Authentication of Chinese Crude Drug Gecko by DNA Barcoding

Gekko gecko, an animal used as a valued traditional Chinese medicine, has been widely used for over 2000 years. Due to localized habitat destruction, the amount of G. gecko has dramatically decreased in recent years. As a result, more and more adulterants have been detected in the traditional medicine, which has resulted in a chaotic market. Therefore, a correct identification method is badly needed. In this study, we employed a new molecular method of DNA barcoding for discriminating gecko from its adulterants. Fifty-seven specimens of gecko and its adulterants were collected as test samples. The full-barcode and mini-barcode sequences of these specimens were separately amplified and sequenced separately. Together with other published barcode sequences, we detected that the intra-specific sequence diversity was far lower than the inter-specific diversity in G. gecko and its adulterants (3% compared with 35% in full-length barcode; 4% compared with 33.5% in mini-barcode). These results showed that both the full-length and mini-barcodes were effective for identifying gecko, which suggested that the DNA barcode could be an effective and powerful tool for identifying the Chinese crude drug gecko.

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Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.

Genome ◽

10.1139/gen-2015-0205 ◽

2016 ◽

Vol 59 (12) ◽

pp. 1150-1156 ◽

Cited By ~ 4

Author(s):

Sundar Poovitha ◽

Nithaniyal Stalin ◽

Raju Balaji ◽

Madasamy Parani

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Dna Barcode ◽

Species Differentiation ◽

Molecular Method ◽

Peninsular India ◽

Plant Materials ◽

Medicinal Value ◽

Formed Part ◽

Suitable Marker

The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%–9.6% with individual markers, which increased to 0%–12.5% and 0.8%–20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.

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An overview of molecular identification of insect fauna with special emphasis on chalcid wasps (Hymenoptera: Chalcidoidea) of India

Acta agriculturae Slovenica ◽

10.14720/aas.2018.111.1.22 ◽

2018 ◽

Vol 111 (1) ◽

pp. 229

Author(s):

Ajaz RASOOL ◽

Tariq AHMAD ◽

Bashir Ahmad GANAI ◽

Shaziya GULL

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Biological Diversity ◽

Global Climate ◽

Biological Effects ◽

Dna Barcode ◽

Habitat Destruction ◽

Insect Fauna ◽

Processed Material ◽

The Face

Identifying organisms has grown in importance as we monitor the biological effects of global climate change and attempt to preserve species diversity in the face of accelerating habitat destruction. Classical taxonomy falls short in this race to catalogue biological diversity before it disappears. Differentiating subtle anatomical differences between closely related species requires the subjective judgment of highly trained specialists – and few are being trained in institutes today. DNA barcodes allow non-experts to objectively identify species – from small, damaged, or even industrially processed material. The aim of DNA barcoding is to establish a shared community resource of DNA sequences commonly used for identification, discrimination or taxonomic classification of organisms. It is a method that uses a short genetic marker in an organism's DNA to identify and distinguish its belonging from particular species, varieties or inter varieties. This simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant-quarantine officers and studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made them a major target of DNA barcoding. In this review, we present an overview of DNA barcoding of insects with emphasis on Chalcid wasps of India.

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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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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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Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

Plants ◽

10.3390/plants10102023 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2023

Author(s):

Suwimol Thariwong ◽

Aekkhaluck Intharuksa ◽

Panee Sirisa-ard ◽

Wannaree Charoensup ◽

Sunee Chansakaow

Keyword(s):

Dna Barcoding ◽

Herbal Remedy ◽

Raw Materials ◽

Dna Barcode ◽

Raw Material ◽

Morinda Citrifolia ◽

Herbal Remedies ◽

Scientific Database ◽

Kidney Deficiency ◽

Fruit Species

The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.

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A DNA barcode reference library of the French Polynesian shore fishes

10.1101/595793 ◽

2019 ◽

Author(s):

Erwan Delrieu-Trottin ◽

Jeffrey T. Williams ◽

Diane Pitassy ◽

Amy Driskell ◽

Nicolas Hubert ◽

...

Keyword(s):

Dna Barcoding ◽

Biological Diversity ◽

Dna Barcode ◽

Reef Fishes ◽

French Polynesia ◽

Morphological Characters ◽

Reference Library ◽

Society Islands ◽

Extensive Collection ◽

I Gene

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

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ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

Insect Systematics and Diversity ◽

10.1093/isd/ixab013 ◽

2021 ◽

Vol 5 (5) ◽

Author(s):

Juha Salokannel ◽

Kyung Min Lee ◽

Aki Rinne ◽

Marko Mutanen

Keyword(s):

Dna Barcoding ◽

Large Scale ◽

Dna Barcode ◽

Nuclear Genome ◽

Distinct Species ◽

Present Species ◽

Cryptic Diversity ◽

Weak Support ◽

Genomic Scale ◽

Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

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Filling gaps in the DNA barcode library - Aquatic insects (Ephemeroptera, Plecoptera, Trichoptera) from semi-mountainous and mountainous rivers of Ecoregion 6 (North Macedonia)

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65053 ◽

2021 ◽

Vol 4 ◽

Author(s):

Biljana Rimcheska ◽

Yanka Vidinova

Keyword(s):

New Species ◽

Dna Barcoding ◽

Aquatic Insects ◽

Molecular Genetic ◽

Dna Barcode ◽

Balkan Peninsula ◽

Molecular Genetic Data ◽

Medium Quality ◽

Total Dna ◽

Data Library

This research provides pivotal molecular genetic data on the community structure of aquatic insects from semi-mountainous and mountainous rivers from the 6th Ecoregion that belongs to the territory of North Macedonia. The aim of this research is to fill the gaps for barcoding the aquatic macroinvertebrates from the Balkan Peninsula and check if the existing barcode library could provide improved identifications for the specimens that were not taxonomically determined to the lowest level possible. We analyzed 95 specimens from which total DNA was extracted and the COI barcode region amplified and sequenced. The taxa were selected from 20 different localities of the territory of western part of North Macedonia. The selected specimens were not determined to species-level in order to test the efficiency of the DNA barcoding methodology and what is missing in the DNA barcoding data library. From the result from one plate (95 specimens) we obtained: 16 samples without barodes, or failed and 10 samples did not have a match in the BOLD database. In the remining 69 samples, three were misidentified. In the total of 69 barcoded species new for the fauna of North Macedonia, 11 are mayflies: Baetis melanonyx, Ecdyonurus vitoshensis, E. macani; stonefly Isoperla vjose; and caddisflies: Agapetus delicatulus, Athripsodes bilineatus, Glossosoma klotho, Lepidostoma basale, Helicopsyche bacescui, Tinodes unicolor and Odontocerum hellenicum. We have also four rarely found species: Zwicknia bifrons, Drussus tenellus, Hydropsyche botosaneanui and Hydropsyche bulbifera, and one species without barcode available as Ecdyonurus sp. SK2 (potential new species). We found 83% efficiency of DNA barcoding, where some samples failed or were with low or medium quality for some specimens, as for the representatives from the genera Baetis, Oxietyra and Rhyacophila. In conclusion we can confirm that 10 of the selected vouchers need to be further identified by morphology and to be added in the BOLD barcode library, and maybe we'll have the possibility to describe a new species as well.

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DNA barcoding a nightmare taxon: assessing barcode index numbers and barcode gaps for sweat bees

Genome ◽

10.1139/gen-2017-0096 ◽

2018 ◽

Vol 61 (1) ◽

pp. 21-31 ◽

Cited By ~ 15

Author(s):

Jason Gibbs

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Error Rates ◽

Nucleotide Substitutions ◽

Single Linkage ◽

Data Set ◽

Index Numbers ◽

Method Error ◽

Specimen Identification ◽

Barcode Gap

There is an ongoing campaign to DNA barcode the world’s >20 000 bee species. Recent revisions of Lasioglossum (Dialictus) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of L. (Dialictus) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method. Error rates were 20% relative to current taxonomic understanding. Barcode Index Numbers (BINs) assigned using Refined Single Linkage Analysis (RESL) and barcode gaps using the Automatic Barcode Gap Discovery (ABGD) method were also assessed. RESL was incongruent for 44.5% of species, although some cryptic diversity may exist. Forty-three of 110 species were part of merged BINs with multiple species. The barcode gap is non-existent for the data set as a whole and ABGD showed levels of discordance similar to the RESL. The viridatum species-group is particularly problematic, so that DNA barcodes alone would be misleading for species delimitation and specimen identification. Character-based methods using fixed nucleotide substitutions could improve specimen identification success in some cases. The use of DNA barcoding for species discovery for standard taxonomic practice in the absence of a well-defined barcode gap is discussed.

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