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.

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.

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 The perspectives for DNA barcoding of Rhaponticum carthamoides (Willd.) Iljin using rbcL gene sequence

2021 ◽  
Vol 908 (1) ◽  
pp. 012030
Author(s):  
M V Protopopova ◽  
N A Shvetsova ◽  
V V Pavlichenko
Keyword(s):  
Dna Barcoding ◽  
Large Subunit ◽  
Dna Barcode ◽  
Natural Populations ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Rhaponticum Carthamoides ◽  
South Siberia ◽  
Illegal Harvesting

Abstract The methods of biological species identification using nucleotide sequences of short genome regions (DNA barcoding) are actively developed. The universal DNA barcode for plants remains to be discovered, and one of the leading candidates is the plastid gene of the large subunit of ribulose-bisphosphate carboxylase gene (rbcL). In our study, we estimated the part of rbcL gene as a possible marker for molecular identification of Rhaponticum carthamoides (Willd.) Iljin. Due to its officinal properties, the species is susceptible to uncontrolled and illegal harvesting from natural populations. Today, the species needs to be protected and therefore is included into the Red Data Books of the Russian Federation and certain regions. The study was carried out using plants from the natural populations sampled from the Khamar-Daban Ridge (South Siberia) and considering now as Rh. carthamoides var. chamarense (Peschkova) O S Zhirova. It was shown that rbcL gene can be used to identify Rh. carthamoides at least from the populations of the Khamar-Daban Ridge using a fragment of the maximum length or its 3’ region. Apparently, the 5’ region of the gene (rbcLa) most often used as DNA barcode for plants may be of lesser importance for Rh. carthamoides. The rbcL gene sequences can be also used for the development of approaches for Rh. carthamoides identification in the medicinal preparations and products containing dried tissues to prevent their falsification and illegal harvesting of this species. The combination of rbcL gene with additional markers seems to be highly desirable to create effective DNA barcodes for Rhaponticum species.

scholarly journals DNA Barcoding Dalugha (Cyrtosperma Merkusii) di Kepulauan Talaud dan Minahasa Selatan Berdasarkan Gen rbcL

2021 ◽  
Vol 11 (2) ◽  
pp. 134
Author(s):  
Marlin Bernadet Taariwuan ◽  
Jantje Ngangi ◽  
Yermia Mokosuli ◽  
Sukmarayu Gedoan
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Local Alignment ◽  
Rbcl Gene ◽  
Endemic Plant ◽  
Bisphosphate Carboxylase ◽  
Large Gene ◽  
North Sulawesi ◽  
Barcode Dna ◽  
Search Tool

(Article History: Received June 28, 2021; Revised August 30, 2021; Accepted Sept 3, 2021) ABSTRAKDalugha (Cyrtospera merkusii (Hassk.)Schott) merupakan tanaman endemik Sulawesi Utara yang digunakan sebagai pangan alternatif (penganti beras). Penelitian ini bertujuan untuk membandingkan spesies daluga di Kepulauan Talaud dan Minahasa Selatan menggunakan DNA barcode gen rbcL (ribulose 1,5 bisphosphate carboxylase large). Perbandingan barcode DNA yang dilakukan pada empat sampel yang berbeda lokasi tersebut keduanya menghasilkan tingkat kesamaan 100% (identik). Dengan demikian, tidak ada variasi intra spesies yang ditemukan dari semua sampel yang ada. Selanjutnya, kemiripan sampel-sampel ini telusuri kemiripannya dengan kerabat terdekat yang tercatat di GenBank menggunakan BLAST (Basic Local Alignment Search Tool).  Tanaman dalugha dalam penelitian ini memiliki kemiripan 99,82% dengan tumbuhan Anaphyllopsis americana (AM905753.1), dan kemiripannya 99,63% dengan Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), dan Podolasia stipitata (AM905752.1). Belum ada rekor sekuens DNA gen rbcL dari spesies ini yang dibisa dibandingkan di GenBank.Kata Kunci: Dalugha; DNA barcoding; gen rbcL ABSTRACTDalugha (Cyrtospera merkusii (Hassk.) Schott) is an endemic plant in North Sulawesi that is used as alternative food (substitute for rice). This research aimed to compare the DNA barcode of dalugha in Talaud Islands and in South Minahasa using rbcL (ribulose 1,5 bisphosphate carboxylase large) gene. The DNA barcoding comparison of all four samples in both area resulted in 100% similarity (identical). Therefore, there is no intraspecific variation found in all samples. Furthermore, the similarity of these samples were conducted with BLAST (Basic Local Alignment Search Tool) to compare with its closest relatives in GenBank. The closest relatives of this plant, based on similarity information, are 99.82% with Anaphyllopsis americana (AM905753.1) and all 99.63% with Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), and Podolasia stipitata (AM905752.1).  There is no record yet of rbcL gene sequence of C. merkusii in GenBank for comparison.Keywords: Dalugha; DNA barcoding; rbcL gene

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.

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.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

scholarly journals Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

2021 ◽  
Author(s):  
Dang Thanh Long ◽  
Hoang Thi Kim Hong ◽  
Le Ly Thuy Tram ◽  
Nguyen Thi Quynh Trang
Keyword(s):  
Chloroplast Genome ◽  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Haplotype Diversity ◽  
Universal Primers ◽  
Nucleotide Position ◽  
Accurate Identification ◽  
Low Levels ◽  
Relationship Of

Background: The DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. Methods: DNA barcoding of 9 chloroplast genes (rbcL, matK, trnH-psbA, accD-psaI, ndhA, psbE-petL, Rpl32-trnL, trnW-psaJ, trnSGCU-trnGGCC) were used to provide the theoretical basis for species identification, genetic diversity analysis of lotus population collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequence products were analyzed using the MEGA X program. Result: The results showed that high levels of haplotype diversity (Hd), ranging from 0.618-0.869 and low levels of nucleotide diversity (Pi), ranging from 0.180 × 10-3-3.280 × 10-3 base on a total of nine gene regions of chloroplast genome. The neutrality tests show an excess of rare nucleotide position variations in individuals’ white lotus and derived haplotypes recent expansion. While the evolution of the individuals in the pink lotus may have to decrease. The phylogenetic analyses indicated that combined sequences were not insufficient to make a difference to the DNA barcoding in the individual’s lotus of the N. nucifera species this is in the study. The standardized and accurate barcode information of lotus is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Nelumbonaceae germplasm resources.

scholarly journals Integrated Approach for Species Identification and Quality Analysis for Labisia pumila Using DNA Barcoding and HPLC

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 717
Author(s):  
Auni Aqilah Ahmad Tarmizi ◽  
Alina Wagiran ◽  
Faezah Mohd Salleh ◽  
Lee Suan Chua ◽  
Farah Izana Abdullah ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Integrated Approach ◽  
Quality Analysis ◽  
Integral Approach ◽  
Medicinal Products ◽  
Herbal Products ◽  
Herbal Medicinal Products ◽  
Herbal Medicinal ◽  
Labisia Pumila

Labisia pumila is a precious herb in Southeast Asia that is traditionally used as a health supplement and has been extensively commercialized due to its claimed therapeutic properties in boosting a healthy female reproductive system. Indigenous people used these plants by boiling the leaves; however, in recent years it has been marketed as powdered or capsuled products. Accordingly, accuracy in determination of the authenticity of these modern herbal products has faced great challenges. Lack of authenticity is a public health risk because incorrectly used herbal species can cause adverse effects. Hence, any measures that may aid product authentication would be beneficial. Given the widespread use of Labisia herbal products, the current study focuses on authenticity testing via an integral approach of DNA barcoding and qualitative analysis using HPLC. This study successfully generated DNA reference barcodes (ITS2 and rbcL) for L.pumila var. alata and pumila. The DNA barcode that was generated was then used to identify species of Labisia pumila in herbal medicinal products, while HPLC was utilized to determine their quality. The findings through the synergistic approach (DNA barcode and HPLC) implemented in this study indicate the importance of both methods in providing the strong evidence required for the identification of true species and to examine the authenticity of such herbal medicinal products.

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