scholarly journals Developing an efficient DNA barcoding system to differentiate between Lilium species

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yixin Liu ◽  
Mingfang Zhang ◽  
Xuqing Chen ◽  
Xi Chen ◽  
Yue Hu ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Identification System ◽  
Representative Species ◽  
Lilium Species ◽  
Edible Species ◽  
Medicinal Properties ◽  
Species Specific ◽  
Genomic Regions

Abstract Background Lilium is an important ornamental bulb, possesses medicinal properties, and is also edible. Species within the Lilium genus share very similar morphology and macroscopic characteristics, thus they cannot be easily and clearly distinguished from one another. To date, no efficient species-specific markers have been developed for classifying wild lily species, which poses an issue with further characterizing its medicinal properties. Results To develop a simple and reliable identification system for Lilium, 45 representative species from 6 sections were used to develop a DNA barcoding system, which was based on DNA sequence polymorphisms. In this study, we assessed five commonly used DNA barcode candidates (ITS, rbcL, ycf1b, matK and psbA-trnH) and five novel barcode candidates obtained from highly variable chloroplast genomic regions (trnL-trnF, trnS-trnG, trnF-ndhJ, trnP-psaJ-rpI33 and psbB-psbH). We showed that a set of three novel DNA barcodes (ITS + trnP-psaJ-rpI33 + psbB-psbH) could be efficiently used as a genetic marker to distinguish between lily species, as assessed by methods including DNAsp, BI and ML tree, and Pair Wise Group (PWG). Conclusions A rapid and reliable DNA barcoding method was developed for all 45 wild Lilium species by using ITS, trnP-psaJ-rpI33, and psbB-psbH as DNA barcoding markers. The method can be used in the classification of wild Lilium species, especially endangered species, and also provides an effective method for selective lily breeding.

scholarly journals Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Viet The Ho ◽  
Thi Kim Phuong Tran ◽  
Thi Thanh Tram Vu ◽  
Sasanti Widiarsih
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Plant Identification ◽  
Genetic Classification ◽  
Discrimination Power ◽  
Orchid Species ◽  
Medicinal Properties ◽  
Jewel Orchid ◽  
Origin Identification

Abstract Background Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. Results The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. Conclusion The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.

Potential Use of DNA Barcodes in Regulatory Science: Applications of the Regulatory Fish Encyclopedia

2008 ◽  
Vol 71 (1) ◽  
pp. 210-217 ◽  
Author(s):  
HAILE F. YANCY ◽  
TYLER S. ZEMLAK ◽  
JACQULINE A. MASON ◽  
JEWELL D. WASHINGTON ◽  
BRADLEY J. TENGE ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Fish Muscle ◽  
The United States ◽  
Identification System ◽  
Dna Barcodes ◽  
Potential Applications ◽  
Species Specific ◽  
Product Forms

The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/~frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.

scholarly journals A Rapid Colorimetric Assay for On-Site Authentication of Cephalopod Species

Biosensors ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 190
Author(s):  
Giuseppina Tatulli ◽  
Paola Cecere ◽  
Davide Maggioni ◽  
Andrea Galimberti ◽  
Pier Paolo Pompa
Keyword(s):  
Dna Barcoding ◽  
Genomic Dna ◽  
Large Scale ◽  
Colorimetric Assay ◽  
Dna Barcode ◽  
Mitochondrial Coi ◽  
Cephalopod Species ◽  
Accurate Design ◽  
Relevant Group ◽  
Species Specific

A colorimetric assay, exploiting the combination of loop-mediated isothermal amplification (LAMP) with DNA barcoding, was developed to address the authentication of some cephalopod species, a relevant group in the context of seafood traceability, due to the intensive processing from the fishing sites to the shelf. The discriminating strategy relies on accurate design of species-specific LAMP primers within the conventional 5’ end of the mitochondrial COI DNA barcode region and allows for the identification of Loligo vulgaris among two closely related and less valuable species. The assay, coupled to rapid genomic DNA extraction, is suitable for large-scale screenings and on-site applications due to its easy procedures, with fast (30 min) and visual readout.

Does GenBank provide a reliable DNA barcode reference to identify small alien oysters invading the Mediterranean Sea?

2014 ◽  
Vol 95 (1) ◽  
pp. 111-122 ◽  
Author(s):  
F. Crocetta ◽  
P. Mariottini ◽  
D. Salvi ◽  
M. Oliverio
Keyword(s):  
Mediterranean Sea ◽  
Native Species ◽  
Dna Barcode ◽  
Genetic Data ◽  
Molecular Data ◽  
The Public ◽  
Variable Species ◽  
The Mediterranean ◽  
Species Specific

The Mediterranean Sea is currently under siege by a conspicuous alien pressure, and, within some families (e.g. the Ostreidae), the number of native species seems to be remarkably outnumbered by that of the alien ones. We wanted to test the reliability of the molecular data currently available on the small alien oysters recently invading the Mediterranean Sea. Samples from Greece and Turkey, encompassing the known species-specific morphological variation, were sequenced for the markers with the widest taxonomic coverage in the group of small oysters (i.e. the 16S rDNA and the COI). The sequences obtained have been compared with those available in GenBank, and a possible identification at the species level has been finally tested in a DNA-barcoding fashion. The present results clearly demonstrated that our samples belong to a single, morphologically highly variable species. Their 16S sequences were closely related to a sequence registered under the name Dendostrea folium, with a genetic distance which does not warrant conspecificity. Additionally, a remarkable number of sequences retrieved from the GenBank (of both genes) did not form a monophyletic group according to the published classification of the vouchers, suggesting—at least in part—an origin from specimens not properly identified. Both genes seem promising for use as DNA-barcode, although the COI will probably prove more effective. Therefore, we urge the availability of a baseline of oyster pedigreed DNA barcode sequences in the public databases, to allow the use of such genetic data to reliably monitor bio-invasions in the Mediterranean Sea.

scholarly journals Oligochaete taxonomy – The rise of earthworm DNA barcode in India

2018 ◽  
Vol 18 (1) ◽  
pp. 1-10 ◽  
Author(s):  
H. Lalthanzara ◽  
Ruth Lalfelpuii ◽  
C. Zothansanga ◽  
M. Vabeiryureilai ◽  
N. Senthil Kumar ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Developmental Stages ◽  
Dna Barcode ◽  
Soil Classification ◽  
Reproductive Organs ◽  
Diagnostic Features ◽  
Protein Coding ◽  
Anatomical Characters ◽  
Ecological Importance

Oligochaeta is a class of segmented worms under the phylum Annelida that are characterised by the presence of tiny setae in each body segment. Earthworms are the main members, consisting of approximately 6200 species. Their ecological importance is well known as they are the major soil macro-fauna; Aristotle had named them as “the intestines of soil”. Classification of earthworms is a controversial issue since the introduction of modern taxonomical system on earthworm by Michaelsen in 1921. This is mainly because conventional identification using morphological and anatomical characters are complicated and confusing. The key diagnostic features such as the position and structure of the reproductive organs, clitellum and the associated tubercular pubertatis are not always reliable, particularly in different developmental stages, especially when the available specimens are the juveniles. DNA barcoding has offered a potential solution, even at the levels of identifying the juveniles or cocoons. Several genes including mitochondrial cytochrome-c oxidase I, 16S, 18S and 28S ribosomal RNAs, and protein-coding histone H3 genes have been introduced in the taxonomy and phylogeny of earthworm. It is anticipated that DNA barcoding will help conflicting taxonomy and further exploration of species diversity in India.

scholarly journals Beyond Bycatch: The Species Diversity of Tonguesole (Pleuronectiformes: Cynoglossidae) in Coastal Fisheries of the Tanintharyi Region, Southern Myanmar

2021 ◽  
Vol 34 (1) ◽  
Author(s):  
IRIS SEGURA-GARCIA ◽  
SABAI SOE ◽  
NYO-NYO TUN ◽  
STEPHEN BOX
Keyword(s):  
Species Diversity ◽  
Dna Barcoding ◽  
Life Histories ◽  
Dna Barcode ◽  
Common Species ◽  
Small Scale ◽  
New Information ◽  
The Family ◽  
Management Plans ◽  
Species Specific

Flatfishes in the family Cynoglossidae are an important coastal fishery in Myanmar. Due to the overlapping morphologies of multiple tonguesole species, caught both as bycatch from trawl fisheries and targeted specifically by small scale fishers, they are all marketed under a single local name, “khwayshar”. This presents a management challenge given the potential differences in the species-specific life-histories, population dynamics, fishing vulnerability and harvest rates. This study investigated the species diversity of tonguesole landings from coastal communities of the Tanintharyi Region of southern Myanmar. DNA barcoding was used to distinguish potentially 10 different species, of which five were identified to species level and five at the genus level. Unconfirmed genetic identifications were based on external morphology. The poor efficacy of DNA barcoding for tonguesole species identification resulted from the limited DNA barcode reference sequences available for the family Cynoglossidae in public databases. An asymmetric occurrence and relative abundance of the identified species in landing sites where samples were collected suggested that the most common species was Cynoglossus oligolepis (Bleeker, 1855), a new species record for Myanmar, followed by Cynoglossus lingua Hamilton, 1822. The results of the present study provide new information to characterise the tonguesole fishery as a first step in the development of management plans for the coastal fishery in Myanmar.

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.

scholarly journals A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 199
Author(s):  
Xiaochun Zhang ◽  
Huan Yu ◽  
Qi Yang ◽  
Ziwei Wang ◽  
Ruocheng Xia ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Barcoding ◽  
High Resolution Melting ◽  
Its Region ◽  
Its Sequencing ◽  
Melting Temperatures ◽  
Hrm Analysis ◽  
National Drug ◽  
Species Specific ◽  
Its1 And Its2

In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.

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