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
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
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
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
DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions(psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS)with potential for use as DNA barcodes were tested for their...DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions(psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS)with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the"DNA barcoding gap"assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.展开更多
We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belongin...We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction （PCR） amplicons in all the accessions tested. However, only 35 （58%） and 4o accessions （66~） yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species （75%） into monophyletic groups and five species into two para- phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species （6o%）, and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence ofnatural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of iTS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.展开更多
Objective: To identify Kadsura interior(Dian Ji Xue Teng, Schisandraceae) by using DNA barcoding.Methods: We analyzed five DNA barcodes(ITS, ITS2, psb A-trn H, mat K and rbc L) using DNA barcoding in terms of distance...Objective: To identify Kadsura interior(Dian Ji Xue Teng, Schisandraceae) by using DNA barcoding.Methods: We analyzed five DNA barcodes(ITS, ITS2, psb A-trn H, mat K and rbc L) using DNA barcoding in terms of distance-based,tree-based and character-based identification to distinguish Kadsura interior and its adulterants.Results: In distance-based and tree-based identification, K. interior could be distinguished easily from the species of Schisandra and K. coccinea.In character-based identification, there are two single nucleotide polymorphisms(SNPs) in ITS and one SNP in psb A-trn H which can be used to distinguish K. interior from K. heteroclita and K. longipedunculata.Conclusion: The results indicate that DNA barcoding can be used to identify K. interior. ITS and psb A-trnH sequence can be the most ideal DNA barcode for discriminating K. interior and its adulterants by the combination analysis of distance-based, tree-based and character-based identification(SNPs).展开更多
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
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
[Objective] A study on the classification of 24 species of Calyptratae entering Ningbo port using DNA barcoding technique was carried out.[Method] The CO I genes of the 24 species of Calyptratae were first sequenced.B...[Objective] A study on the classification of 24 species of Calyptratae entering Ningbo port using DNA barcoding technique was carried out.[Method] The CO I genes of the 24 species of Calyptratae were first sequenced.Based on the comparison and analysis of the obtained sequences,the phylogenetic tree was constructed using MEGA6.0.[Result] The cluster analysis showed the classification of the 24 species of Calyptratae was consistent with the morphological classification at the family and genus levels.However,the cluster analysis could not fully distinguish the closely-related species.[Discussion] The DNA barcoding technique cannot be singly used for classifying and identifying Calyptratae.It should be combined with morphological classification methods,and can be treated as a beneficial supplement for morphological classification methods.展开更多
[Objective] This study aimed to provide reference and reduce the workload for screening standard DNA barcoding genes of plants. [Method] Three DNA barcoding genes ITS, ITS2 and rbcL were amplified from seven Xanthium ...[Objective] This study aimed to provide reference and reduce the workload for screening standard DNA barcoding genes of plants. [Method] Three DNA barcoding genes ITS, ITS2 and rbcL were amplified from seven Xanthium species under the same PCR condition： PCR amplification was started with initial denaturation at 95 ℃ for 4 min, followed by 35 cycles of denaturation at 94 ℃ for 30 s, annealing at 52 ℃ for 45 s, and extension at 72 ℃ for 45 s; the amplification was completed by holding the reaction mixture at 72 ℃ for 10 min to allow complete extension of PCR, and the PCR products were stored at 4 ℃. [Result] Three DNA barcoding genes ITS, ITS2 and rbcL were all amplified successfully. [Conclusion] This study indicates that PCR amplification conditions for DNA barcoding genes ITS,ITS2 and rbcL in plants may be consistent.展开更多
基金supported by the National Natural Science Foundation of China(31471958,31272298)the Youth Innovation Promotion Association of the CAS(2013183)the Open Project of Key Laboratory of Insect Developmental and Evolutionary Biology,CAS(2009DP17321409)
文摘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.
基金supported by the National Natural Science Foundation of China(31300551)the Anhui Outstanding Young Talent Support Program(gxfx2017059)
文摘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.
基金supported by the National Special Research Fund for Non-Profit Sector (Agriculture) (No. 200903030)the National Natural Science Foundation of China (No.41176135)
文摘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.
基金supported by the Fundamental Research Funds for the Central Universities(grant no.TD2012-04)the Scientific Research Foundation of the State Human Resource Ministry and the Education Ministry for Returned Chinese Scholars(to L.Xie)+2 种基金the State Key Laboratory Program from the State Key Laboratory of Systematic and Evolutionary Botany(grant no.LSEB2011-07)the Main Direction Program of Knowledge Innovation of the Chinese Academy of Sciences(grant no.KSCX2-EW-Z-1)the National Natural Science Foundation of China(grant nos.31170201,81072317,31110103911)
文摘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.
基金supported by the National International Cooperation Program(Grant No.2007DFA30990)Special Scientific Research Project of Health Profession(Grant No.200802043)
文摘DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions(psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS)with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the"DNA barcoding gap"assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.
基金financial support (BT/ PR8349/NDB/51/136/2006 19/01/2007–19-01/2010) from the Department of Biotechnology, Government of India
文摘We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction （PCR） amplicons in all the accessions tested. However, only 35 （58%） and 4o accessions （66~） yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species （75%） into monophyletic groups and five species into two para- phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species （6o%）, and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence ofnatural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of iTS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.
基金the support of the National Natural Science Foundation of China(Project No.81373913)
文摘Objective: To identify Kadsura interior(Dian Ji Xue Teng, Schisandraceae) by using DNA barcoding.Methods: We analyzed five DNA barcodes(ITS, ITS2, psb A-trn H, mat K and rbc L) using DNA barcoding in terms of distance-based,tree-based and character-based identification to distinguish Kadsura interior and its adulterants.Results: In distance-based and tree-based identification, K. interior could be distinguished easily from the species of Schisandra and K. coccinea.In character-based identification, there are two single nucleotide polymorphisms(SNPs) in ITS and one SNP in psb A-trn H which can be used to distinguish K. interior from K. heteroclita and K. longipedunculata.Conclusion: The results indicate that DNA barcoding can be used to identify K. interior. ITS and psb A-trnH sequence can be the most ideal DNA barcode for discriminating K. interior and its adulterants by the combination analysis of distance-based, tree-based and character-based identification(SNPs).
基金supported by the funds from Natural Science Foundation of Hebei Province(C2022402017).
文摘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.
文摘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.
文摘[Objective] A study on the classification of 24 species of Calyptratae entering Ningbo port using DNA barcoding technique was carried out.[Method] The CO I genes of the 24 species of Calyptratae were first sequenced.Based on the comparison and analysis of the obtained sequences,the phylogenetic tree was constructed using MEGA6.0.[Result] The cluster analysis showed the classification of the 24 species of Calyptratae was consistent with the morphological classification at the family and genus levels.However,the cluster analysis could not fully distinguish the closely-related species.[Discussion] The DNA barcoding technique cannot be singly used for classifying and identifying Calyptratae.It should be combined with morphological classification methods,and can be treated as a beneficial supplement for morphological classification methods.
基金Supported by Science and Technology Project of Jiangsu Entry-Exit Inspection and Quarantine Bureau(2012KJ54)~~
文摘[Objective] This study aimed to provide reference and reduce the workload for screening standard DNA barcoding genes of plants. [Method] Three DNA barcoding genes ITS, ITS2 and rbcL were amplified from seven Xanthium species under the same PCR condition： PCR amplification was started with initial denaturation at 95 ℃ for 4 min, followed by 35 cycles of denaturation at 94 ℃ for 30 s, annealing at 52 ℃ for 45 s, and extension at 72 ℃ for 45 s; the amplification was completed by holding the reaction mixture at 72 ℃ for 10 min to allow complete extension of PCR, and the PCR products were stored at 4 ℃. [Result] Three DNA barcoding genes ITS, ITS2 and rbcL were all amplified successfully. [Conclusion] This study indicates that PCR amplification conditions for DNA barcoding genes ITS,ITS2 and rbcL in plants may be consistent.
