scholarly journals DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

2019 ◽  
Vol 47 (2) ◽  
pp. 333-342
Author(s):  
Abu Faiz Md Aslam ◽  
Sharmin Sultana ◽  
Sumita Rani Das ◽  
Abdul Jabber Howlader
Keyword(s):  
Dna Barcoding ◽  
Tribolium Castaneum ◽  
Life Stage ◽  
Dna Barcode ◽  
Tribolium Confusum ◽  
Likelihood Method ◽  
Coi Gene ◽  
Pest Species ◽  
Stored Grain ◽  
Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

scholarly journals Molecular characterization and identification of three stored grain pests based on mitochondrial cytochrome C oxidase subunit I (COI) gene sequences

2019 ◽  
Vol 47 (1) ◽  
pp. 1-11
Author(s):  
Abu Faiz Md Aslam ◽  
Sharmin Sultana ◽  
Faria Farhana Rain ◽  
Sumita Rani Das ◽  
Ayesha Siddika ◽  
...  
Keyword(s):  
Insect Pests ◽  
Sitophilus Oryzae ◽  
Dna Barcode ◽  
Control Measures ◽  
Coi Gene ◽  
Composition Analysis ◽  
Callosobruchus Chinensis ◽  
Pest Species ◽  
Stored Grain ◽  
Stored Grain Pests

Stored grain pests are discovered in food as immature stages, which further complicates the identification process. A DNA barcode dataset of some important pests that can be used for easy and confirm identification in stages of life is constructed. COI genes of three stored grain insect pests i.e,, Sitophilus oryzae, Callosobruchus chinensis and Oryzaephilus surinamensis were sequenced. The sequenced genes were submitted to NCBI GenBank and obtained accession numbers MG967331.1, MG967332.1, MG967333.1 and MK041216.1. BLAST analysis showed 99 to 100% homology with existing GenBank sequences. The nucleotide composition analysis revealed that the value of A+T (64.8%) is greater than G+C (35.2%). Genetic distance among four sequences of three store pests were ranged from 0.00293-0.32807. Phylogenetic analysis showed that these three species are originated from different clades. Haplotype analysis of mitochondrial COI gene of the stored grain insect pests showed high genetic diversity among them. C. chinensis, O. surinamensis and S. oryzae were separated from their common ancestor by 80, 73 and 64 mutational steps. These information may be helpful for attempting any successful control measures against the pest species. In conclusion, present author established the first DNA barcode dataset of three store grain pests and confirmed its efficiency for identifying these pests. Bangladesh J. Zool. 47(1): 1-11, 2019

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

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.

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

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.

A multiplex PCR method for identification of two common true cutworm species (Lepidoptera: Noctuidae) tested in the central plain of Guilan province, Iran

Zootaxa ◽  
2018 ◽  
Vol 4420 (2) ◽  
pp. 243
Author(s):  
REZA HOSSEINI ◽  
KHADIJEH MADAHI
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Coi Gene ◽  
Molecular Diagnostic ◽  
Pest Species ◽  
Immature Stages ◽  
Nucleotide Polymorphisms ◽  
Peridroma Saucia ◽  
Lepidoptera Noctuidae ◽  
Guilan Province

Many species of cutworms (Lepidoptera: Noctuidae) are important agricultural pest. They feed on roots and foliage of their host plants. Traditionally these species are identified based on morphological characteristics of adults. Hence identification of specimens in poor condition, immature stages and also closely related species or cryptic species is a difficult task. The basics of biological and ecological studies largely rely on an accurate species identification; consequently these investigations are impacted by potential misidentifications. In this study, we amplified 5' region of mitochondrial c cytochrome oxidase subunit I (COI) gene (DNA barcode region) of various common true cutworm species including Agrotis ipsilon (Hufnagel, 1766), Agrotis exclamationis (Linnaeus, 1758), Peridroma saucia (Hübner, 1808) and Xestia c-nigrum (Linnaeus, 1758) from agricultural fields of Guilan province (North of Iran). We were able to detect 66 conservative Single Nucleotide Polymorphisms (SNPs) among the targeted pest species and eventually design specific primers and develop a multiplex polymerase chain reaction assay as a molecular diagnostic tool for immature stages of two the most common and abundant species including A. ipsilon and X. c-nigrum in Guilan province. 

scholarly journals An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1410
Author(s):  
Inkyu Park ◽  
Sungyu Yang ◽  
Goya Choi ◽  
Byeong Cheol Moon ◽  
Jun-Ho Song
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Northeast Asia ◽  
Herbal Medicines ◽  
Integrated Approach ◽  
Rbcl Gene ◽  
Accurate Identification ◽  
Diagnostic Characteristics ◽  
Microscopic Techniques ◽  
Cuscuta Species

To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia; however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.

A test of DNA barcoding in crayfish of the upper James River basin, Virginia

2015 ◽  
Vol 21 (1) ◽  
pp. 179-183
Author(s):  
Paul R. Cabe ◽  
Bradleigh E. Navalsky ◽  
Ainsley K. Bloomer ◽  
Ryan Doherty ◽  
Jordan Edgren ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
River Basin ◽  
Native Species ◽  
Biological Diversity ◽  
Coi Gene ◽  
Test Case ◽  
Accurate Identification ◽  
James River ◽  
Coi Sequences ◽  
Current Sequence

Abstract Crayfish populations in North America face many conservation threats, including habitat loss, degradation, and the introduction of non-native species. The management of biological diversity requires accurate identification of species, and for crayfish, many species are difficult to identify using standard morphological approaches. We investigated DNA barcoding using cytochrome oxidase I (COI) gene sequences to determine if this widely used method is useful in the identification of crayfish. As a test case, we sampled crayfish from the middle and upper James River basin in Virginia. This area had been recently surveyed by experienced crayfish biologists, and hosts a moderate number of species. We collected nearly 300 COI sequences, which clustered clearly into seven groups, mirroring the seven species reported for this watershed. Despite the unambiguous clustering, the range of sequence variation within species overlapped the range of variation between species; we detected no clear "barcode gap." Although this method holds promise as an aid to crayfish identification, current sequence databases (GenBank, BOLD) do not contain enough appropriate COI sequences to allow unequivocal identification in this unique and understudies fauna.

scholarly journals Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

2022 ◽  
Vol 2022 ◽  
pp. 1-19
Author(s):  
Sarfraz Ahmed ◽  
Muhammad Ibrahim ◽  
Chanin Nantasenamat ◽  
Muhammad Farrukh Nisar ◽  
Aijaz Ahmad Malik ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Species Level ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bacterial Strains ◽  
Accurate Identification ◽  
Bisphosphate Carboxylase ◽  
Parallel Acquisition ◽  
Invertebrate Animal

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

Species Delimitation of Scavenger Flies in the Valley of Mexico

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.

A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 773-789 ◽  
Author(s):  
Gary W. Saunders
Keyword(s):  
Species Diversity ◽  
Dna Barcoding ◽  
Life Histories ◽  
Dna Barcode ◽  
Genetic System ◽  
Marine Macroalgae ◽  
Accurate Identification ◽  
Additional Species ◽  
Large Numbers ◽  
Red Algal

The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.

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