcodes matK+ITS and ITS+ycf1 were the best-performing combinations,allowing up to 69%and 70%,respectively,correct identification.However,DNA barcoding failed in phylogenetically close groups,such as many Mediterranean species.The use of SSR can aid the identification of species,and the combination of both types of data(DNA barcoding and SSR)improved the success.The combination of data was especially relevant in detecting the presence of hybridization processes,which are common in the genus.However,caution must be exercised when choosing the clustering methods for the SSR data since diferent methods can lead to very different results. 展开更多
关键词 DNA barcoding identification methods Mediteanean Basin microsatllites Tamarix
The Potential of DNA Barcode-Based Delineation Using Seven Putative Candidate Loci of the Plastid Region in Inferring Molecular Diversity of Cowpea at Sub-Species Level 认领 引用
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作者 Patrick Okoth John Muoma +3 位作者 Mulaya Emmanuel Wekesa Clabe Dennis O. Omayio Paul O. Angienda 《American Journal of Molecular Biology》 CAS 2016年第4期138-158,共21页
The novelty and suitability of the mitochondrial gene CO1 in DNA barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochond... The novelty and suitability of the mitochondrial gene CO1 in DNA barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochondrial cytochrome c oxidase-1 gene (CO1) which has the necessary universality and variability making it a generally acceptable barcode region. CO1 is a haploid single locus that is uniparentally-inherited. Protein-coding regions are present in high-copy numbers making it an ideal barcode. The mitochondrial oxidase subunit I (COI) gene is a robust barcode with a suitable threshold for delineating animals and is not subject to drastic length variation, frequent mononucleotide repeats or microinversions. However, a low nucleotide substitution rate of plant mitochondrial genome [mtDNA] precludes the use of CO1 as a universal plant DNA barcode and makes the search for alternative barcode regions necessary. Currently, there exists no universal barcode for plants. The plastid region reveals leading candidate loci as appropriate DNA barcodes yet to be explored in biodiversity studies in Kenya. Four of these plastid regions are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and three noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbL) which emerge as ideal candidate DNA loci. While different research groups propose various combinations of these loci, there exists no consensus;the lack thereof impedes progress in getting a suitable universal DNA barcode. Little research has attempted to investigate and document the applicability and extend of effectiveness of different DNA regions as barcodes to delineate cowpea at subspecies level. In this study we sought to test feasibility of the seven putative candidate DNA loci singly and in combination in order to establish a suitable single and multi-locus barcode regions that can have universal application in delineating diverse phylogeographic groups of closely related Kenyan cowpea variants. In this study, our focus was based on genetic parameters including analyses of intra- and infra-specific genetic divergence based on intra- and infra-specific K2P distances;calculation of Wilcoxon signed rank tests of intra-specific divergence among loci and coalescence analyses to delineate independent genetic clusters. Knowledge of DNA candidate loci that are informative will reveal the suitability of DNA barcoding as a tool in biodiversity studies. Results of this study indicate that: matK, trnH-psbA, psbK-psbL, and rbcL are good barcodes for delineating intra and infraspecific distances at single loci level. However, among the combinations, matK + trnH-psbA, rpoB + atpF-atpH + matK are the best barcodes in delineating cowpea subvariants. rbcL gene can be a suitable barcode marker at single locus level, but overall, multi locus approach appears more informative than single locus approach. The present study hopes to immensely contribute to the scanty body of knowledge on the novelty of DNA barcoding in cataloguing closely related cowpea variants at molecular level and hopes to open up future research on genomics and the possibility of use of conserved regions within DNA in inferring phylogenetic relationships among Kenyan cowpea variants. 展开更多
关键词 DNA Barcoding Plastid Region DNA Sequencing Intergenic Spacers cp DNA Mo-lecular Phylogenetics Intraspecific Infraspecific
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Screening of DNA Barcode of Quarantine Phytophthora 认领 引用
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作者 Ruifang GAO Yinghui CHENG +3 位作者 Ying WANG Ying WANG Liyun GUO Guiming ZHANG 《Agricultural Biotechnology》 2017年第1期46-51,54,共6页
Phytophthora is genus of plant-damaging Oomycetes, whose member species are capable of causing enormous economic losses on crops worldwide. In the present study, four candidate genes ITS, CO1, EF-1α and β-tubulin we... Phytophthora is genus of plant-damaging Oomycetes, whose member species are capable of causing enormous economic losses on crops worldwide. In the present study, four candidate genes ITS, CO1, EF-1α and β-tubulin were tested using 123 strains of 80 species of Phytophthora to investigate the feasibility of ser- ving as DNA barcoding markers. The results showed that among the four candidate genes, ITS and CO1 had the highest success rate of PCR amplification and se- quencing, up to 100% and 96.7%. There were obvious barcode gaps in ITS, CO1 andβ-tubulin, but their frequency distributions of intra- and interspecific genetic distances were slightly overlapped. Wilcoxon rank sum test on intraspecific genetic distances of the four genes showed ITS = CO1 = β - tubulin = EF-1α indicating they bad the same effect on intraspecific discrimination, while the test on interspecific genetic distances of the four genes showed ITS 〉 C01 〉 β- tubulin 〉 EF - 1α. In summary, ITS and COl should be used in combination as the primary barcodes, β-tubulin as the complementary barcede for the identification of 11 quaran- tine Phytophthora species. 展开更多
关键词 Quarantine Phytophthora DNA barcoding Genetic distance Barcoding gap
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Spatiotemporal patterns of bird strikes at civil airports across China inferred from DNA barcoding(2012–2024) 认领 引用 被引量：1
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作者 Jie Zhang Wan Chen +5 位作者 Jiajie Li Yang Liu Feng Zhang Peng Li Chaochao Hu Qing Chang 《Avian Research》 SCIE CAS CSCD 2026年第2期520-528,共9页
Wildlife strikes,particularly bird strikes,pose a persistent threat to aviation safety worldwide.Although wildlife aircraft collisions in North America and Europe airports have been extensively studied,large-scale ass... Wildlife strikes,particularly bird strikes,pose a persistent threat to aviation safety worldwide.Although wildlife aircraft collisions in North America and Europe airports have been extensively studied,large-scale assessments remain scarce in rapidly developing regions such as China,despite its rapidly expanding aviation industry.Between 2012 and 2024,13,732 wildlife strike remains were collected at civil airports in China,of which 12,327 samples(89.8%)were successfully identiffiified by DNA barcoding and used for subsequent taxonomic and spatiotemporal analyses,including 10,261 birds,2035 mammals,and 31 other animals.We identiffiified 410 bird species(19 orders,68 families),with strikes strongly dominated by a few high-risk migratory species,particularly the Barn Swallow,Eurasian Skylark,and Red-rumped Swallow.The number of strikes events and species richness increased over time,with signiffiificant seasonal and geographical variations.Autumn exhibited the highest strike frequency(3668 incidents,320 species),whereas winter showed the lowest(467 incidents,120 species).Spatially,East China recorded the greatest number of strikes and species,reffllflecting its position along major migratory ffllflyways and the presence of key stopover habitats.Additionally,2035 bat strike samples were detected,indicating that the role of bats in aviation hazards may be underestimated.Our ffiifindings demonstrate that wildlife strike risk in China is shaped by migration dynamics and regional biogeography,underscoring the importance of seasonally adaptive and region-speciffiific management strategies that incorporate both birds and bats into airport wildlife hazard programs. 展开更多
关键词 Airport Bird diversity Bird strike DNA barcode Wildlife strike
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