scholarly journals DNA Barcoding Subtropical Aphids and Implications for Population Differentiation

Insects ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 11 ◽  
Author(s):  
Qiang Li ◽  
Jun Deng ◽  
Cui Chen ◽  
Linda Zeng ◽  
Xiaolan Lin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Population Differentiation ◽  
Dna Barcode ◽  
Threshold Value ◽  
Aphid Species ◽  
Sampling Effort ◽  
Pest Species ◽  
Aphis Spiraecola ◽  
Geographical Regions ◽  
Taxonomic Groups

DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.

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

A complement to DNA barcoding reference library for identification of fish from the Northeast Pacific

Genome ◽  
2021 ◽  
Author(s):  
Sergei V Turanov ◽  
Yuri Ph. Kartavtsev
Keyword(s):  
Dna Barcoding ◽  
North Pacific Ocean ◽  
Molecular Genetic ◽  
Dna Barcode ◽  
Fish Fauna ◽  
Threshold Value ◽  
Published Data ◽  
Northeast Pacific ◽  
Barcoding Gap ◽  
The North

The seas of the North Pacific Ocean are characterized by a large variety of fish fauna, including endemic species. Molecular genetic methods, often based on DNA barcoding approaches, have been recently used to determine species boundaries and identify cryptic diversity within these species. This study complements the DNA barcode library of fish from the Northeast Pacific area. A library based on 154 sequences of the mitochondrial <i>COI</i> gene from 44 species was assembled and analyzed. It was found that 39 species (89%) can be unambiguously identified by the clear thresholds forming a barcoding gap. Deviations from the standard 2% threshold value resulted in detection of the species <i>Enophrys lucasi </i>in the sample, which is not typical for the eastern part of the Bering Sea. This barcoding gap also made it possible to identify naturally occurring low values of interspecific divergence of eulittoral taxa <i>Aspidophoroides</i> and the deep-sea genus <i>Coryphaenoides</i>. Synonymy of the genus <i>Albatrossia</i> in favor of the genus <i>Coryphaenoides</i> is suggested based on both the original and previously published data.

scholarly journals Gap Analysis for DNA Barcode Reference Libraries for Aquatic Macroinvertebrate Species in the Apulia Region (Southeast of Italy)

2020 ◽  
Vol 8 (7) ◽  
pp. 538
Author(s):  
Valeria Specchia ◽  
Eftychia Tzafesta ◽  
Gabriele Marini ◽  
Salvatore Scarcella ◽  
Simona D’Attis ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Gap Analysis ◽  
Dna Barcode ◽  
Regional Level ◽  
New Combination ◽  
Dna Barcodes ◽  
Aquatic Macroinvertebrate ◽  
Apulia Region ◽  
Taxonomic Groups ◽  
Macroinvertebrate Species

The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more effective DNA barcode implementation effort and extensive use of the metabarcoding method. In this paper, a new combination of primers has revealed its experimental effectiveness at least on the species belonging to the three most represented taxa in the aquatic ecosystems of the Apulia region, highlighting the opportunity to develop combinations of primers useful at the regional level and the importance of studying DNA barcode gaps at the local/regional level. The DNA barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Acquatina di Frigole” in the Apulia region) and we sampled two macroinvertebrate species lacking DNA barcodes from “Aquatina di Frigole” NATURA 2000 Site IT9150003, Fabulina fabula and Tritia nitida, generated two new CO1 barcodes and added them to a DNA barcode reference library.

scholarly journals Complete DNA barcode reference library for a country's butterfly fauna reveals high performance for temperate Europe

2010 ◽  
Vol 278 (1704) ◽  
pp. 347-355 ◽  
Author(s):  
Vlad Dincă ◽  
Evgeny V. Zakharov ◽  
Paul D. N. Hebert ◽  
Roger Vila
Keyword(s):  
Dna Barcoding ◽  
High Performance ◽  
Dna Barcode ◽  
Taxonomic Status ◽  
Reference Database ◽  
The European Union ◽  
Early Application ◽  
Geographical Regions ◽  
Butterfly Fauna ◽  
Taxonomic Framework

DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive sampling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development.

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

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.

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.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

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

Plants ◽  
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.

scholarly journals A DNA barcode reference library of the French Polynesian shore fishes

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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