scholarly journals Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids

Genome ◽  
2017 ◽  
Vol 60 (8) ◽  
pp. 665-671 ◽  
Author(s):  
Iffat Parveen ◽  
Hemant K. Singh ◽  
Saloni Malik ◽  
Saurabh Raghuvanshi ◽  
Shashi B. Babbar
Keyword(s):  
Dna Barcoding ◽  
Habitat Destruction ◽  
Species Discrimination ◽  
Medicinal Species ◽  
Orchid Species ◽  
Illicit Trade ◽  
Discrimination Capability ◽  
Discrimination Rate ◽  
Identification Tags ◽  
Species Specific

Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand owing to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS, matK, rbcL, rpoB, and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species. ITS provided the highest species discrimination rate of 94.9%. While, among the chloroplast loci, matK provided the highest species discrimination rate of 85.7%. None of the tested loci individually discriminated 100% of the species. Therefore, multi-locus combinations of up to five loci were tested for their species resolution capability. Among two-locus combinations, the maximum species resolution (86.7%) was provided by ITS+matK. ITS and matK sequences of the medicinal orchids were species specific, thus providing unique molecular identification tags for their identification and detection. These observations emphasize the need for the inclusion of ITS in the core barcode for plants, whenever required and available.

scholarly journals The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8755
Author(s):  
Adrian Kannan ◽  
Suganiya Rama Rao ◽  
Shyamala Ratnayeke ◽  
Yoon-Yen Yow
Keyword(s):  
16S Rdna ◽  
Dna Barcoding ◽  
Peninsular Malaysia ◽  
Coi Gene ◽  
Diagnostic Tools ◽  
Species Discrimination ◽  
Pomacea Canaliculata ◽  
Agricultural Wetlands ◽  
Barcoding Gap ◽  
Species Specific

Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.

scholarly journals Identification of CITES-Listed Euphorbia royleana through DNA Barcoding Technology: A New Facet in Wildlife Forensics

2021 ◽  
Vol 3 (2) ◽  
pp. 260-272
Author(s):  
Mukesh Thakar ◽  
Tina Sharma
Keyword(s):  
Genetic Distance ◽  
Dna Barcoding ◽  
Related Species ◽  
Species Discrimination ◽  
Closely Related Species ◽  
Wildlife Forensics ◽  
Interspecific Genetic Distance ◽  
Species Specific ◽  
Endangered Status ◽  
Discrimination Method

Disorganized and chaotic collection of the Euphorbia plant species from the wild is one of the major reasons for its endangered status. According to CITES, the trade in Euphorbia royleana species is prohibited under Appendix II. However, the trade continues unabated as current identification methods do not discriminate between closely related species.  In the present study, a DNA barcoding method has been used to establish inter- and intra-specific divergences of both matK and rbcL regions by using pairwise genetic distance measurement methods for evaluating the maximum barcoding gap. The matk and rbcL yielded a 100% amplification and sequencing success rate to distinguish closely related species of Euphorbia royleana unambiguously. The matk and rbcL showed average interspecific genetic distance divergence values of 0.031and 0.015, respectively. The maximum number of species-specific SNPs was observed in matK sequences at seven consecutive sites, which could distinguish Euphorbia royleana from closely related species.  The best candidate barcoding region to identify Euphorbia royleana was found to be matK with a single-locus barcoding approach. Furthermore, the species discrimination method was developed with the help of species-specific SNPs derived from the matK barcoding region to accurately authenticate Euphorbia royleana, and it provided 100% species resolution

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.

Temporal Detection Limits of Remnant Larval Bloodmeals in Nymphal Ixodes scapularis (Say, Ixodida: Ixodidae) Using Two Next-Generation Sequencing DNA Barcoding Assays

2020 ◽  
Author(s):  
Genevieve A M Lumsden ◽  
Evgeny V Zakharov ◽  
Sarah Dolynskyj ◽  
J Scott Weese ◽  
L Robbin Lindsay ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Barcoding ◽  
Ixodes Scapularis ◽  
Life Stage ◽  
Next Generation ◽  
Host Detection ◽  
Host Identification ◽  
Species Specific ◽  
Generation Sequencing ◽  
Assay Detection

Abstract Using next-generation sequencing DNA barcoding, we aimed to determine: 1) if the larval bloodmeal can be detected in Ixodes scapularis nymphs and 2) the post-moult temporal window for detection of the larval bloodmeal. Subsets of 30 nymphs fed on a domestic rabbit (Oryctolagus cuniculus Linnaeus, Lagomorphia: Leporidae) as larvae were reared and frozen at 11 time points post-moult, up to 150 d. Vertebrate DNA was amplified using novel universal (UP) and species-specific primers (SSP) and sequenced for comparison against cytochrome c oxidase subunit I barcodes to infer host identification. Detectable bloodmeals decreased as time since moult increased for both assays. For the SSP assay, detection of bloodmeals decreased from 96.7% (n = 29/30) in day 0 nymphs to 3.3% (n = 1/30) and 6.7% (n = 2/30) at 4- and 5-mo post-moult, respectively. A shorter temporal detection period was achieved with the UP assay, declining from 16.7% (n = 5/30) in day 0 nymphs to 0/30 in 3-d-old nymphs. Bloodmeal detection was nonexistent for the remaining cohorts, with the exception of 1/30 nymphs at 2-mo post-moult. Host detection was significantly more likely using the SSP assay compared to the UP assay in the first three time cohorts (day 0: χ 2 = 39.1, P < 0.005; day 2: χ 2 = 19.2, P < 0.005; day 3: χ 2 = 23.3, P < 0.005). Regardless of the primer set used, the next-generation sequencing DNA barcoding assay was able to detect host DNA from a larval bloodmeal in the nymphal life stage; however, a short window with a high proportion of detection post-moult was achieved.

Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patella spp.) from non-destructive sampling

2016 ◽  
Vol 97 (7) ◽  
pp. 1479-1482 ◽  
Author(s):  
Thomas J. Ashton ◽  
Meriem Kayoueche-Reeve ◽  
Andrew J. Blight ◽  
Jon Moore ◽  
David M. Paterson
Keyword(s):  
Dna Barcoding ◽  
Species Abundance ◽  
Microscopic Analysis ◽  
Cost Effective ◽  
Field Studies ◽  
Similar Species ◽  
Species Determination ◽  
Destructive Sampling ◽  
Species Specific ◽  
Non Destructive

Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

ISSR-Derived Species-Specific SCAR Marker for Rapid and Accurate Authentication of Ocimum tenuiflorum L.

Planta Medica ◽  
2017 ◽  
Vol 84 (02) ◽  
pp. 117-122 ◽  
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Priyanka Mishra ◽  
Kuppusamy Baskaran ◽  
Ashutosh Shukla ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
High Volume ◽  
Inter Simple Sequence Repeat ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Accurate Identification ◽  
Sequence Characterized Amplified Region ◽  
Medicinal Value ◽  
Ocimum Tenuiflorum ◽  
Species Specific

Abstract Ocimum tenuiflorum has been widely used in traditional medicine and has high medicinal value. High volume trade of this potential medicinal plant species led to unscrupulous adulteration of both crude drugs as well as formulations. Morphology-based authentication is difficult in cases of incomplete or damaged samples and in dried herbal materials. In such cases, PCR-based molecular methods may aid in accurate identification. The present study aimed at developing species-specific DNA marker(s) for the authentication of O. tenuiflorum. A species-specific amplicon (279 bp) generated through an inter-simple sequence repeat marker (UBC 835) in all individuals of O. tenuiflorum was cloned, sequenced, and a primer pair was developed (designated as CIM-OT-835F/CIM-OT-835R). The newly developed sequence characterized amplified region marker was validated through PCR amplification in all available seven species of Ocimum, and its specificity for O. tenuiflorum was confirmed with the consistent generation of an amplicon of 177 bp. The developed marker can be used for accurate and rapid identification of the species for certification purposes and will be useful in quality control of medicinal preparations containing this important medicinal species.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

Integrative description of five Pseudechiniscus species (Heterotardigrada: Echiniscidae: the suillus-facettalis complex)

Zootaxa ◽  
2020 ◽  
Vol 4763 (4) ◽  
pp. 451-484 ◽  
Author(s):  
MILENA ROSZKOWSKA ◽  
DARIA GROBYS ◽  
TOMASZ BARTYLAK ◽  
MAGDALENA GAWLAK ◽  
HANNA KMITA ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Genetic Data ◽  
Integrative Taxonomy ◽  
Genetic Distances ◽  
Morphological Features ◽  
Species Discrimination ◽  
Coi Sequences ◽  
Morphology And Morphometry ◽  
Species Specific

Pseudechiniscus is a morphologically homogeneous heterotardigrade genus with a relatively low number of morphological features useful for the species discrimination. The species of the Pseudechiniscus suillus-facettalis complex are some of the most challenging tardigrades to identify. Here, we examine several populations from Antarctica, Italy, Madagascar and Norway that would have most likely been attributed to Pse. suillus prior to the recent redescription of the species. Populations were analysed using integrative taxonomy—a combination of classical morphology and morphometry, as well as genetic data. Besides minute differences in dorsal sculpture and morphometry, we found clear, species-specific differences in ventral sculpture which are very useful in discrimination of Pseudechiniscus species. Based on morphology (mainly ventral sculpture) and significant genetic distances in COI and ITS-2 sequences, we describe five new species: Pse. angelusalas sp. nov. from Madagascar, Pse. dastychi sp. nov. from Antarctica, Pse. ehrenbergi sp. nov. from Italy as well as Pse. indistinctus sp. nov. and Pse. lacyformis sp. nov. from Norway. Finally, we provide an updated phylogenetic tree of the genus Pseudechiniscus based on COI sequences. 

High diversity in the Pseudechiniscus suillus–facettalis complex (Heterotardigrada: Echiniscidae) with remarks on the morphology of the genus Pseudechiniscus

2020 ◽  
Vol 188 (3) ◽  
pp. 733-752 ◽  
Author(s):  
Daria Grobys ◽  
Milena Roszkowska ◽  
Magdalena Gawlak ◽  
Hanna Kmita ◽  
Andrzej Kepel ◽  
...  
Keyword(s):  
Molecular Data ◽  
Integrative Taxonomy ◽  
Morphological Features ◽  
Species Discrimination ◽  
Extensive Discussion ◽  
Morphology And Morphometry ◽  
Species Specific ◽  
High Diversity ◽  
General Appearance

Abstract Pseudechiniscus is a morphologically homogeneous genus of tardigrades. The morphological features commonly used for species discrimination in this genus are the dorsal sculpture, the shape and number of dorsal plates and trunk appendages. Species of the Pseudechiniscus suillus–facettalis complex are one of the most challenging tardigrades to identify. All species are similar in their general appearance and all lack trunk appendages. Moreover, not only the nominal Pseudechiniscus suillus, but also other members of the suillus–facettalis complex have been insufficiently described. In our study, we examined several populations from the Northern and the Southern Hemispheres that could be traditionally attributed to Pse. suillus. These populations were analysed using integrative taxonomy – a combination of classical morphology and morphometry with molecular data. Besides the differences in the dorsal sculpture and morphometry, we also found species-specific differences in ventral sculpture, which were originally used for discrimination of Pseudechiniscus species. Moreover, we provide an extensive discussion on all morphological and morphometric differences used in Pseudechiniscus taxonomy and indicate main taxonomic problems with this genus. Finally, we redescribe the nominal Pse. suillus from Italy.

scholarly journals Authentication of Chinese Crude Drug Gecko by DNA Barcoding

2011 ◽  
Vol 6 (1) ◽  
pp. 1934578X1100600 ◽  
Author(s):  
Hai-Feng Gu ◽  
Yun Xia ◽  
Rui Peng ◽  
Bang-Hui Mo ◽  
Li Li ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Habitat Destruction ◽  
Full Length ◽  
Correct Identification ◽  
Molecular Method ◽  
Specific Sequence ◽  
Gekko Gecko ◽  
Crude Drug

Gekko gecko, an animal used as a valued traditional Chinese medicine, has been widely used for over 2000 years. Due to localized habitat destruction, the amount of G. gecko has dramatically decreased in recent years. As a result, more and more adulterants have been detected in the traditional medicine, which has resulted in a chaotic market. Therefore, a correct identification method is badly needed. In this study, we employed a new molecular method of DNA barcoding for discriminating gecko from its adulterants. Fifty-seven specimens of gecko and its adulterants were collected as test samples. The full-barcode and mini-barcode sequences of these specimens were separately amplified and sequenced separately. Together with other published barcode sequences, we detected that the intra-specific sequence diversity was far lower than the inter-specific diversity in G. gecko and its adulterants (3% compared with 35% in full-length barcode; 4% compared with 33.5% in mini-barcode). These results showed that both the full-length and mini-barcodes were effective for identifying gecko, which suggested that the DNA barcode could be an effective and powerful tool for identifying the Chinese crude drug gecko.

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