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
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 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 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
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
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
[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
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
[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
DNA barcoding is an increasingly prevalent molecular biological technology which uses a short and conserved DNA fragment to facilitate rapid and accurate species identification. Kalidium species are distributed i...DNA barcoding is an increasingly prevalent molecular biological technology which uses a short and conserved DNA fragment to facilitate rapid and accurate species identification. Kalidium species are distributed in saline soil habitat throughout Southeast Europe and Northwest Asia, and used mainly as forage grass in China. The discrimination of Ka-lidium species was based only on morphology-based identification systems and limited to recognized species. Here, we tested four DNA candidate loci, one nuclear locus （ITS, internal transcribed spacer） and three plastid loci （rbcL9 matK and ycflb）, to select potential DNA barcodes for identifying different Kalidium species. Results showed that the best DNA barcode was ITS locus, which displayed the highest species discrimination rate （100%）, followed by matK （33.3%）,ycflb （16.7%）, and rbcL （16.7%）. Meanwhile, four loci clearly identified the variant species, Kalidium cuspidatum （Ung.-Stemb.） Gmb.var.A. J. Li,as a single species in Kalidium.展开更多
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.
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.
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 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.
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.
基金the National Key Research and Development Program of China(No.2019YFD0901000)the Natural Science Foundation of Shandong Pro-vince,China(No.ZR2020MC194).
文摘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.
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.
基金The National Natural Science Foundation of China under contract No.41006078the Fundamental Research Funds for the Central Universities under contract No.2010121037+1 种基金the Public Science and Technology Research Funds Projects of Ocean under contract Nos 201005012-3 and 201005015-5the Natural Science Foundation of Fujian Province of China under contract No.2011J05116
文摘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.
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 the Program for New Century Excellent Talents in the Ministry of Education in China(NCET-09-0446)lzujbky-2012-k22 to Yu Xia Wu
文摘DNA barcoding is an increasingly prevalent molecular biological technology which uses a short and conserved DNA fragment to facilitate rapid and accurate species identification. Kalidium species are distributed in saline soil habitat throughout Southeast Europe and Northwest Asia, and used mainly as forage grass in China. The discrimination of Ka-lidium species was based only on morphology-based identification systems and limited to recognized species. Here, we tested four DNA candidate loci, one nuclear locus （ITS, internal transcribed spacer） and three plastid loci （rbcL9 matK and ycflb）, to select potential DNA barcodes for identifying different Kalidium species. Results showed that the best DNA barcode was ITS locus, which displayed the highest species discrimination rate （100%）, followed by matK （33.3%）,ycflb （16.7%）, and rbcL （16.7%）. Meanwhile, four loci clearly identified the variant species, Kalidium cuspidatum （Ung.-Stemb.） Gmb.var.A. J. Li,as a single species in Kalidium.
