scholarly journals Species Identification of Marine Fishes in China with DNA Barcoding

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Junbin Zhang
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Introgressive Hybridization ◽  
Genetic Distances ◽  
Gene Coi ◽  
Interspecific Comparisons ◽  
Mitochondrial Cytochrome Oxidase ◽  
Two Parameter ◽  
Identification Tool

DNA barcoding is a molecular method that uses a short standardized DNA sequence as a species identification tool. In this study, the standard 652 base-pair region of the mitochondrial cytochrome oxidase subunit I gene (COI) was sequenced in marine fish specimens captured in China. The average genetic distance was 50-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 15.742% among congeners and only 0.319% for intraspecific individuals. There are no overlaps of pairwise genetic variations between conspecific and interspecific comparisons apart from the generaPampusin which the introgressive hybridization was detected. High efficiency of species identification was demonstrated in the present study by DNA barcoding. Due to the incidence of cryptic species, an assumed threshold is suggested to expedite discovering of new species and biodiversity, especially involving biotas of few studies.

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

Diagnostic and phylogenetic utility of the first DNA barcode library for longhorn beetles (Coleoptera: Cerambycidae) from the Russian Far East

Zootaxa ◽  
2017 ◽  
Vol 4276 (3) ◽  
pp. 441 ◽  
Author(s):  
VASILY V. GREBENNIKOV ◽  
EDUARD JENDEK ◽  
MAXIM ED. SMIRNOV
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Signal ◽  
Russian Far East ◽  
Far East ◽  
Dna Barcode ◽  
Longhorn Beetles ◽  
Gene Coi ◽  
Online Library ◽  
Identification Tool ◽  
The Russian Far East

One hundred forty two specimens representing 56 species of longhorn beetles (Cerambycidae) from the Russian Far East were sequenced for a 658 bp fragment of the 5' end of the mitochondrial cytochrome oxidase subunit I gene (COI, =DNA barcode). The data are publicly available in an open access online library (dx.doi.org/10.5883/DS-CERRF). All analysed species could be differentiated using the standard online DNA barcode identification tool, except for a group of three sympatric colour-defined Menesia species. Seven Menesia records share the same Barcode Identification Number (=BIN), while the single specimen of M. flavotecta shares the same haplotype as some of M. sulphurata. Excluding the Menesia case, the Barcode Index Numbers (BINs) uniquely correspond to the analysed species, in all but the four specimens of Chlorophorus simillimus where they share two BINs. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data and in the Maximum Likelihood analysis, all four subfamilies were recovered as monophyletic. Notwithstanding the few detected deviations from the absolute taxonomic/phylogenetic match, DNA barcoding is a powerful identification tool with a capacity to place an undocumented record among its closest relatives. 

scholarly journals Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

2021 ◽  
Author(s):  
Chuanjiang Zhou ◽  
Mengxia Feng ◽  
Yongtao Tang ◽  
Changxing Yang ◽  
Xiaolin Meng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Morphological Characteristics ◽  
Henan Province ◽  
Coi Gene ◽  
Morphological Identification ◽  
Freshwater Shrimp

Freshwater shrimp is an extremely rich species group with a long and problematic taxonomic history, attributed to its wide distribution, numerous species and similar morphology. Shrimp diversity and species identification is utmost important for fisheries management. However, identification based on morphological characteristics is difficult and complex for a non-specialist to perform. The water system of Henan Province is relatively abundant, but there are few investigations of freshwater shrimps and no description of molecular features. The aim of this study was to uncover the species diversity and phylogenetic of freshwater shrimp in Henan province by combining morphological identification and molecular species delimitation (barcoding gene: COI gene). About 1,200 freshwater shrimp samples from 46 sampling sites were collected for preliminary traditional morphological identification, 222 samples of these were been further microscopic examination and molecular delimitation. Here we used tree based method (NJ, ML) and distance based method (ABGD, bPTP) mainly to define species, detect the cryptic species and assess the validity of the barcoding in molecular. Comprehensive morphological identification and molecular delimitation results, there were 9 effective species and more than one cryptic species of freshwater shrimp in the province and moreover all of them can be identified by DNA barcoding. The results of morphological identification and molecular identification show high consistency, which proves the high efficiency in freshwater shrimp species identification of the DNA barcoding and the presence of cryptic species.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta) based on COI and ITS2 genes in China

2021 ◽  
Author(s):  
Tingting Zhou ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Morphological Identification ◽  
Lumbriculus Variegatus ◽  
Mitochondrial Coi ◽  
Aquatic Oligochaete ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaete could serve as an excellent indicator in aquatic monitoring programs. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial COI gene and nuclear ITS2 gene of 83 specimens belonging to 36 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae, and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree based on ITS2 gene, which was coincident with morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even aquatic oligochaete.

scholarly journals DNA barcoding of twelve shrimp species (Crustacea: Decapoda) from Turkish seas reveals cryptic diversity

2014 ◽  
Vol 16 (1) ◽  
pp. 36 ◽  
Author(s):  
R. BILGIN ◽  
M. A. UTKAN ◽  
E. KALKAN ◽  
S. U. KARHAN ◽  
M. BEKBÖLET
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Coastal Waters ◽  
Cryptic Diversity ◽  
Nuclear Markers ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Shrimp Species ◽  
Gene Coi ◽  
First Time ◽  
Mitochondrial Cytochrome Oxidase

DNA barcoding is a useful tool for the identification and potential discovery of new species. In this study, DNA barcoding was employed by sequencing the mitochondrial cytochrome oxidase subunit I gene (COI) to characterize the genetic diversity of 12 shrimp species inhabiting Turkish coastal waters and, when possible, to compare with the genetic data available from different parts of the Mediterranean and eastern Atlantic. This study also comprises the first DNA barcoding study performed in the Turkish Seas using COI. A total of 40 shrimp specimens were collected and analyzed from 9 sites. Generally, the barcoding gap criterion was successful at identifying species; hence COI appeared to be a good marker of choice for DNA barcoding in this group. Out of the 12 species investigated, five were barcoded for the first time. In six species two intraspecific clades were retrieved after the analyses. The results suggest the presence of cryptic diversity in a genetically understudied marine area, Turkish coastal waters, and further investigation in these species using population genetics, taxonomic approaches and nuclear markers is likely to result in designation of new species.

scholarly journals Chemistry and Molecular Characteristics of Premna flavescens Wall. ex C. B. Clarke in Vietnam

2021 ◽  
Vol 16 (9) ◽  
pp. 1934578X2110314
Author(s):  
Le Minh Ha ◽  
Ngo Thi Phuong ◽  
Nguyen Thi Phuong Trang ◽  
Dinh Thi Thu Thuy ◽  
Le Ngoc Hung
Keyword(s):  
Essential Oil ◽  
Dna Barcoding ◽  
Species Identification ◽  
Folk Medicine ◽  
Molecular Characteristics ◽  
The Family ◽  
First Time ◽  
Identification Tool ◽  
Inflammatory Effect

Premna flavescens Wall. ex C. B. Clarke, a medicinal plant in the family Lamiaceae, was used for the treatment of arthritis in folk medicine. From the essential oil extracted from the leaves of this plant we have identified 51 components, with β-caryophyllene as the major component (26.3%). The essential oil showed a strong anti-inflammatory effect in vitro with an IC50 of 5.88 µg/mL. DNA barcoding is an useful tool for species identification based on the standardized genomic DNA fragments, but the molecular database of P flavescens is still lacking from Genebank. A molecular species identification tool for P flavescens was developed for the first time using DNA barcoding. The sequences of rbcL, trnH–psbA, internal transcribed spacer, and 18S barcodes of P flavescens were submitted to the Genebank with the accession numbers MW553265, MW553266, MT935698.1, and MW485128.1, respectively. This will be highly useful for the molecular authentication of the marker samples.

scholarly journals African freshwater eel species (Anguilla spp.) identification through DNA barcoding

2020 ◽  
Vol 71 (11) ◽  
pp. 1543
Author(s):  
Céline Hanzen ◽  
Martyn C. Lucas ◽  
Gordon O'Brien ◽  
Colleen T. Downs ◽  
Sandi Willows-Munro
Keyword(s):  
Dna Barcoding ◽  
Environmental Dna ◽  
Western Indian Ocean ◽  
Genetic Distances ◽  
Kwazulu Natal ◽  
Coi Barcoding ◽  
Ocean Region ◽  
Coi Sequences ◽  
Freshwater Eels ◽  
Identification Tool

Freshwater eels (Anguilla spp.) have a long and complex catadromous life cycle. This unique feature, coupled with difficulty in separating species based on morphology, makes them complex targets for conservation. In this study we evaluated the utility of DNA barcoding using cytochrome oxidase I (COI) to delimit the four species of African eels found in the western Indian Ocean region. We collected 76 individual fin clips from the four eel species (A. mossambica, n=51; A. marmorata, n=17; A. bengalensis, n=6; A. bicolor, n=2) in the rivers of KwaZulu–Natal, South Africa, in 2016–18. Phylogenetic analysis of the COI sequences recovered all four species as monophyletic. Barcoding gap analyses were performed and there was no found overlap in inter- and intraspecific genetic distances. Consequently, the use of COI barcoding as an identification tool was found to be reliable for identifying African eels to the species level, which suggests that this marker should be included in future environmental DNA or metabarcoding studies.

scholarly journals Potential of DNA Barcoding for Detecting Quarantine Fungi

2013 ◽  
Vol 103 (11) ◽  
pp. 1103-1107 ◽  
Author(s):  
Ruifang Gao ◽  
Guiming Zhang
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Internal Transcribed Spacer ◽  
Pathogenic Fungi ◽  
International Standards ◽  
Detection Methods ◽  
Dna Barcodes ◽  
Interstate Disputes ◽  
The Status ◽  
Identification Tool

The detection of live quarantine pathogenic fungi plays an important role in guaranteeing regional biological safety. DNA barcoding, an emerging species identification technology, holds promise for the reliable, quick, and accurate detection of quarantine fungi. International standards for phytosanitary guidelines are urgently needed. The varieties of quarantine fungi listed for seven countries/regions, the currently applied detection methods, and the status of DNA barcoding for detecting quarantine fungi are summarized in this study. Two approaches have been proposed to apply DNA barcoding to fungal quarantine procedures: (i) to verify the reliability of known internal transcribed spacer (ITS)/cytochrome c oxidase subunit I (COI) data for use as barcodes, and (ii) to determine other barcodes for species that cannot be identified by ITS/COI. As a unique, standardizable, and universal species identification tool, DNA barcoding offers great potential for integrating detection methods used in various countries/regions and establishing international detection standards based on accepted DNA barcodes. Through international collaboration, interstate disputes can be eased and many problems related to routine quarantine detection methods can be solved for global trade.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

2021 ◽  
Vol 9 ◽  
Author(s):  
Tingting Zhou ◽  
Wei Jiang ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Its2 Region ◽  
Aquatic Oligochaetes ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

DNA barcoding of Antarctic marine zooplankton for species identification and recognition

2014 ◽  
Vol 24 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Fangping CHENG ◽  
Minxiao WANG ◽  
Song SUN ◽  
Chaolun LI ◽  
Yongshan ZHANG
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Marine Zooplankton ◽  
Antarctic Marine
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