DNA barcoding for identification of species in mushrooms: A component of product certification

Forensic entomology uses insects to determine the time, cause and place of death. To this end, two entomological methods are used. The development-based method uses the patterns of insect larvae development under the specific thermal and environmental conditions. The succession-based method analyzes the sequence of insect succession on the body in various environmental conditions. The proper insect species identification is essential in both methods. In this article, the molecular methods of species, age and sex identification are presented such as DNA barcoding or DNA-HRM-PCR.

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COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae)

Amphibia-Reptilia ◽

10.1163/15685381-00003012 ◽

2015 ◽

Vol 36 (4) ◽

pp. 361-372 ◽

Cited By ~ 4

Author(s):

Qin Liu ◽

Fei Zhu ◽

Guanghui Zhong ◽

Yunyu Wang ◽

Min Fang ◽

...

Keyword(s):

Dna Barcoding ◽

Intraspecific Variability ◽

Gene Fragment ◽

Reference Library ◽

Threshold Method ◽

Cytochrome Oxidase Subunit ◽

Barcoding Gap ◽

Putative Species ◽

Interspecific Divergence ◽

Identification Of Species

DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.

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The molecular identification of Zanthoxylum armatum DC of Pakistan based on DNA barcoding

Bangladesh Journal of Plant Taxonomy ◽

10.3329/bjpt.v27i2.50671 ◽

2020 ◽

Vol 27 (2) ◽

pp. 323-333

Author(s):

Shakila Umer ◽

Nayab Safdar ◽

Khushi Muhammad

Keyword(s):

Dna Barcoding ◽

Molecular Identification ◽

Sequence Similarity ◽

Pcr Analysis ◽

Dna Barcodes ◽

Zanthoxylum Armatum ◽

The Family ◽

Plant Taxon ◽

Identification Of Species ◽

Zanthoxylum Bungeanum

Zanthoxylum armatum DC., belonged to the family Ruteacea, is a medicinal plant used to cure many diseases. DNA barcoding was used as a tool for molecular identification of Zanthoxylum armatum DC. species from Balakot Pakistan. In the present study four DNA barcodes including matk, rbcl, ITS and trnH-psbA were used. The sequenced data were analyzed by using BLASTn at NCBI, FASTA and Mega 7.0 software. During PCR analysis, 3 DNA barcodes ITS, rbcl and trnh-psbA were successfully amplified and showed the 100% sequencing success. Furthermore, these barcode markers showed 99-100% sequence similarity with the reference sequences at the BLASTn. The further analysis revealed the sequence similarity of investigating marker with Zanthoxylum armatum (MH016484.1), Zanthoxylum nitidum (FN599471.1) and Zanthoxylum bungeanum (MF097123.1) respectively. The current finding provides the basis for sequenced data of Z. armatum to be used in future for molecular discrimination among the plant species from Pakistan and it is concluded that combination of diverse kind of barcoding markers could be helpful in proper identification of species at lower taxonomic level. Bangladesh J. Plant Taxon. 27(2): 323-333, 2020 (December)

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Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding

Genome ◽

10.1139/gen-2015-0225 ◽

2017 ◽

Vol 60 (2) ◽

pp. 139-146 ◽

Cited By ~ 7

Author(s):

Stalin Nithaniyal ◽

Sophie Lorraine Vassou ◽

Sundar Poovitha ◽

Balaji Raju ◽

Madasamy Parani

Keyword(s):

Medicinal Plants ◽

Medicinal Plant ◽

Alternative Medicine ◽

Dna Barcoding ◽

Species Identification ◽

Dna Barcode ◽

Regulatory Agencies ◽

Vernacular Names ◽

Identification Of Species ◽

Whole Plants

Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.

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Species Delimitation of Scavenger Flies in the Valley of Mexico

Journal of Medical Entomology ◽

10.1093/jme/tjab094 ◽

2021 ◽

Author(s):

Carlos Pedraza-Lara ◽

Marco A Garduño-Sánchez ◽

Isabel Téllez-García ◽

Stephany Rodríguez-González ◽

Eduardo Nuple-Juárez ◽

...

Keyword(s):

Species Richness ◽

Dna Barcoding ◽

Species Delimitation ◽

Nature Reserve ◽

New Records ◽

Dna Barcode ◽

Coi Gene ◽

Baseline Knowledge ◽

Identification Of Species ◽

Diverse Groups

Abstract Identification of species involved in cadaveric decomposition, such as scavenger Diptera, is a fundamental step for the use of entomological evidence in court. Identification based on morphology is widely used in forensic cases; however, taxonomic knowledge of scavenger fauna is poor for many groups and for many countries, particularly Neotropical ones. A number of studies have documented the utility of a DNA barcoding strategy to assist in the identification of poorly known and diverse groups, particularly in cases involving immature states or fragmented organisms. To provide baseline knowledge of the diversity of scavenger Diptera in the Valley of Mexico, we generated a DNA barcode collection comprised of sequences of the cytochrome c oxidase subunit 1 (COI) gene for all families sampled at a nature reserve located in this region. We collected and identified specimens on the basis of morphology and a species delimitation analysis. Our analyses of 339 individuals delineated 42 species distributed across nine families of Diptera. The richest families were Calliphoridae (9 species), Sarcophagidae (7 species), and Phoridae (6 species). We found many of the species previously recorded for the Valley of Mexico, plus 18 new records for the region. Our study highlights the utility of DNA barcoding as a first-step strategy to assess species richness of poorly studied scavenger fly taxa.

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Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding

Current Zoology ◽

10.1093/czoolo/55.2.158 ◽

2009 ◽

Vol 55 (2) ◽

pp. 158-164 ◽

Cited By ~ 22

Author(s):

Zhong-e Hou ◽

Zhu Li ◽

Shu-qiang Li

Keyword(s):

Cryptic Species ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Neighbor Joining ◽

Cytochrome C Oxidase I ◽

Widespread Species ◽

Intraspecific Divergence ◽

Gammarus Lacustris ◽

Interspecific Divergence ◽

Identification Of Species

Abstract Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21. 9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

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DNA Barcoding: A Reliable Method for the Identification of Thrips Species (Thysanoptera, Thripidae) Collected on Sticky Traps in Onion Fields

Insects ◽

10.3390/insects11080489 ◽

2020 ◽

Vol 11 (8) ◽

pp. 489 ◽

Cited By ~ 1

Author(s):

Rita Marullo ◽

Francesco Mercati ◽

Gregorio Vono

Keyword(s):

Dna Barcoding ◽

Insect Pests ◽

Small Body ◽

Correct Identification ◽

Cytochrome C Oxidase I ◽

Sticky Traps ◽

Thrips Species ◽

The Family ◽

Identification Of Species ◽

Morphological Differences

Several thrips species (Insecta, Thysanoptera) are globally known as important crop pests and vectors of viral diseases, but their identification is difficult because of their small body size and inconspicuous morphological differences. Sequencing variation in the mitochondrial cytochrome c oxidase I (COI) region has been proven to be useful for the identification of species of many groups of insect pests. Here, DNA barcoding has been used to identify thrips species collected with the use of sticky traps placed in an open onion field. A total of 238 thrips specimens were analyzed, 151 of which could be identified to species and 27 to genera belonging to the family Thripidae. Fifty-one specimens could not be assigned to any genus, with the closest BLAST match in the GenBank queries being below 98%, whilst six specimens were not recognized as Thysanoptera. The results indicate that, although there are a few pest thrips species not yet barcoded, most of the species that may cause damage to crops in Europe are represented in GenBank and other databases, enabling correct identification. Additionally, DNA barcoding can be considered a valuable alternative to the classic morphology method for identification of major thrips species.

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DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

Neotropical Ichthyology ◽

10.1590/1982-0224-20160147 ◽

2017 ◽

Vol 15 (1) ◽

Cited By ~ 7

Author(s):

Josiane Ribolli ◽

Bianca Maria Scaranto ◽

Oscar Akio Shibatta ◽

Robie Allan Bombardelli ◽

Evoy Zaniboni-Filho

Keyword(s):

Dna Barcoding ◽

River Basin ◽

Molecular Taxonomy ◽

Distinct Species ◽

Operational Taxonomic Units ◽

Identification Of Species ◽

Cytogenetic Analyses ◽

Taxonomic Studies ◽

Optimum Threshold ◽

Iguaçu River

ABSTRACT DNA barcoding is a widely utilized molecular-based identification of species and taxonomic resolutions. Until recently, Rhamdia voulezi and Rhamdia branneri were considered species synonyms of Rhamdia quelen; however, morphological and cytogenetic analyses have suggested the validity of distinct species. Due to the absence of molecular taxonomy of R. voulezi and R. branneri, the objective of this study was to test its validity through traditional DNA barcoding and the GMYC (General Mixed Yule Coalescent) COI-based analyses in 19 specimens from the Iguaçu River Basin. In both methodologies, three MOTUs (Molecular Operational Taxonomic Units) were identified based on the estimated optimum threshold (OT = 0.77). The average inter-MOTU distance (NJ, K2P) between R. branneri and R. voulezi was 1.4%, and 0% intra-MOTU distance in both species. The two species identified as R. branneri and R. voulezi showed correspondence with taxonomic and morphological identifications. With regard to R. quelen, the average intra-MOTU distance was greater than OT (2.7%), indicating that this species can be formed by different MOTUs. We suggest that molecular and taxonomic studies should be employed concurrently in R. quelen, to prevent contamination of wild species by hybridizations.

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Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2005.1715 ◽

2005 ◽

Vol 360 (1462) ◽

pp. 1835-1845 ◽

Cited By ~ 217

Author(s):

Daniel H Janzen ◽

Mehrdad Hajibabaei ◽

John M Burns ◽

Winnie Hallwachs ◽

Ed Remigio ◽

...

Keyword(s):

Dna Barcoding ◽

Cloud Forest ◽

Tropical Dry Forest ◽

Sympatric Species ◽

Dry Forest ◽

Full Potential ◽

Resource Base ◽

Biodiversity Inventory ◽

Large Numbers ◽

Identification Of Species

By facilitating bioliteracy, DNA barcoding has the potential to improve the way the world relates to wild biodiversity. Here we describe the early stages of the use of cox1 barcoding to supplement and strengthen the taxonomic platform underpinning the inventory of thousands of sympatric species of caterpillars in tropical dry forest, cloud forest and rain forest in northwestern Costa Rica. The results show that barcoding a biologically complex biota unambiguously distinguishes among 97% of more than 1000 species of reared Lepidoptera. Those few species whose barcodes overlap are closely related and not confused with other species. Barcoding also has revealed a substantial number of cryptic species among morphologically defined species, associated sexes, and reinforced identification of species that are difficult to distinguish morphologically. For barcoding to achieve its full potential, (i) ability to rapidly and cheaply barcode older museum specimens is urgent, (ii) museums need to address the opportunity and responsibility for housing large numbers of barcode voucher specimens, (iii) substantial resources need be mustered to support the taxonomic side of the partnership with barcoding, and (iv) hand-held field-friendly barcorder must emerge as a mutualism with the taxasphere and the barcoding initiative, in a manner such that its use generates a resource base for the taxonomic process as well as a tool for the user.

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