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
[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
[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
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
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
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
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
Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae.Currently,the taxonomy of Chrysopidae lacks a comprehensive revision,which im...Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae.Currently,the taxonomy of Chrysopidae lacks a comprehensive revision,which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents.We have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling(95.63%)in 25 of the 34 provincial regions in China,comprising 1119 barcodes of 25 genera and 197 species(representing 85%genera and 43.62%species from China).Combining other 1049 high quality green lacewing DNA barcodes,we first inferred the optimal threshold of interspecific genetic divergence(1.87%)for successful species identification in multiple simulated scenarios based on present data.We further inferred the threshold of genetic divergence(7.77%)among genera with biocontrol significance.The inference and performance of the threshold appears to be mainly associated with the completeness of sampling,the proportion of closely related species,and the analytical approaches.Six new combinations,Apertochrysa platypa(Yang&Yang,1991)comb.nov.,Apertochrysa shennongana(Yang&Wang,1990)comb.nov.,Apertochrysa pictifacialis(Yang,1988)comb.nov.,Apertochrysa helana(Yang,1993)comb.nov.,Plesiochrysa rosulata(Yang&Yang,2002)comb.nov.,and Signochrysa hainana(Yang&Yang,1991),are proposed according to integrative species delimitation.Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings.Our study also provides a methodological reference in molecular delimitation of other insects.展开更多
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
The first record of abnormal body coloration in Sebastes koreanus Kim and Lee,1994,from the Yellow Sea of China,was documented based on morphological characteristics and DNA barcoding.The two rockfish specimens were c...The first record of abnormal body coloration in Sebastes koreanus Kim and Lee,1994,from the Yellow Sea of China,was documented based on morphological characteristics and DNA barcoding.The two rockfish specimens were collected from the coastal waters of Qingdao,China,and the whole body and all fins of them were red.Of the two red-colored rockfish,there were tiny deep red spots on each fin,2 red radial stripes behind and below the eyes and 1 large deep red blotch on the opercula,while the similar stripe and spot patterns are also present in the S.koreanus specimens with normal body coloration.The countable characteristics of the two specimens are in the range of the morphometry of S.koreanus.To further clarify the species identity and taxonomic status of the two specimens,DNA barcode analysis was carried out.The genetic distance between the red-colored rockfish and S.koreanus was 0,and the minimum net genetic distances between the red-colored rockfish and other Sebastes species except for S.koreanus were 3.0%,which exceeds the threshold of species delimitation.The phylogenetic analysis showed that the DNA barcoding sequences of the two red-colored rockfish clustered with the S.koreanus sequences.The above results of DNA barcode analysis also support that the two red-colored rockfish could be identified as the species of S.koreanus.The mechanism of color variation in S.koreanus is desirable for further research and the species could be an ideal model to study the color-driven speciation of the rockfishes.展开更多
The genus Pyrrosia belongs to the family Polypodiaceae and are medium-sized epiphytic ferns,where the dried leaves of Pyrrosia lingua,Pyrrosia sheareri,Pyrrosia lanceolata,and Pyrrosia calvata are commonly used in med...The genus Pyrrosia belongs to the family Polypodiaceae and are medium-sized epiphytic ferns,where the dried leaves of Pyrrosia lingua,Pyrrosia sheareri,Pyrrosia lanceolata,and Pyrrosia calvata are commonly used in medicinal practice.In this study,the authenticity of the collected medicinal plant samples of Shiwei was identified with the help of DNA barcoding technology using the internal transcribed spacer 2(ITS2)as the identifying sequence.The experimental samples were analyzed using the basic local alignment search tool(BLAST)and the authenticity of the samples was further verified with the results of similarity comparison.The results proved that the sequences of the experimentally collected samples of Pyrrosia lingua,Pyrrosia sheareri,Pyrrosia lanceolata,and Pyrrosia calvata had a similarity of more than 97%when compared with the corresponding sequences that were uploaded on the Internet.展开更多
The introduction of invasive insect pests across national borders has become a major concern in crop production. Accordingly, national plant protection organizations are challenge to reinforce their monitoring strateg...The introduction of invasive insect pests across national borders has become a major concern in crop production. Accordingly, national plant protection organizations are challenge to reinforce their monitoring strategies, which are hampered by the weight and size of inspection equipment, as well as the taxonomic extensiveness of interrupted species. Moreover, some insect pests that impede farmer productivity and profitability are difficult for researchers to address on time due to a lack of appropriate plant protection measures. Farmers’ reliance on synthetic pesticides and biocontrol agents has resulted in major economic and environmental ramifications. DNA barcoding is a novel technology that has the potential to improve Integrated Pest Management decision-making, which is dependent on the ability to correctly identify pest and beneficial organisms. This is due to some natural traits such as phenology or pesticide susceptibility browbeaten by IPM strategies to avert pest establishment. Specifically, Deoxyribonucleic acid (DNA) sequence information was applied effectively for the identification of some micro-organisms. This technology, DNA barcoding, allows for the identification of insect species by using short, standardized gene sequences. DNA barcoding is basically based on repeatable and accessible technique that allows for the mechanisation or automation of species discrimination. This technique bridges the taxonomic bio-security gap and meets the International Plant Protection Convention diagnostic standards for insect identification. This review therefore discusses DNA barcoding as a technique for insect pests’ identification and its potential application for crop protection.展开更多
Objective To select a more suitable DNA barcode to identify the species in Artemisia L. Methods ITS, ITS2, and three other major universal barcode candidates（mat K, rbc L, and psb A-trn H） were evaluated in the iden...Objective To select a more suitable DNA barcode to identify the species in Artemisia L. Methods ITS, ITS2, and three other major universal barcode candidates（mat K, rbc L, and psb A-trn H） were evaluated in the identification efficiency using a total of 1433 sequences downloaded from Gen Bank representing 343 species in Artemisia L. ITS and ITS2 were evaluated in the PCR and sequencing rate, sequencing peak quality（Q value）, and misread rate. One hundred and twelve A. annua samples were collected from 11 populations across over China, which were amplified with universal primers on the ITS and ITS2 regions. Results ITS and ITS2 shared a higher identification efficiency and exhibited 71.43% and 64.11% detectability at the species level, respectively. The Q values of ITS and ITS2 showed that the direct PCR sequencing data were reliable for the ITS2 region and ITS exhibited poor sequencing trace quality. In certain sites, the ITS sequences exhibited reading ambiguities and errors, indicating that the misread and deletion sites in the ITS region would incorrectly inflate the identification ratio. Conclusion ITS2 is a suitable barcode for identification of species in Artemisia L., which enlarges the optimal range of divergence levels for taxonomic inferences using ITS2 sequences.展开更多
Boerhavia diffusa （B. diffusa）, also known as Punarnava, is an indigenous plant in India and an important component in traditional Indian medicine. The accurate identification and collection of this medicinal herb i...Boerhavia diffusa （B. diffusa）, also known as Punarnava, is an indigenous plant in India and an important component in traditional Indian medicine. The accurate identification and collection of this medicinal herb is vital to enhance the drug＇s efficacy and biosafety. In this study, a DNA barcoding technique has been applied to identify and distinguish B. diffusa from its closely-related species. The phylogenetic analysis was carried out for the four species of Boerhavia using barcode candidates including nuclear ribosomal DNA regions ITS, ITS1, ITS2 and the chloroplast plastid gene psbA-trnH. Sequence alignment revealed 26% polymorphic sites in ITS, 30% in ITS1, 16% in ITS2 and 6% in psbA-trnH, respectively. Additionally, a phylogenetic tree was constructed for 15 species using ITS sequences which clearly distinguished B. diffusa from the other species. The ITS1 demonstrates a higher transition/transversion ratio, percentage of variation and pairwise distance which differentiate B. diffusa from other species of Boerhavia. Our study revealed that 1TS and ITS1 could be used as potential candidate regions for identifying B. diffusa and for authenticating its herbal products.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
Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine...Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.展开更多
Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan c...Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.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.
文摘[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.
基金Supported by Hainan Provincial Natural Science Foundation of China,High-level Talent Project(321RC587),Classification of sea snakes in the South Sea China based on molecular Systematics,morphology and climate modelSpecial Scientific Research Trial Production Project of Sanya City(2016KS05),Identification of sea snake species and construction of DNA barcoding based on molecular systematics.
文摘[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.
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 Public Science and Technology Research Funds Projects of Ocean(Nos.201105021,201305030)the National Natural Science Foundation of China(No.41276137)
文摘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.
基金Supported by Science and Technology Plan Project of Shenzhen Entry-Exit Inspection and Quarantine Bureau(SZ2015101)National Key Technology Research and Development Program of China during the 12~(th)Five-Year Plan Period(2012BAK11B06)Science and Technology Plan Project of General Administration of Quality Supervision,Inspection and Quarantine of People's Republic of China(2016IK239)
文摘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.
文摘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.
基金supported by the Beijing Natural Science Foundation(No.5212011)the National Natural Science Foundation of China(Nos.32170448,32130012)+1 种基金the 2115 Talent Development Program of China Agricultural Universitythe National Animal Collection Resource Center,China.
文摘Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae.Currently,the taxonomy of Chrysopidae lacks a comprehensive revision,which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents.We have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling(95.63%)in 25 of the 34 provincial regions in China,comprising 1119 barcodes of 25 genera and 197 species(representing 85%genera and 43.62%species from China).Combining other 1049 high quality green lacewing DNA barcodes,we first inferred the optimal threshold of interspecific genetic divergence(1.87%)for successful species identification in multiple simulated scenarios based on present data.We further inferred the threshold of genetic divergence(7.77%)among genera with biocontrol significance.The inference and performance of the threshold appears to be mainly associated with the completeness of sampling,the proportion of closely related species,and the analytical approaches.Six new combinations,Apertochrysa platypa(Yang&Yang,1991)comb.nov.,Apertochrysa shennongana(Yang&Wang,1990)comb.nov.,Apertochrysa pictifacialis(Yang,1988)comb.nov.,Apertochrysa helana(Yang,1993)comb.nov.,Plesiochrysa rosulata(Yang&Yang,2002)comb.nov.,and Signochrysa hainana(Yang&Yang,1991),are proposed according to integrative species delimitation.Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings.Our study also provides a methodological reference in molecular delimitation of other insects.
基金funded by the U.S.National Science Foundation(Award DEB-1916263 to M.S.C.)the Clemson University Experiment Station(SC-1700596 to M.S.C.).
文摘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.
基金Supported by the National Key R&D Program of China (No.2018YFD0900803)the China Agriculture Research System of MOF and MARA (No.CARS-47)the Central Public-Interest Scientific Institution Basal Research Fund (Nos.2021JC01,20603022022024)
文摘The first record of abnormal body coloration in Sebastes koreanus Kim and Lee,1994,from the Yellow Sea of China,was documented based on morphological characteristics and DNA barcoding.The two rockfish specimens were collected from the coastal waters of Qingdao,China,and the whole body and all fins of them were red.Of the two red-colored rockfish,there were tiny deep red spots on each fin,2 red radial stripes behind and below the eyes and 1 large deep red blotch on the opercula,while the similar stripe and spot patterns are also present in the S.koreanus specimens with normal body coloration.The countable characteristics of the two specimens are in the range of the morphometry of S.koreanus.To further clarify the species identity and taxonomic status of the two specimens,DNA barcode analysis was carried out.The genetic distance between the red-colored rockfish and S.koreanus was 0,and the minimum net genetic distances between the red-colored rockfish and other Sebastes species except for S.koreanus were 3.0%,which exceeds the threshold of species delimitation.The phylogenetic analysis showed that the DNA barcoding sequences of the two red-colored rockfish clustered with the S.koreanus sequences.The above results of DNA barcode analysis also support that the two red-colored rockfish could be identified as the species of S.koreanus.The mechanism of color variation in S.koreanus is desirable for further research and the species could be an ideal model to study the color-driven speciation of the rockfishes.
文摘The genus Pyrrosia belongs to the family Polypodiaceae and are medium-sized epiphytic ferns,where the dried leaves of Pyrrosia lingua,Pyrrosia sheareri,Pyrrosia lanceolata,and Pyrrosia calvata are commonly used in medicinal practice.In this study,the authenticity of the collected medicinal plant samples of Shiwei was identified with the help of DNA barcoding technology using the internal transcribed spacer 2(ITS2)as the identifying sequence.The experimental samples were analyzed using the basic local alignment search tool(BLAST)and the authenticity of the samples was further verified with the results of similarity comparison.The results proved that the sequences of the experimentally collected samples of Pyrrosia lingua,Pyrrosia sheareri,Pyrrosia lanceolata,and Pyrrosia calvata had a similarity of more than 97%when compared with the corresponding sequences that were uploaded on the Internet.
文摘The introduction of invasive insect pests across national borders has become a major concern in crop production. Accordingly, national plant protection organizations are challenge to reinforce their monitoring strategies, which are hampered by the weight and size of inspection equipment, as well as the taxonomic extensiveness of interrupted species. Moreover, some insect pests that impede farmer productivity and profitability are difficult for researchers to address on time due to a lack of appropriate plant protection measures. Farmers’ reliance on synthetic pesticides and biocontrol agents has resulted in major economic and environmental ramifications. DNA barcoding is a novel technology that has the potential to improve Integrated Pest Management decision-making, which is dependent on the ability to correctly identify pest and beneficial organisms. This is due to some natural traits such as phenology or pesticide susceptibility browbeaten by IPM strategies to avert pest establishment. Specifically, Deoxyribonucleic acid (DNA) sequence information was applied effectively for the identification of some micro-organisms. This technology, DNA barcoding, allows for the identification of insect species by using short, standardized gene sequences. DNA barcoding is basically based on repeatable and accessible technique that allows for the mechanisation or automation of species discrimination. This technique bridges the taxonomic bio-security gap and meets the International Plant Protection Convention diagnostic standards for insect identification. This review therefore discusses DNA barcoding as a technique for insect pests’ identification and its potential application for crop protection.
基金National Natural Science Foundation of China(No.81473303)Major Scientific and Technological Special Project for "Significant New Drugs Creation"(No.2014ZX09304307001)
文摘Objective To select a more suitable DNA barcode to identify the species in Artemisia L. Methods ITS, ITS2, and three other major universal barcode candidates（mat K, rbc L, and psb A-trn H） were evaluated in the identification efficiency using a total of 1433 sequences downloaded from Gen Bank representing 343 species in Artemisia L. ITS and ITS2 were evaluated in the PCR and sequencing rate, sequencing peak quality（Q value）, and misread rate. One hundred and twelve A. annua samples were collected from 11 populations across over China, which were amplified with universal primers on the ITS and ITS2 regions. Results ITS and ITS2 shared a higher identification efficiency and exhibited 71.43% and 64.11% detectability at the species level, respectively. The Q values of ITS and ITS2 showed that the direct PCR sequencing data were reliable for the ITS2 region and ITS exhibited poor sequencing trace quality. In certain sites, the ITS sequences exhibited reading ambiguities and errors, indicating that the misread and deletion sites in the ITS region would incorrectly inflate the identification ratio. Conclusion ITS2 is a suitable barcode for identification of species in Artemisia L., which enlarges the optimal range of divergence levels for taxonomic inferences using ITS2 sequences.
基金the financial support from UGC (Grant No. 34-272/2008(SR))
文摘Boerhavia diffusa （B. diffusa）, also known as Punarnava, is an indigenous plant in India and an important component in traditional Indian medicine. The accurate identification and collection of this medicinal herb is vital to enhance the drug＇s efficacy and biosafety. In this study, a DNA barcoding technique has been applied to identify and distinguish B. diffusa from its closely-related species. The phylogenetic analysis was carried out for the four species of Boerhavia using barcode candidates including nuclear ribosomal DNA regions ITS, ITS1, ITS2 and the chloroplast plastid gene psbA-trnH. Sequence alignment revealed 26% polymorphic sites in ITS, 30% in ITS1, 16% in ITS2 and 6% in psbA-trnH, respectively. Additionally, a phylogenetic tree was constructed for 15 species using ITS sequences which clearly distinguished B. diffusa from the other species. The ITS1 demonstrates a higher transition/transversion ratio, percentage of variation and pairwise distance which differentiate B. diffusa from other species of Boerhavia. Our study revealed that 1TS and ITS1 could be used as potential candidate regions for identifying B. diffusa and for authenticating its herbal products.
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 grants from CAS' Largescale Scientific Facilities (Grant No.2017-LSF-GBOWS-02)the Key R & D Program of Yunnan Province,China (Grant No.20210 3AC100003)Ten Thousand Talent Program of Yunnan Province (Grant No.YNWR-QNBJ-2020-297)。
文摘Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.
基金Supported by the Zhejiang Provincial Key Research and Development Program (No.2021C02047)。
文摘Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.
