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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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DNA metabarcoding analysis of the North China and Amur Leopards’feeding habits 认领 引用
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作者 Hailong Dou Wenjing Liu +1 位作者 Limin Feng Haitao Yang 《Current Zoology》 SCIE CAS CSCD 2026年第1期95-105,共11页
Leopards Panthera pardus are top predators that play a crucial role in maintaining ecosystem balance and stability by exerting top-down control on prey species populations through direct predation.Despite their wide d... Leopards Panthera pardus are top predators that play a crucial role in maintaining ecosystem balance and stability by exerting top-down control on prey species populations through direct predation.Despite their wide distribution,in recent years leopard populations have become endangered in many regions due to increasing anthropogenic activity.Studying the feeding habits of endangered species provides insight into their survival from the perspective of their trophic niche and can help identify factors contributing to their decline,aiding in the development of targeted conservation strategies.In this study,the North China leopard(P.p.japonensis)and Amur leopard(P.p.orientalis)were selected as the study objects.A total of 97 fecal samples were collected throughout their typical habitats,83 of which were confirmed as originating from leopards using molecular identification.DNA metabarcoding identified 13 prey species for the North China leopard and 15 for the Amur leopard,with small-and medium-sized prey(5.8%)highlights the impact of anthropogenic activities on leopard feeding habits.To support leopard conservation,it is recommended to protect all prey species within reserves and reduce anthropogenic interference in these habitats. 展开更多
关键词 biomass carnivore DNA barcode diet analysis
Assembly-free reads accurate identification(AFRAID)approach outperforms other methods of DNA barcoding in the walnut family(Juglandaceae) 认领 引用 被引量：1
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作者 Yanlei Liu Kai Chen +6 位作者 Lihu Wang Xinqiang Yu Chao Xu Zhili Suo Shiliang Zhou Shuo Shi Wenpan Dong 《Plant Diversity》 SCIE CAS CSCD 2025年第1期115-126,共12页
DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Jugl... DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification(AFRAID)method of species identification,a novel approach for precise species identification in plants.Specifically,we determined(1)the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae,(2)the minimum size of chloroplast dataset for species discrimination,and(3)minimum amount of next generation sequencing(NGS)data required for species identification.We found that species identification rates were highest when whole chloroplast genomes were used,followed by taxon-specific DNA barcodes,and then universal DNA barcodes.Species identification of 100%was achieved when chloroplast genome sequence coverage reached 20%and the original sequencing data reached 500,000 reads.AFRAID accurately identified species for all samples tested after 500,000 clean reads,with far less computing time than common approaches.These results provide a new approach to accurately identify species,overcoming limitations of traditional DNA barcodes.Our method,which uses next generation sequencing to generate partial chloroplast genomes,reveals that DNA barcode regions are not necessarily fixed,accelerating the process of species identification. 展开更多
关键词 DNA barcode Species identification Random DNA barcode Juglandaceae Assembly-free
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Identification of Ichthyoplankton Species in the East China Sea off the Coast of Zhoushan Archipelago Using An Integrated Strategy of Morphology and DNA Barcoding 认领 引用
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作者 LIANG Zibin JIANG Rijin +3 位作者 MCHURA Magati Tereza YIN Rui ZHOU Yongdong CHEN Yongjiu 《浙江海洋大学学报（自然科学版）》 CAS 2025年第1期49-59,共11页
The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term o... The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term overfishing,the ichthyoplankton structure has been dramatically altered.Understanding the species composition and distribution of fish eggs and larvae is one of the most essential tasks to accurately regulate fishery resources and formulate effective management policies;however,little is known about the ichthyoplankton in this region.In this study,an integrated strategy of morphology identification(MI)and mitochondrial COI DNA barcoding was used to identify species of fish eggs and larvae collected from the ECSCZA.MI revealed 15 fish egg species belonging to 12 families and 12 fish larva species belonging to 12 families;in contrast,DNA barcoding altogether identified 30 species,including 18 fish egg species and 13 fish larva species.One species was shared between the egg and larva samples.Our study offers useful tools and critical scientific information for further understanding the diversity,distribution,and conservation management of various ichthyoplankton species in the marine environment. 展开更多
关键词 Zhoushan Archipelago ichthyoplankton morphology DNA barcoding species diversity conservation management
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DNA Barcoding and Mini-DNA Barcoding Reveal Mislabeling of Salmonids in Different Distribution Channels in the Qingdao Area 认领 引用 被引量：5
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作者 HAN Cui DONG Shuanglin +2 位作者 LI Li GAO Qinfeng ZHOU Yangen 《Journal of Ocean University of China》 SCIE CAS CSCD 2021年第6期1537-1544,共8页
There is an increasing demand for salmonid authentication due to the globalization of the salmonid trade.DNA barcoding and mini-DNA barcoding are widely used for identifying fish species based on a fragment of the mit... There is an increasing demand for salmonid authentication due to the globalization of the salmonid trade.DNA barcoding and mini-DNA barcoding are widely used for identifying fish species based on a fragment of the mitochondrial cytochrome c oxidase subunit I(COI)sequence.In this study,rainbow trout(Oncorhynchus mykiss),steelhead trout(O.mykiss),and Atlantic salmon(Salmo salar)collected from two salmonid aquaculture bases in China were authenticated by DNA barcoding(about 650 bp)and mini-DNA barcoding(127 bp)to evaluate the accuracy of the two methods in the identification of different salmonid species.The results revealed that both methods could effectively distinguish O.mykiss and S.salar with 100%accuracy.However,the two methods failed to separate rainbow trout(O.mykiss)and steelhead trout(O.mykiss),which are the same species but cultured in different water environments.Moreover,salmonid samples from three main distribution channels in the Qingdao area(traditional supermarkets,online supermarkets,and sushi bars)were identified by the two methods.Substitution of S.salar with O.mykiss was discovered,and the 27.78%overall substitution rate of salmonids in the Qingdao area was higher than those in other regions reported in previous studies.In addition,the mislabeling rates of salmonids from traditional supermarkets,online supermarkets,and sushi bars were compared in this study.The mislabeling rate was significantly greater in sushi bars(50%)than in the other two channels(16.67%),suggesting that stronger monitoring and enforcement measures are necessary for the aquatic food catering industry. 展开更多
关键词 salmonid DNA barcoding mini-DNA barcoding species authentication mislabeling rate
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Species identification of poisonous medicinal plant using DNA barcoding 认领 引用 被引量：15
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作者 LIU Miao LI Xi-Wen +2 位作者 LIAO Bao-Sheng LUO Lu REN Yue-Ying 《Chinese Journal of Natural Medicines》 SCIE CAS CSCD 2019年第8期585-590,共6页
The aim is to select a universal DNA barcode for identifying all poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants. We chose 4 commonly used regions as candidate DN... The aim is to select a universal DNA barcode for identifying all poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants. We chose 4 commonly used regions as candidate DNA barcodes(ITS2, psb A-trn H,matK and rbc L) and compared their identification efficiency in 106 species from 27 families and 65 genera totally. Data analysis was performed including the information of sequence alignment, inter/intra-specific genetic distance and data distribution, identification efficiency and the situation of Neighbor-Joining(NJ) phylogenetic trees. We found ITS2 sequence region had high variation, stable genetic distance and identification efficiency relatively. The topological structure of NJ phylogenetic tree showed monophyletic. Our findings show that ITS2 can be applied as a universal barcode for identifying poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants. 展开更多
关键词 Sequence Poisonous herbal medicine Genetic distance DNA barcoding ITS2 Blast
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Identification of processed Chinese medicinal materials using DNA mini-barcoding 认领 引用 被引量：11
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作者 SONG Ming DONG Gang-Qiang +2 位作者 ZHANG Ya-Qin LIU Xia SUN Wei 《Chinese Journal of Natural Medicines》 SCIE CAS CSCD 2017年第7期481-486,共6页
Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and ident... Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psb A-trn H, rbc L, mat K, trnL(UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL(UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%——20% of the processed samples, while the amplification rates of the trnL(UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL(UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control. 展开更多
关键词 DNA barcoding trnL(UAA)intron P6 loop Identification Processed medicinal materials Mini-barcode
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Testing four proposed barcoding markers for the identification of species within Ligustrum L.(Oleaceae) 认领 引用 被引量：10
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作者 Jing GU jun-Xia SU +2 位作者 Ruo-Zhu LIN Rui-Qi LI Pei-Gen XIAO 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期213-224,共12页
DNA barcoding is a biological technique that uses short and standardized genes or DNA regions to facilitate species identification. DNA barcoding has been used successfully in several animal and plant groups. Ligustr... DNA barcoding is a biological technique that uses short and standardized genes or DNA regions to facilitate species identification. DNA barcoding has been used successfully in several animal and plant groups. Ligustrum （Oleaceae） species occur widely throughout the world and are used as medicinal plants in China. Therefore, the accurate identification of species in this genus is necessary. Four potential DNA barcodes, namely the nuclear ribosomal internal transcribed spacer （ITS） and three chloroplast （cp） DNA regions （rbcL, matK, and trnH-psbA）, were used to differentiate species within Ligustrum. BLAST, character-based method, tree-based methods and TAXONDNA analysis were used to investigate the molecular identification capabilities of the chosen markers for discriminating 92 samples representing 20 species of this genus. The results showed that the ITS sequences have the most variable information, followed by trnH-psbA, matK, and rbcL. All sequences of the four regions correctly identified the species at the genus level using BLAST alignment. At the species level, the discriminating power of rbcL, marK, trnH-psbA, and ITS based on neighbor-joining （NJ） trees was 36.8%, 38.9%, 77.8%, and 80%, respectively. Using character-based and maximum parsimony （MP） tree methods together, the discriminating ability of trnH-psbA increased to 88.9%. All species could be differentiated using ITS when combining the NJ tree method with character-based or MP tree methods. Overall, the results indicate that DNA barcoding is an effective molecular identification method for Ligustrum species. We propose the nuclear ribosomal ITS as a plant barcode for plant identification and trnH-psbA as a candidate barcode sequence. 展开更多
关键词 DNA barcoding internal transcribed spacer （ITS） Ligustrum matK trnH-psbA rbcL.
Testing four barcoding markers for species identification of Potamogetonaceae 认领 引用 被引量：8
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作者 Zhi-Yuan DU Alitong QIMIKE +2 位作者 Chun-Feng YANG jin-Ming CHEN Qing-Feng WANG 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期246-251,共6页
The pondweeds （Potamogetonaceae） are among the most important plant groups in the aquatic envi- ronment. Owing to their high morphological and ecological diversity, species identification of this aquatic family rema... The pondweeds （Potamogetonaceae） are among the most important plant groups in the aquatic envi- ronment. Owing to their high morphological and ecological diversity, species identification of this aquatic family remains problematic. DNA barcoding involves sequencing a standard DNA region and has been shown to be a powerful tool for species identification. In the present study, we tested four barcoding markers （rbcL, matK, internal transcribed spacer （ITS）, and trnH-psbA） in 15 Potamogeton species and two Stuckenia species, representing most species of the Potamogetonaceae in China. The results show that all four regions can distinguish and support the newly proposed genera of Stuckenia from Potamogeton. Using ITS and trnH-psbA, significant interspecific genetic variability was shown. However, intraspecific genetic variability of trnH-psbA is high and so it is not suitable for barcoding in Potamogetonaceae. The ITS and matK regions showed good discrimination. However, matK was not easy to sequence using universal primers. The best performing single locus was ITS, making it a potentially useful DNA barcode in Potamogetonaceae. 展开更多
关键词 DNA barcoding internal transcribed spacer （ITS） matK Potamogetonaceae rbcL trnH-psbA.
New universal matK primers for DNA barcoding angiosperms 认领 引用 被引量：25
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作者 Jing YU jian-Hua XUE Shi-Liang ZHOU 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期176-181,共6页
The chloroplast maturase K gene （matK） is one of the most variable coding genes of angiosperms and has been suggested to be a ＂barcode＂ for land plants. However, matK exhibits low amplification and sequencing rate... The chloroplast maturase K gene （matK） is one of the most variable coding genes of angiosperms and has been suggested to be a ＂barcode＂ for land plants. However, matK exhibits low amplification and sequencing rates due to low universality of currently available primers and mononucleotide repeats. To resolve these technical problems, we evaluated the entire matK region to find a region of 600-800 bp that is highly variable, represents the best of all rnatK regions with priming sites conservative enough to design universal primers, and avoids the mononucleotide repeats. After careful evaluation, a region in the middle was chosen and a pair of primers named matK472F and matK1248R was designed to amplify and sequence the matK fragment of approximately 776 bp. This region encompasses the most variable sites, represents the entire mark region best, and also exhibits high amplification rates and quality of sequences. The universality of this primer pair was tested using 58 species from 47 families of angiosperm plants. The primers showed a strong amplification （93.1%） and sequencing （92.6%） successes in the species tested. We propose that the new primers will solve, in part, the problems encountered when using matK and promote the adoption of matK as a DNA barcode for angiosperms. 展开更多
关键词 angiosperm DNA barcoding matK primer.
High universality of matK primers for barcoding gymnosperms 认领 引用 被引量：9
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作者 Yan LI Lian-Ming GAO +2 位作者 Ram C. POUDEL De-Zhu Li Alan FORREST 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期169-175,共7页
DNA barcoding is a tool to provide rapid and accurate taxonomic identification using a standard DNA region. A two-marker combination of matK＋rbcL was formally proposed as the core barcode for land plants by the Conso... DNA barcoding is a tool to provide rapid and accurate taxonomic identification using a standard DNA region. A two-marker combination of matK＋rbcL was formally proposed as the core barcode for land plants by the Consortium for the Barcode of Life Plant Working Group. However, there are currently no barcoding primers for matK showing high universality in gymnosperms. We used 57 gymnosperm species representing 40 genera, 11 families and four subclasses to evaluate the universality of nine candidate matK primers and one rbcL primer in this study. Primer （1F/724R） of rbcL is proposed here as a universal primer for gymnosperms due to high universality. One of the nine candidate matK primers （Gym_F 1A/Gym_R1A） is proposed as the best ＂universal＂ matK primer for gymnosperms because of high polymerase chain reaction success and routine generation of high quality bidirectional sequences. A specific matK primer for Ephedra was newly designed in this study, which performed well on the sampled species. The primers proposed here for rbcL and matK can be easily and successfully amplified for most gymnosperms. 展开更多
关键词 DNA barcoding matK gymnosperm primer universality.
Testing four candidate barcoding markers in temperate woody bamboos (Poaceae: Bambusoideae) 认领 引用 被引量：11
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作者 Zhao-Ming CAI Yu-Xiao ZHANG +2 位作者 Li-Na ZHANG Lian-Ming GAO De-Zhu LI 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2012年第6期527-539,共13页
Bambusoideae is an important subfamily of the grass family Poaceae that has considerable economic, ecologic and cultural value. In addition, Bambusoideae species are important constituents of the forest vegetation in ... Bambusoideae is an important subfamily of the grass family Poaceae that has considerable economic, ecologic and cultural value. In addition, Bambusoideae species are important constituents of the forest vegetation in China. Because of the paucity of flower-bearing specimens and homoplasies of morphological characters, it is difficult to identify species of Bambusoideae using morphology alone, especially in the case of temperate woody bamboos （i.e. Arundinarieae）. To this end, DNA barcoding has shown great potential in identifying species. The present study is the first attempt to test the feasibility of four proposed DNA barcoding markers （matK, rbcL, trnH-psbA, and internal transcribed spacer [ITS]） in identifying 27 species of the temperate woody bamboos. Three plastid markers showed high levels of universality, whereas the universality of ITS was comparatively low. A single plastid marker provided low levels of discrimination success at both the genus and species levels （〈 12%）. Among the combinations of plastid markers, the highest discriminatory power was obtained using the combination of rbcL ＋ matK （14.8%）. Using a combination of three markers did not increase species discrimination. The nuclear region ITS alone could identify 66.7% of species, although fewer taxa were included in the ITS analyses than in the plastid analyses. When ITS was integrated with a single or combination of plastid markers, the species discriminatory power was significantly improved. We suggest that a combination ofrbcL ＋ ITS, which exhibited the highest species identification power of all combinations in the present study, could be used as a potential DNA barcode for temperate woody bamboos. 展开更多
关键词 DNA barcoding internal transcribed spacer （ITS） matK rbcL temperate woody bamboos.
DNA barcoding in closely related species:A case study of Primula L.sect.Proliferae Pax(Primulaceae) in China 认领 引用 被引量：10
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作者 Hai-Fei YAN Gang HAO +1 位作者 Chi-Ming HU Xue-Jun GE 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期225-236,共12页
DNA barcoding is a method of identifying species by analyzing one or a few short standardized DNA sequences. There are particular challenges in barcoding plants, especially for distinguishing closely related species. ... DNA barcoding is a method of identifying species by analyzing one or a few short standardized DNA sequences. There are particular challenges in barcoding plants, especially for distinguishing closely related species. Hence, there is an urgent need to evaluate the performance of candidate loci for distinguishing between species, especially closely related species, to complement the rbcL ＋ matK combination suggested as the core barcode for land plants. We sampled 48 individuals representing 12 species in Primula sect. Proliferae Pax in China to evaluate the performance of eight leading candidate barcode loci （matK, rbcL, rpoB, rpoC1, trnH-psb.4, psbK-psbI, atpF- atpH, and internal transcribed spacer （ITS））. The core combination rbcL ＋ matK gave only 50% species resolution in sect. Proliferae. In terms ofintraspecies and interspecies divergence, degree of monophyly, and sequence similarity, ITS, trnH-psbA, and psbK-psbI showed good performance as single-locus barcodes. Internal transcribed spacer displayed the highest genetic divergence and best discriminatory power, both alone and in combination with rbcL ＋ matK （83.3% species resolution）. We recommend evaluating the use of ITS for barcoding in other species. Low or single copy nuclear regions would provide more sophisticated barcoding tools in the long term, even though further research is required to find suitable loci. 展开更多
关键词 DNA barcoding ITS plastid candidates Primlula sect. Proliferae species discrimination.
Identification of species within Tetrastigma(Miq.)Planch.(Vitaceae)based on DNA barcoding techniques 认领 引用 被引量：21
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作者 Yuan-Miao FU Wei-Mei JIANG Cheng-Xin FU 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期237-245,共9页
Many species of Tetrastigma(Miq.)Planch.(Vitaceae)have long been used as medicinal plants in China,and some are endangered due to overexploitation.Although adulterants are often added to traditional Chinese medicines,... Many species of Tetrastigma(Miq.)Planch.(Vitaceae)have long been used as medicinal plants in China,and some are endangered due to overexploitation.Although adulterants are often added to traditional Chinese medicines,there is no reliable or practical method for identifying them.In this study,we used four markers(rbcL,matK,trnH-psbA,and internal transcribed spacer[ITS])as DNA barcodes to test their ability to distinguish species of Tetrastigma.The results indicated that the best barcode was ITS,which showed significant inter-specific genetic variability,and thus its potential as a DNA barcode for identifying Tetrastigma.Multiple loci provided a greater ability to distinguish species than single loci.We recommend using the combined rbcL+matK+ITS barcode for the genus.Phylogenetic trees from each barcode were compared.Analyses using the unweighted pair group method with arithmetic mean discriminated an equal or greater percentage of resolvable species than did neighbor joining,maximum likelihood,or maximum parsimony analyses.Additionally,five medicinal species of Tetrastigma,especially T.hemsleyanum,could be identified precisely using DNA barcoding. 展开更多
关键词 DNA barcoding medicinal plants species identification Tetrastigma.
Are nuclear loci ideal for barcoding plants? A case study of genetic delimitation of two sister species using multiple loci and multiple intraspecific individuals 认领 引用 被引量：13
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作者 Qian WANG Qiu-Shi YU Jian-Quan LIU 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第3期182-188,共7页
Considerable debate remains as to which DNA region should be used to barcode plants. Several different chloroplast （cp） DNA regions （rbcL, marK, and trnH-psbA） and nuclear ribosomal internal transcribed regions （... Considerable debate remains as to which DNA region should be used to barcode plants. Several different chloroplast （cp） DNA regions （rbcL, marK, and trnH-psbA） and nuclear ribosomal internal transcribed regions （ITS） have been suggested as suitable barcodes in plants. Recently, low-copy nuclear loci were also suggested to be potentially ideal barcode regions. The aim of the present study was to test the effectiveness of these proposed DNA fragments and five additional low-copy loci （CHS, DET1, COP1, PGIC1, and RPS2; comprising both coding and non-coding regions） in barcoding closely related species. We examined the divergences within and between two species ofPugionium （Brassicaceae）. We failed to find any interspecific variation from three cpDNA fragments with which to discriminate the two species. However, a single base mutation in the internal transcribed spacer （ITS） could discriminate between the two species consistently. We found more variations among all individuals of the two species using each of the other five low-copy nuclear loci. However, only alleles from one locus （DET1） of the five low-copy loci related to flowering regulations was able to distinguish the sampled individuals into two species. We failed to amplify the corresponding fragments out of Brassicaceae using the designed DET1 primers. We further discussed the discrimination power of different loci due to incomplete lineage sorting, gene flow, and species-specific evolution. Our results highlight the possibility of using the nuclear ITS as a core or complementary fragment to barcode recent diverged species. 展开更多
关键词 chloroplast DNA DNA barcoding internal transcribed spacer （ITS） low-copy nuclear loci Pugionium.
DNA barcoding and molecular phylogeny of Dumasia(Fabaceae:Phaseoleae)reveals a cryptic lineage 认领 引用 被引量：3
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作者 Kai-Wen Jiang Rong Zhang +2 位作者 Zhong-Fu Zhang Bo Pan Bin Tian 《Plant Diversity》 SCIE CAS CSCD 2020年第5期376-385,共10页
Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we ev... Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we evaluated the ability of six DNA barcoding sequences,one nuclear(ITS)and five chloroplast regions(trnH-psbA,matK,rbcL,trnL-trnF,psbB-psbF),to efficiently identify Dumasia species.Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation.Most combined analyses including ITS showed good species resolution and identification efficiency.We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia.The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches,which may result from cryptic differentiation.Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species. 展开更多
关键词 Cryptic species DNA barcoding Dumasia Internal transcribed spacer(ITS) Plastid genome
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DNA barcoding of Gaultheria L. in China(Ericaceae:Vaccinioideae) 认领 引用 被引量：3
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作者 He REN Lu LU +1 位作者 Hong WANG De-Zhu LI 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第5期411-424,共14页
Four DNA barcoding loci,chloroplast loci rbcL,matK,trnH-psbA,and nuclear locus internal transcribed spacer（ITS）,were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific... Four DNA barcoding loci,chloroplast loci rbcL,matK,trnH-psbA,and nuclear locus internal transcribed spacer（ITS）,were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific and interspecific pairwise P-distance,Wilcoxon signed rank test,and tree-based analyses.This study included 186 individuals from 89 populations representing 30 species.For all individuals,single locus markers showed high levels of sequencing universality but were ineffective for species resolvability.Polymerase chain reaction amplification and sequencing were successful for all four loci.Both ITS and matK showed significantly higher levels of interspecific species delimitation than rbcL and trnH-psbA.A combination of matK and ITS was the most efficient DNA barcode among all studied regions,however,they do not represent an appropriate candidate barcode for Chinese Gaultheria,by which only 11 out of 30 species can be separated.Loci rbcL,matK,and trnH-psbA,which were recently proposed as universal plant barcodes,have a very poor capacity for species separation for Chinese Gaultheria.DNA barcodes may be reliable tools to identify the evolutionary units of this group,so further studies are needed to develop more efficient DNA barcodes for Gaultheria and other genera with complicated evolutionary histories. 展开更多
关键词 DNA barcoding Ericaceae Gaultheria species discrimination taxonomy Vaccinioideae.
DNA barcoding of East Asian Amentotaxus (Taxaceae): Potential new species and implications for conservation 认领 引用 被引量：3
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作者 Lian-Ming Gao Yan Li +5 位作者 Loc Ke Phan Li-Jun Yan Philip Thomas Long Ke Phan Michael Mbller De-Zhu Li 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2017年第1期16-24,共9页
DNA barcoding is a useful tool for species identification using standardized genomic DNA fragments. The genus Amentotaxus, consisting of five or six species, is confined to South China, Northeast India, Laos, and Viet... DNA barcoding is a useful tool for species identification using standardized genomic DNA fragments. The genus Amentotaxus, consisting of five or six species, is confined to South China, Northeast India, Laos, and Vietnam. All species have been assessed as globally or nationally threatened. However, there is uncertainty about the number of species involved, especially in the border areas of southern China, northern Vietnam, and Laos. We selected five DNA barcodes （rbcL, matK, trnH-psbA, trnL-F, and internal transcribed spacer （ITS）） to evaluate their discrimination ability in this genus, and to investigate the current taxonomy of Amentotaxus. Our results indicate that all the selected barcoding regions showed a high level of universality for PCR and sequencing. When six species are recognized, the nuclear ribosomal DNA region ITS and the chloroplast DNA region trnL-F used on their own provided the highest identification success （60%）. Two barcode combinations that included either ITS or trnL-F had the same species discrimination ability. Combinations using additional barcodes did not improve the species identification success. When only five species are recognized, with A. hatuyenensis T. H. Nguyen treated as a synonym of A. yunnanensis H. L. Li, the discrimination rate rises to 100%. Our results also indicate that recent collections from Yunnan province, China, Lao Cai province, Vietnam, and Laos may represent a potential new species. The findings from this study will be very useful for the formulation of appropriate conservation strategies for threatened Amentotaxus species in national and trans-boundary regions. 展开更多
关键词 Amentotaxus biodiversity conservation DNA barcoding new species discovery species discrimination.
DNA barcoding of the main cultivated yams and selected wild species in the genus Dioscorea 认领 引用 被引量：3
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作者 Gezahegn Girma Charles Spillane Melaku Gedil 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2016年第3期228-237,共10页
Distinguishing yam species based on morphological traits is extremely difficult and unreliable, posing a challenge to breeders and genebank curators. Development of a molecular assay based on DNA barcoding can facilit... Distinguishing yam species based on morphological traits is extremely difficult and unreliable, posing a challenge to breeders and genebank curators. Development of a molecular assay based on DNA barcoding can facilitate rapid and accurate identification of important Dioscorea species. To develop a DNA barcoding system for Dioscorea species identification, the rbcL and mark loci （in unison and in combination）, the non-coding intergenic spacer trnH-psbA of the chloroplast genome, and the nuclear ITS regions were investigated using criteria for developing candidate DNA barcodes. All DNA barcoding sequences were assessed for ease of PCR amplification, sequence quality and species discriminatory power. Amongst the markers investigated, the matK locus performed well in terms of species identification （63.2%）, in addition to detecting high interspecific variation with mean divergence of 0.0196 （SD=0.0209）. The combination of the two coding regions （rbcL ＋ matK） was determined to be the optimal （76.2%） DNA barcoding approach as 16 out of 21 species could be defined. While the rbcL exhibited good PCR amplification efficiency and sequence quality, its species discriminatory power was relatively poor with 47.6% identification. Similarly, the trnH-psbA region had a weak discrimination efficiency of only .36.8%. While the development of more robust DNA barcoding systems is an ongoing challenge, our results indicate that the rbcL ＋ matK combination can be utilized as multi-locus DNA barcode regions for Dioscorea species identification. 展开更多
关键词 Dioscorea DNA barcoding matK rbcL trnH-psbA.
16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China 认领 引用 被引量：10
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作者 ZHENG Lianming HE Jinru +2 位作者 LIN Yuanshao CAO Wenqing ZHANG Wenjing 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2014年第4期55-76,共22页
Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for specie... Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for species identification, however, the choice between mitochondrial cytochrome c oxidase subunit I（COI） and large subunit ribosomal RNA gene（16S） as a standard barcode for hydrozoans is subject to debate. Herein, we directly compared the barcode potential of COI and 16S in hydrozoans using 339 sequences from 47 pelagic hydrozoan species. Analysis of Kimura 2-parameter genetic distances（K2P） documented the mean intraspecific/interspecific variation for COI and 16S to be 0.004/0.204 and 0.003/0.223, respectively. An obvious ＂barcoding gap＂ was detected for all species in both markers and all individuals of a species clustered together in both the COI and 16S trees. These results suggested that the species within the studied taxa can be efficiently and accurately identified by COI and 16S. Furthermore, our results confirmed that 16S was a better phylogenetic marker for hydrozoans at the genus level, and in some cases at the family level. Considering the resolution and effectiveness for barcoding and phylogenetic analyses of Hydrozoa, we strongly recommend 16S as the standard barcode for hydrozoans. 展开更多
关键词 DNA barcoding hydrozoan COI 16S rRNA
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