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

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)

scholarly journals Demersal Fish Diversity and Molecular Taxonomy in the Bering Sea and Chukchi Sea

2021 ◽  
Author(s):  
xuehua wang ◽  
Yuan Li ◽  
Nan Zhang ◽  
Puqing Song ◽  
Ran Zhang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Bering Sea ◽  
Chukchi Sea ◽  
Molecular Taxonomy ◽  
Demersal Fish ◽  
Fish Diversity ◽  
Dna Barcodes ◽  
The Family ◽  
Arctic Fish ◽  
The Bering Sea

Abstract DNA barcoding by sequencing a standard region of cytochrome c oxidase subunit I (COⅠ) provides an accurate, rapid method for identifying different species. In this study, we provide a molecular taxonomic assessment of demersal fishes in the Bering Sea and Chukchi Sea based on DNA barcoding, and a total of 123 mitochondrial COⅠ partial fragments with a length of 652 bp were obtained. The consensus among all sequences was determined by alignment via a BLAST search in GenBank. Phylogenetic relationships were reconstructed on the basis of neighbor-joining (NJ) trees and barcoding gaps. The 39 species investigated in this analysis were distributed among 10 families. Five families within Scorpaeniformes including 19 species accounted for almost half of the species. The next largest group was Perciformes, with 9 species, followed by Pleuronectiformes and Gadiformes, with 5 species each, and the smallest number of species belonged to Rajiformes. At the family level, Cottidae was the largest family, followed by Zoarcidae, accounting for 8 species. The other eight families—Gadidae, Pleuronectidae, Psychrolutidae, Agonidae, Liparidae, Ammodytidae, Hexagrammidae, and Rajidae—accounted for a smaller proportion of species. In brief, our study shows that DNA barcodes are an effective tool for studying fish diversity and phylogeny in the Bering Sea and Chukchi Sea. The contribution of DNA barcoding to identifying Arctic fish species may benefit further Arctic fish studies on biodiversity, biogeography and conservation in the future.

scholarly journals Newly Emerging Pest in China, Rhynchaenus maculosus (Coleoptera: Curculionidae): Morphology and Molecular Identification with DNA Barcoding

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 568
Author(s):  
Rui-Sheng Yang ◽  
Ming-Yang Ni ◽  
Yu-Jian Gu ◽  
Jia-Sheng Xu ◽  
Ying Jin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Molecular Identification ◽  
Morphological Characters ◽  
Information Storage ◽  
Morphological Description ◽  
Quick Response ◽  
Dna Barcodes ◽  
Pairwise Divergence ◽  
Coding Capacity

The oak flea weevil, Rhynchaenus maculosus Yang et Zhang 1991, is a newly emerging pest that severely damages oak (genus Quercus) in China. The first R. maculosus outbreak occurred in 2020 and caused spectacular damage to all oak forests in Jilin province, northeast China. The lack of key morphological characters complicates the identification of this native pest, especially in larva and pupa stages. This is problematic because quick and accurate species identification is crucial for early monitoring and intervention during outbreaks. Here, we provided the first detailed morphological description of R. maculosus at four life stages. Additionally, we used DNA barcodes from larva and pupa specimens collected from three remote locations for molecular identification. The average pairwise divergence of all sequences in this study was 0.51%, well below the 2% to 3% (K-2-parameter) threshold set for one species. All sample sequences matched the R. maculosus morphospecies (KX657706.1 and KX657707.1), with 99.23% to 100% (sequence identity, E value: 0.00) matching success. The tree based on barcodes placed the specimens into the Rhynchaenus group, and the phylogenetic relationship between 62 sequences (30 samples and 32 from GeneBank) had high congruence with the morphospecies taxa. The traditional DNA barcodes were successfully transformed into quick response codes with larger coding capacity for information storage. The results showed that DNA barcoding is reliable for R. maculosus identification. The integration of molecular and morphology-based methods contributes to accurate species identification of this newly emerging oak pest.

scholarly journals Identification of species and materia medica withinSaussureasubg.Amphilaenabased on DNA barcodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6357 ◽  
Author(s):  
Jie Chen ◽  
Yong-Bao Zhao ◽  
Yu-Jin Wang ◽  
Xiao-Gang Li
Keyword(s):  
Internal Transcribed Spacer ◽  
Evolutionary History ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Additional Species ◽  
Plant Materials ◽  
Materia Medica ◽  
The Family ◽  
Identification Of Species ◽  
Medical Plants

Saussureais one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed.Saussureasubg.Amphilaenais one of the four subgenera ofSaussureaand it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) +rbcL or ITS +rbcL +psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS +rbcL as the DNA barcode forS.subg.Amphilaenaor the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.

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

Insects ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 489 ◽  
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.

scholarly journals Assessment of the DNA Barcodes Characteristic of Phalaenopsis deliciosa based on matK, rbcL, and ITS

2020 ◽  
Vol 8 (2) ◽  
pp. 138
Author(s):  
Nada Nisrina Maulidya ◽  
Siti Rohimah ◽  
Zakiyah Ramadany ◽  
Tri Ratnasari ◽  
Mukhamad Su'udi
Keyword(s):  
Dna Barcoding ◽  
Plant Species ◽  
Molecular Identification ◽  
High Specificity ◽  
Morphological Characters ◽  
Flowering Period ◽  
Dna Barcodes ◽  
Alternative Method

Indonesia has high biodiversity for plant species, including orchids with medicinal potential such as Phalaenopsis deliciosa. Generally, morphological characters, especially in flowers are used for orchids identification. However, when the plants are not in the flowering period, the identification becomes difficult. Therefore an alternative method, such as molecular identification (DNA barcoding) needs to be applied for the best solution. This research, which was conducted with three different markers found that the identity level of matK, rbcL, and ITS to other orchids species was 99-98%, 98%, and 94-96%, respectively. Furthermore, matK and ITS showed high specificity for Phalaenopsis deliciosa, and are therefore recommended as the best molecular identification marker of genus Phalaenopsis.

scholarly journals Molecular identification of Lavendula dentata L., Mentha longifolia (L.) Huds. and Mentha × piperita L. by DNA barcodes

2018 ◽  
Vol 25 (2) ◽  
pp. 149-157
Author(s):  
Shawkat Mahmoud Ahmed
Keyword(s):  
Saudi Arabia ◽  
Dna Barcoding ◽  
Molecular Identification ◽  
Phylogenetic Trees ◽  
Mentha Piperita ◽  
Dna Barcodes ◽  
Mentha Longifolia ◽  
The Relationship

Five DNA barcodes were tested for identification and discrimination of Lavendula dentata L., Mentha longifolia (L.) Huds. and Mentha × piperita L. New DNA barcodes have been registered for L. dentata from Taif, Saudi Arabia. The separate clading of L. dentata and M. longifolia through the phylogenic analyses proved their endemism to Saudi Arabia. The phylogenetic trees revealed from the ITS2, matK and trnH data demonstrated that all Mentha species formed monophyletic clusters except hybrid M. × piperita from Taif which formed separate clades distinguishing it from the two parents; M. aquatica L. and M. spicata L. DNA barcoding could be considered as a good approach for distinguishing and identifying the mint plants, though it was not possible to confirm the relationship between hybrids and their putative parents.

DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 348-357 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Fernanda Montes De Oca ◽  
Sean W.J. Prosser ◽  
Paul D.N. Hebert ◽  
T. Ryan Gregory ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Black Flies ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
Species Groups

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

scholarly journals Diversity and Life-cycle Analysis of Pacific Ocean Zooplankton by Videomicroscopy and DNA Barcoding. I. Cnidaria

2019 ◽  
Author(s):  
Peter J. Bryant ◽  
Timothy E. Arehart
Keyword(s):  
Life Cycle ◽  
Pacific Ocean ◽  
Dna Barcoding ◽  
Dna Barcodes ◽  
Putative Species ◽  
The Pacific ◽  
Solid Substrates ◽  
The Family ◽  
The Pacific Ocean ◽  
The University

AbstractMost, but not all cnidarian species in the classes Hydrozoa, Scyphozoa and Anthozoa have a life cycle in which a colonial, asexually reproducing hydroid phase alternates with a free-swimming, sexually reproducing medusa phase that, in the hydrozoans, is usually microscopic. Hydrozoan medusae were collected by zooplankton tows in Newport Bay and the Pacific Ocean near Newport Beach, California, and hydroid colonies were collected from solid substrates in the same areas. Specimens were documented by videomicroscopy, preserved in ethanol, and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for DNA barcoding.Among the order Anthomedusae (athecate hydroids), DNA barcoding allowed for the discrimination between the medusae of eight putative species of Bougainvillia, and the hydroid stages were documented for two of these. The medusae of three putative species of Amphinema were identified, and the hydroid stages were identified for two of them. DNA barcodes were obtained from medusae of one species of Cladonema, one adult of the By-the wind Sailor, Velella Velella, five putative species of Corymorpha with the matching hydroid phase for one; and Coryne eximia, Turritopsis dohrnii and Turritopsis nutricula with the corresponding hydroid phases. The actinula larvae and hydroid for the pink-hearted hydroid Ectopleura crocea were identified and linked by DNA barcoding.Among the order Leptomedusae (thecate hydroids) medusae were identified for Clytia elsaeoswaldae, Clytia gracilis and Clytia sp. 701 AC and matched with the hydroid phases for the latter two species. Medusae were matched with the hydroid phases for two species of Obelia (including O. dichotoma) and Eucheilota bakeri. Obelia geniculata was collected as a single hydroid. DNA barcodes were obtained for hydroids of Orthopyxis everta and three other species of Orthopyxis.The medusa of one member of the family Solmarisidae, representing the order Narcomedusae, and one member (Liriope tetraphylla) of the order Trachymedusae were recognized as medusae.In the Scyphozoa, DNA barcoding confirmed the planktonic larval stage (ephyra) of the Moon Jelly, Aurelia aurita, the adult medusa of which is occasionally common in and around Newport Bay. In the Anthozoa, antipathula larvae were identified from the Onion Anemone, Paranthus rapiformis and a cerinula larva was identified from the Tube-dwelling Anemone, Isarachnanthus nocturnus. We have yet to find the adults of these species locally.

scholarly journals DNA barcoding of Zygaenidae (Lepidoptera): results and perspectives

2019 ◽  
Vol 42 (2) ◽  
pp. 137-150
Author(s):  
Konstantin A. Efetov ◽  
Anna V. Kirsanova ◽  
Zoya S. Lazareva ◽  
Ekaterina V. Parshkova ◽  
Gerhard M. Tarmann ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Coi Gene ◽  
Dna Barcodes ◽  
The Family ◽  
The World ◽  
Biological Characters

The present study provides a DNA barcode library for the world Zygaenidae (Lepidoptera). This study reports 1031 sequence data of the COI gene DNA barcodes for more than 240 species in four of the five subfamilies of the family Zygaenidae. This is about 20% of the world Zygaenidae species. Our results demonstrate the specificity of the COI gene sequences at the species level in most of the studied Zygaenidae and agree with already established taxonomic opinions. The study confirms the effectiveness of DNA barcoding as a tool for determination of most Zygaenidae species. However, some of the results are contradictory. Some cases of shared barcodes have been found, as well as cases of deep intraspecific sequence divergence in species that are well separated by morphological and biological characters. These cases are discussed in detail. Overall, when combined with morphological and biochemical data, as well as biological and ecological observations, DNA barcoding results can be a useful support for taxonomic decisions.

scholarly journals The Future of DNA Barcoding: Reflections from Early Career Researchers

Diversity ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 313
Author(s):  
Danielle M. Grant ◽  
Ole Bjørn Brodnicke ◽  
Ann M. Evankow ◽  
André O. Ferreira ◽  
João T. Fontes ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Swot Analysis ◽  
Low Cost ◽  
Early Career ◽  
The Novel ◽  
Dna Barcodes ◽  
Early Career Researchers ◽  
The Future ◽  
Identification Of Species

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.

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