Contribution of DNA barcoding to the study of the bees (Hymenoptera: Apoidea) of Canada: progress to date

AbstractBees (Hymenoptera: Apoidea, Apiformes) are taxonomically and ecologically diverse, with a wide range of social complexity, nesting preferences, floral associations, and biogeographic restrictions. A Canadian bee checklist, greatly assisted by the gene-assisted approach of DNA barcoding, is nearing completion. Previous evaluation of bee diversity in Canada, assisted by DNA barcoding, was restricted to Nova Scotia, which contains about 25% of the bee species in the country. Here, we summarise efforts to date to build a comprehensive DNA barcode library supporting bee taxonomic studies in Canada, consisting of more than 12 500 barcode-compliant sequences yielding 811 distinct barcode index numbers (BINs). This appears to represent ~95% of the 856 bee species presently recorded from Canada, but comparison with known morphological species in each genus shows that some genera are still under-sampled or may contain cryptic taxa, with much taxonomic work still to be done on bees in Canada. This is particularly true within the taxonomically difficult generaAndrenaFabricius (Andrenidae), HylaeusFabricius (Colletidae),MelissodesLatreille (Apidae),NomadaScopoli (Apidae),OsmiaPanzer (Megachilidae), andSphecodesLatreille (Halictidae). DNA analysis will likely be a key asset in resolving bee taxonomic issues in Canada in the future, and to date has even assisted studies of well-known bee taxa. Here we present summaries of our results, and discuss the use of DNA barcoding to assist future taxonomic work, faunal lists, and ecological studies.

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Single-Laboratory Validation of a Two-Tiered DNA Barcoding Method for Raw Botanical Identification

Journal of AOAC International ◽

10.1093/jaoac/102.5.1435 ◽

2019 ◽

Vol 102 (5) ◽

pp. 1435-1447 ◽

Cited By ~ 1

Author(s):

Zhengfei Lu ◽

Christopher M Thompson ◽

Tiffany Chua ◽

Silva Babajanian ◽

Yanjun Zhang ◽

...

Keyword(s):

Dna Barcoding ◽

Raw Materials ◽

Dna Barcode ◽

Sampling Technique ◽

Regulatory Compliance ◽

Raw Material ◽

Animal Products ◽

Policy Makers ◽

Plant Parts ◽

Wide Range

Abstract Background: The applications of deoxyribonucleic acid (DNA) barcoding methods have been extended from authenticating taxonomic provenance of animal products to identifying botanicals used as herbal medicine and in botanical dietary supplements. DNA barcoding methods for botanical identification must be adequately validated to meet regulatory compliance. Objective: The goal of this study is to provide a validation protocol for a two-tiered DNA barcoding method that aims to identify raw botanicals. Methods: A barcode database was computationally validated to define the barcode combinations that can unambiguously identify botanicals in the database. A maximum variation sampling technique was used to capture a wide range of perspectives relating to DNA barcode-based botanical identification, including plant parts and species distance, for the experimental validation. Twenty-two authenticated botanicals were purposively sampled from different plant parts—covering both closely related and distantly related species—to validate the two-tiered DNA barcoding method. The performance of the method was assessed on accuracy, precision, ruggedness, and uncertainty. Results: High accuracy (100%) and precision (1.0) were obtained from the validation samples. The method was also found to be rugged and have acceptable uncertainty. Conclusions: The method was validated and suitable for DNA-based identification of botanical raw materials listed in the current database. Highlights: This work will provide support guidance for manufacturers and regulatory policy makers to implement equivalent validated and compliant DNA-based testing in quality control processes to improve botanical raw material identification and authentication.

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First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean

Genome ◽

10.1139/gen-2019-0226 ◽

2020 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Tomasz Rewicz ◽

Arnold Móra ◽

Grzegorz Tończyk ◽

Ada Szymczak ◽

Michal Grabowski ◽

...

Keyword(s):

Dna Barcoding ◽

Related Species ◽

Dna Barcode ◽

Taxonomic Status ◽

Index Number ◽

Reference Library ◽

Nuclear Markers ◽

Closely Related Species ◽

Maltese Islands ◽

Morphological Species

We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.

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Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d180411 ◽

2017 ◽

Vol 18 (4) ◽

pp. 1358-1366

Author(s):

MOHD LUTFI ABDULLAH ◽

SITI AZIZAH MOHD NOR ◽

DARLINA MD. NAIM

Keyword(s):

Dna Barcoding ◽

Fish Species ◽

Incomplete Lineage Sorting ◽

Molecular Taxonomy ◽

Dna Barcode ◽

Coi Gene ◽

Lineage Sorting ◽

Taxonomic Studies ◽

Mitochondrial Cytochrome Oxidase ◽

Blast Result

Abdullah ML, Nor SAM, Naim DMd. 2017. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas 18: 1358-1366. The genus Ariidae contains many valuable fish species threatened by overfishing, but knowledge on distribution and threats is still limited due to taxonomic ambiguities. The aim of this study was to apply DNA barcoding techniques to establish a resource of DNA for identification of Ariidae species in Malaysia. A 621 bp of mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to resolve phylogenetic relationships and molecular taxonomy of eight presumed Malaysian Ariid species. We found the monophyly of most species was well established with a mean Kimura-2 parameter (K2P) interspecies distance of 9.6% except for two species, Arius venosus, and Nemapteryx caelata that have very low interspecies genetic distance. The BLAST result shows only two species matched the presumably eight identified fish species. Such discrepancies could arise as a result of misidentifications or errors in GenBank database input, hybridization or incomplete lineage sorting. We suggest the use of DNA barcoding is integrated into the workflow during taxonomic studies as it could significantly increase knowledge about species distributions.

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Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

10.1101/087437 ◽

2016 ◽

Cited By ~ 11

Author(s):

Shadi Shokralla ◽

Joel F. Gibson ◽

Ian King ◽

Donald J. Baird ◽

Daniel H. Janzen ◽

...

Keyword(s):

Environmental Samples ◽

High Throughput Sequencing ◽

Dna Analysis ◽

Dna Barcode ◽

Environmental Dna ◽

Amplicon Sequencing ◽

Marker Genes ◽

Hybridization Capture ◽

Sequence Capture ◽

Wide Range

ABSTRACTEnvironmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.

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A revision of European species of the genus Tetrastichus Haliday (Hymenoptera: Eulophidae) using integrative taxonomy

Biodiversity Data Journal ◽

10.3897/bdj.8.e59177 ◽

2020 ◽

Vol 8 ◽

Author(s):

Christer Hansson ◽

Stefan Schmidt

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Host Record ◽

Current Data ◽

Biological Information ◽

Morphological Data ◽

Integrative Approach ◽

Similar Species ◽

European Species ◽

Wide Range

The European species of the genus Tetrastichus (Insecta, Hymenoptera, Eulophidae, Tetrastichinae) are revised with 93 species, including 50 species described as new. The revision was conducted using an integrative taxonomic approach, based on DNA barcoding in combination with morphological characters. The Tetrastichinae are a biologically diverse and species-rich group of parasitoid wasps with numerous complexes of morphologically often very similar species that attack a wide range of hosts in over 100 insect families in 10 different orders. The genus Tetrastichus is, with almost 500 described species, the third largest genus of Tetrastichinae. Although biological information is lacking for most species, current data indicate that Tetrastichus species are gregarious koinobiont endoparasitoids developing on juvenile stages of mainly holometabolous insects. Due to their host specificity, several species of Tetrastichus are used as biological control agents. The European species of Tetrastichus Haliday (Hymenoptera: Eulophidae) are revised using a combination of externo-morphological and DNA barcoding data. This is the first integrative approach for any of the large genera of the Tetrastichinae. A total of 93 species are included, of which 50 are described as new: T. agonus sp. n., T. antonjanssoni sp. n., T. argei sp. n., T. argutus sp. n., T. asilis sp. n., T. ballotus sp. n., T. bledius sp. n., T. broncus sp. n., T. calcarius sp. n., T. calmius sp. n., T. clisius sp. n., T. cosidis sp. n., T. cumulus sp. n., T. cyprus sp. n., T. delvarei sp. n., T. doczkali sp. n., T. elanus sp. n., T. elodius sp. n., T. ennis sp. n., T. enodis sp. n., T. erinus sp. n., T. evexus sp. n., T. fadus sp. n., T. fenrisi sp. n., T. flaccius sp. n., T. gredius sp. n., T. iasi sp. n., T. illydris sp. n., T. incanus sp. n., T. inscitus sp. n., T. intruitus sp. n., T. johnnoyesi sp. n., T. lacustrinus sp. n., T. ladrus sp. n., T. lanius sp. n., T. lazius sp. n., T. lixalius sp. n., T. lycus sp. n., T. marcusgrahami sp. n., T. minius sp. n., T. mixtus sp. n., T. nataliedaleskeyae sp. n., T. nymphae sp. n., T. pixius sp. n., T. scardiae sp. n., T. splendens sp. n., T. sti sp. n., T. suecus sp. n., T. tacitus sp. n. and T. tartus sp. n. Two keys for the identification of species are presented, one for females and one for males. Based on DNA barcode sequences for 70 of the species, a Maximum Likelihood tree to assess phylogenetic relationships within the genus is presented. These 70 species are also characterised by a combination of CO1 and morphological data. The remaining 23 species, without a DNA barcode, are characterised by morphological data. Using a combination of data from the morphology and CO1 or morphological data only, the species are separated into three species groups (clito-, hylotomarum-, murcia-groups) with 41 unplaced species outside these groups. Hosts are known for 27 of the species and they are gregarious, koinobiont endoparasitoids on a wide range of immature stages of holometabolous insects and appear to be very host specific. The first host record for Lepidoptera (Tineidae) in Europe is included.

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DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Genome ◽

10.1139/gen-2016-0024 ◽

2016 ◽

Vol 59 (11) ◽

pp. 933-945 ◽

Cited By ~ 30

Author(s):

Muhammad Ashfaq ◽

Paul D.N. Hebert

Keyword(s):

Dna Barcoding ◽

Life Stage ◽

Dna Barcode ◽

Dna Barcodes ◽

Plant Pests ◽

The Past ◽

Arthropod Species ◽

Global Agriculture ◽

Major Pest ◽

Cryptic Taxa

Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.

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Differentiation of Mitragyna speciosa, a narcotic plant, from allied Mitragyna species using DNA barcoding-high-resolution melting (Bar-HRM) analysis

Scientific Reports ◽

10.1038/s41598-021-86228-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Chayapol Tungphatthong ◽

Santhosh Kumar J. Urumarudappa ◽

Supita Awachai ◽

Thongchai Sooksawate ◽

Suchada Sukrong

Keyword(s):

High Resolution ◽

Dna Barcoding ◽

High Resolution Melting ◽

Dna Barcode ◽

Herbal Medicines ◽

Efficient Tool ◽

Hrm Analysis ◽

Mitragyna Speciosa ◽

Leaf Powder

AbstractMitragyna speciosa (Korth.) Havil. [MS], or “kratom” in Thai, is the only narcotic species among the four species of Mitragyna in Thailand, which also include Mitragyna diversifolia (Wall. ex G. Don) Havil. [MD], Mitragyna hirsuta Havil. [MH], and Mitragyna rotundifolia (Roxb.) O. Kuntze [MR]. M. speciosa is a tropical tree belonging to the Rubiaceae family and has been prohibited by law in Thailand. However, it has been extensively covered in national and international news, as its abuse has become more popular. M. speciosa is a narcotic plant and has been used as an opium substitute and traditionally used for the treatment of chronic pain and various illnesses. Due to morphological disparities in the genus, the identification of plants in various forms, including fresh leaves, dried leaf powder, and finished products, is difficult. In this study, DNA barcoding combined with high-resolution melting (Bar-HRM) analysis was performed to differentiate M. speciosa from allied Mitragyna and to assess the capability of Bar-HRM assays to identify M. speciosa in suspected kratom or M. speciosa-containing samples. Bar-HRM analysis of PCR amplicons was based on the ITS2, rbcL, trnH-psbA, and matK DNA barcode regions. The melting profiles of ITS2 amplicons were clearly distinct, which enabled the authentication and differentiation of Mitragyna species from allied species. This study reveals that DNA barcoding coupled with HRM is an efficient tool with which to identify M. speciosa and M. speciosa-containing samples and ensure the safety and quality of traditional Thai herbal medicines.

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Parasites in Antarctic krill guts inferred from DNA sequences

Antarctic Science ◽

10.1017/s0954102018000469 ◽

2019 ◽

Vol 31 (1) ◽

pp. 16-22 ◽

Cited By ~ 2

Author(s):

Alison C. Cleary ◽

Maria C. Casas ◽

Edward G. Durbin ◽

Jaime Gómez-Gutiérrez

Keyword(s):

Dna Sequences ◽

High Frequency ◽

Dna Analysis ◽

Antarctic Krill ◽

Euphausia Superba ◽

Gut Contents ◽

The West ◽

West Antarctic ◽

Wide Range

AbstractThe keystone role of Antarctic krill,Euphausia superbaDana, in Southern Ocean ecosystems, means it is essential to understand the factors controlling their abundance and secondary production. One such factor that remains poorly known is the role of parasites. A recent study of krill diet using DNA analysis of gut contents provided a snapshot of the parasites present within 170E. superbaguts in a small area along the West Antarctic Peninsula. These parasites includedMetschnikowiaspp. fungi,Haptoglossasp. peronosporomycetes,LankesteriaandParalecudinaspp. apicomplexa,Stegophorussp. nematodes, andPseudocolliniaspp. ciliates. Of these parasites,Metschnikowiaspp. fungi andPseudocolliniaspp. ciliates had previously been observed inE. superba, as had other genera of apicomplexans, though notLankesteriaandParalecudina.In contrast, nematodes had previously only been observed in eggs ofE. superba, and there are no literature reports of peronosporomycetes in euphausiids.Pseudocolliniaspp., parasitoids which obligately kill their host, were the most frequently observed infection, with a prevalence of 12%. The wide range of observed parasites and the relatively high frequency of infections suggest parasites may play a more important role than previously acknowledged inE. superbaecology and population dynamics.

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Research Paper DNA barcode identification of fish products from Guiyang markets in southwest China

Journal of Food Protection ◽

10.4315/jfp-21-258 ◽

2022 ◽

Author(s):

Qian Tang ◽

Qi Luo ◽

Qian Duan ◽

Lei Deng ◽

Renyi Zhang

Keyword(s):

Dna Barcoding ◽

Molecular Identification ◽

Fish Consumption ◽

Southwest China ◽

Dna Barcode ◽

Guizhou Province ◽

Accurate Identification ◽

Continuous Growth ◽

Fish Products ◽

Fresh Frozen

Nowadays, the global fish consumption continues to rise along with the continuous growth of the population, which has led to the dilemma of overfishing of fishery resources. Especially high-value fish that are overfished are often replaced by other fish. Therefore, the accurate identification of fish products in the market is a problem worthy of attention. In this study, full-DNA barcoding (FDB) and mini-DNA barcoding (MDB) used to detect the fraud of fish products in Guiyang, Guizhou province in China. The molecular identification results showed that 39 of the 191 samples were not consistent with the labels. The mislabelling of fish products for fresh, frozen, cooked and canned were 11.70%, 20.00%, 34.09% and 50.00%, respectively. The average kimura 2 parameter distances of MDB within species and genera were 0.27% and 5.41%, respectively; while average distances of FDB were 0.17% within species and 6.17% within genera. In this study, commercial fraud is noticeable, most of the high-priced fish were replaced of low-priced fish with a similar feature. Our study indicated that DNA barcoding is a valid tool for the identification of fish products and that it allows an idea of conservation and monitoring efforts, while confirming the MDB as a reliable tool for fish products.

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Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

10.21203/rs.3.rs-844711/v1 ◽

2021 ◽

Author(s):

Sonexay Rasphone ◽

Long Thanh Dang ◽

Hoan Nguyen ◽

Ngoc Quang Nguyen ◽

Oanh Thi Duong ◽

...

Keyword(s):

Dna Barcoding ◽

Ribosomal Dna ◽

Maximum Likelihood Method ◽

Dna Barcode ◽

Population Expansion ◽

Nuclear Ribosomal Dna ◽

Likelihood Method ◽

Gene Region ◽

Universal Primers ◽

Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

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