scholarly journals DNA barcoding of medicinal orchids in Asia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bhakta Bahadur Raskoti ◽  
Rita Ale
Keyword(s):  
Herbal Medicine ◽  
Dna Barcoding ◽  
Global Markets ◽  
Morphological Observation ◽  
Correct Identification ◽  
Illegal Trade ◽  
Natural Habitats ◽  
Accurate Identification ◽  
Orchid Species ◽  
Important Method

AbstractGrowing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3516 ◽  
Author(s):  
Sohath Z. Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation forLucilia eximia, Lucilia retroversa, Lucilia ricaandChloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

2017 ◽  
Author(s):  
Sohath Z Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

2017 ◽  
Author(s):  
Sohath Z Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals Yeast Species Associated with Orange Juice: Evaluation of Different Identification Methods

2002 ◽  
Vol 68 (4) ◽  
pp. 1955-1961 ◽  
Author(s):  
Covadonga R. Arias ◽  
Jacqueline K. Burns ◽  
Lorrie M. Friedrich ◽  
Renee M. Goodrich ◽  
Mickey E. Parish
Keyword(s):  
Orange Juice ◽  
Restriction Pattern ◽  
Partial Sequence ◽  
Rrna Gene ◽  
Correct Identification ◽  
Internal Transcribed Spacer Region ◽  
Accurate Identification ◽  
Hanseniaspora Uvarum ◽  
Classical Methodology ◽  
26S Rrna

ABSTRACT Five different methods were used to identify yeast isolates from a variety of citrus juice sources. A total of 99 strains, including reference strains, were identified using a partial sequence of the 26S rRNA gene, restriction pattern analysis of the internal transcribed spacer region (5.8S-ITS), classical methodology, the RapID Yeast Plus system, and API 20C AUX. Twenty-three different species were identified representing 11 different genera. Distribution of the species was considerably different depending on the type of sample. Fourteen different species were identified from pasteurized single-strength orange juice that had been contaminated after pasteurization (PSOJ), while only six species were isolated from fresh-squeezed, unpasteurized orange juice (FSOJ). Among PSOJ isolates, Candida intermedia and Candida parapsilosis were the predominant species. Hanseniaspora occidentalis and Hanseniaspora uvarum represented up to 73% of total FSOJ isolates. Partial sequence of the 26S rRNA gene yielded the best results in terms of correct identification, followed by classical techniques and 5.8S-ITS analysis. The commercial identification kits RapID Yeast Plus system and API 20C AUX were able to correctly identify only 35 and 13% of the isolates, respectively. Six new 5.8S-ITS profiles were described, corresponding to Clavispora lusitaniae, Geotrichum citri-aurantii, H. occidentalis, H. vineae, Pichia fermentans, and Saccharomycopsis crataegensis. With the addition of these new profiles to the existing database, the use of 5.8S-ITS sequence became the best tool for rapid and accurate identification of yeast isolates from orange juice.

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 The fishing and illegal trade of the angelshark: DNA barcoding against misleading identifications

2018 ◽  
Vol 206 ◽  
pp. 193-197 ◽  
Author(s):  
Ingrid Vasconcellos Bunholi ◽  
Bruno Lopes da Silva Ferrette ◽  
Juliana Beltramin De Biasi ◽  
Carolina de Oliveira Magalhães ◽  
Matheus Marcos Rotundo ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Illegal Trade

DNA barcoding for wood identification: global review of the last decade and future perspective

IAWA Journal ◽  
2020 ◽  
Vol 41 (4) ◽  
pp. 620-643 ◽  
Author(s):  
Lichao Jiao ◽  
Yang Lu ◽  
Tuo He ◽  
Juan Guo ◽  
Yafang Yin
Keyword(s):  
Dna Barcoding ◽  
Extraction Methods ◽  
Future Perspective ◽  
Future Research ◽  
Reference Database ◽  
Wood Identification ◽  
Accurate Identification ◽  
Research Orientation ◽  
Timber Trade ◽  
Dna Extraction Methods

Abstract DNA barcoding technology has emerged as one of the most promising tools available to identify timber at the species level, contributing to the monitoring of the timber trade and the conservation of forestry sources. This paper reviews the progress, challenges, and existing problems in the development of DNA barcoding for wood identification in the last ten years. There is a focus on the optimization of DNA extraction methods for processed or ancient wood, the strategy of screening high-resolution DNA barcodes suitable for wood identification, the development of a wood DNA reference database especially for priority taxa, and the comparison and comprehensive application of sequence analytical methods to achieve accurate identification. In addition to DNA barcoding, the feasibility of other genetic methods for wood identification is also discussed. Furthermore, future research orientation and strategy of wood DNA barcoding are presented. We argue that wood DNA barcoding integrated with other methodologies including wood anatomy can offer an effective approach and a new perspective to promote legal logging for timber trade custody and global biodiversity conservation.

Genetic Diversity of Pediculus humanus capitis (Phthiraptera: Pediculidae) in Peninsular Malaysia and Molecular Detection of Its Potential Associated Pathogens

2019 ◽  
Vol 57 (3) ◽  
pp. 915-926
Author(s):  
Aida Syafinaz Mokhtar ◽  
Yee Ling Lau ◽  
John-James Wilson ◽  
Noraishah Mydin Abdul-Aziz
Keyword(s):  
Genetic Diversity ◽  
Dna Barcoding ◽  
Pathogenic Bacteria ◽  
Peninsular Malaysia ◽  
Molecular Evidence ◽  
Head Lice ◽  
Pediculus Humanus Capitis ◽  
Accurate Identification ◽  
Pediculosis Capitis ◽  
Pediculus Humanus

Abstract Pediculosis capitis caused by Pediculus humanus capitis (De Geer) is endemic all over the world, and children are mostly affected, particularly those living in overcrowded institutions. Several studies have shown that P. h. capitis carried human pathogenic bacteria, suggesting the potential role of head lice in the transmission of pathogens to humans. In this study, we determined the genetic diversity of head lice collected from welfare homes sheltering underprivileged children by using DNA barcoding and demonstrated the presence of Acinetobacter spp., Serratia marcescens, and Staphylococcus aureus in head lice, which have never been investigated before in Malaysia. Cox1 DNA barcoding identified the head lice, P. h. capitis collected from welfare homes across two geographical areas of Peninsular Malaysia as belonging to clades A, B, and D. Acinetobacter bacteria: Acinetobacter guillouiae, Acinetobacter junii, Acinetobacter baumannii, and Acinetobacter nosocomialis were detected in head lice belonging to clades A and also D. In addition, DNA from S. marcescens and S. aureus were also detected in both clades A and D. To our knowledge, this is the first report on the genetic diversity of head lice in Malaysia through DNA barcoding, as well as the first to provide molecular evidence on the type of bacteria occurring in head lice in Malaysia. It is anticipated that the DNA barcoding technique used in this study will be able to provide rapid and accurate identification of arthropods, in particular, medically important ectoparasites.

scholarly journals PCR-RFLP of 16S ribosomal DNA to confirm the identification of Enterococcus gallinarum and Enterococcus casseliflavus isolated from clinical and food samples

2010 ◽  
Vol 43 (1) ◽  
pp. 100-101 ◽  
Author(s):  
Aline Weber Medeiros ◽  
Pedro d'Azevedo ◽  
Rebeca Inhoque Pereira ◽  
Ana Paula Cassenego ◽  
Sueli Van Der Sand ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Food Samples ◽  
Correct Identification ◽  
Accurate Identification ◽  
16S Ribosomal Dna ◽  
Pcr Rflp ◽  
Enterococcus Casseliflavus ◽  
Dna Pattern ◽  
Enterococcus Gallinarum ◽  
Rdna Analysis

INTRODUCTION: This study aimed to confirm the identification of Enterococcus gallinarum and Enterococcus casseliflavus isolated from clinical and food samples by PCR-RFLP. METHODS: Fifty-two strains identified by conventional biochemical exams were submitted to PCR amplification and digested with HinfI. Only 20 (38.5%) of the 52 strains showed a DNA pattern expected for E. gallinarum and E. casseliflavus. RESULTS: Analysis of the results of this study showed that E. gallinarum and E. casseliflavus are occasionally erroneously identified and confirmed the potential application of 16S rDNA analysis for accurate identification of these species. CONCLUSIONS: A correct identification is important to distinguish between intrinsic and acquired vancomycin resistance.

scholarly journals Medicinal Orchids of Nepal: Are They Well Protected?

Our Nature ◽  
1970 ◽  
Vol 8 (1) ◽  
pp. 82-91 ◽  
Author(s):  
K.P. Acharya ◽  
M.B. Rokaya
Keyword(s):  
Species Richness ◽  
Herbal Medicine ◽  
Protected Areas ◽  
Distribution Pattern ◽  
Negative Correlation ◽  
Medicinal Purpose ◽  
Orchid Species ◽  
Medicinal Orchid

This paper aims to explore distribution pattern of orchids used for medicinal purpose and their conservation aspect. We compiled information on 82 species of orchids which are used as herbal medicine. Maximum richness of medicinal orchids was observed at an elevation of 1700 msl but, the maximum numbers of protected areas are located at an elevation of 3000 to 3500 msl. There is a negative correlation between number of protected areas and medicinal orchid species richness mentioning that the protected areas are less synchronized with medicinal orchids of Nepal.DOI: 10.3126/on.v8i1.4315

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