scholarly journals Review: Progress and potential of DNA barcoding for species identification of fish species

2017 ◽  
Vol 18 (4) ◽  
pp. 1394-1405
Author(s):  
AYESHA IMTIAZ ◽  
SITI AZIZAH MOHD NOR ◽  
DARLINA MD. NAIM
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Biological Species ◽  
Molecular Technique ◽  
Base Pairs ◽  
Main Challenge ◽  
The Status ◽  
Group A

Imtiaz A, Mohd Nor SA, Md. Naim D. 2017. Review: Progress and potential of DNA barcoding for species identification of fish species. Biodiversitas 18: 1394-1405. DNA barcoding is a molecular technique to identify species by utilizing 600-800 base pairs genetic primer segments of mitochondrial gene cytochrome oxidase I. DNA barcoding has high potential to identify species into taxa, resolves ambiguousness in species identification, helps in accurate species identification, categorize species for conservation and also communize the information in the form of database system. The main challenge to this technique is regarding the use of barcoding information on ‘biological species concept’. The extreme diversity of fish and their economic importance has made this group a major target of DNA barcoding. DNA barcoding can assign the status of known to unknown sample but it also has the ability to detect previously un-sampled species as distinct. In this review, we present an overview of DNA barcoding and introduce current advances and limitation of this promising technique.

Identification of common cladocerans and calanoids in two south Australian reservoirs using DNA barcoding and morphological analysis: an integrative approach

Crustaceana ◽  
2014 ◽  
Vol 87 (7) ◽  
pp. 834-855 ◽  
Author(s):  
P. Sharma ◽  
M. Elias Gutierrez ◽  
T. Kobayashi
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Mitochondrial Gene ◽  
A Priori ◽  
South Australia ◽  
Integrative Approach ◽  
The Status ◽  
Population Structures ◽  
Coi Sequences ◽  
Abundance And Diversity

Valid identification of species of freshwater zooplankton is the first step to understand population structures, abundance, and diversity in the pelagic environment. While some Australian taxa can be easily identified morphologically, e.g.,Calamoecia ampulla(Searle, 1911), most other species of freshwater micrometazoans are difficult to identify without specialised training, resulting in limited and even incorrect identification of the various taxa. The use of DNA barcodes, for species identification and discrimination, has added a new dimension to the traditional phenotypic approach and allows researchers to understand the patterns of genetic variability and to overcome taxonomic difficulties in the identification of the species from different life history stages. We used mitochondrial gene cytochrome coxidase I (COI) to examine the species status of common planktonic microcrustaceans in two South Australian reservoirs. COI analyses indicated that the zooplankton specimens examined from the order Diplostraca and the class Maxillopoda, which were assigned binomial names a priori from the generaBosmina,Boeckella,Chydorus,CalamoeciaandDaphnia, possessed distinct COI sequences and nested cohesively within the genealogy, except for individuals ofCeriodaphniacf.cornutaand aCeriodaphniaspecies complex that formed 4 clusters. These clusters were not explicitly identified morphologically. The present study does improve and contribute to the understanding of the status of taxonomy and biogeography of micro-crustaceans in South Australia. This information is crucial for the application of these species in studies of local and regional environmental change over varying time scales. We recommend the integration of traditional morphology with DNA barcoding-based examination, to facilitate species identification, especially for applied research.

scholarly journals Molecular Identification of Mudskipper Fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta

2021 ◽  
Vol 6 (3) ◽  
pp. 66391
Author(s):  
Katon Waskito Aji ◽  
Tuty Arisuryanti
Keyword(s):  
Genetic Distance ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Universal Primers ◽  
Molecular Approaches ◽  
Morphological Studies ◽  
The Family ◽  
Pcr Method

Mudskipper fish is amphibious fish belonging to the family Gobiidae. Coastal communities widely consume mudskipper to meet their animal protein needs. Mudskipper is primarily cryptic species that are morphologically difficult to identify and distinguish from other mudskipper fish species. Consequently, it can be confused with the naming of mudskipper fish species and can affect the conservation efforts of the fish in their habitat. One of the molecular approaches that can be used to identify the fish species quickly and accurately is DNA barcoding using the COI mitochondrial gene. However, the research on the identification of mudskipper fish in Indonesia is still very limited. Therefore, this study aimed to identify 26 mudskipper fish from Baros Beach, Bantul, Yogyakarta, using COI mitochondrial gene as a molecular marker for DNA barcoding. The method used in this study was a PCR method with universal primers, FishF2 and FishR2. The data obtained were then analyzed using GeneStudio, DNASTAR, BLAST, Identification Engine, Mesquite, MEGAX, and BEAST. The analysis was conducted to obtain similarity, genetic distance and reconstruct a phylogenetic tree. The result revealed that all 26 samples of mudskippers collected from Baros Beach were identified in one genus, namely Periophthalmus, and consisted of 3 species, namely P. kalolo (16 samples), P. argentilineatus (9 samples), and P. novemradiatus (1 sample). Furthermore, this study also discovered a suspected cryptic species in P. argentilineatus with a genetic distance of 5.46-5.96% between clade E, F compared with clade G. Further morphological studies are needed to confirm the species status of these three clades before solidly proclaim that they are cryptic species. 

A case study for application of DNA barcoding in identifying species and genetic diversity of fish from the Suez city market, Egypt

2020 ◽  
Vol 33 ◽  
pp. 11
Author(s):  
Omir Abdalwahhab ◽  
Asmaa Galal-Khallaf ◽  
Samy Abd El-Latif Saber ◽  
Alaa GM Osman ◽  
Khaled Mohammed-Geba
Keyword(s):  
Dna Barcoding ◽  
Red Sea ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Fish Market ◽  
Standard Procedures ◽  
Gene Coi ◽  
Northern Red Sea ◽  
Fish Species Diversity

The Red Sea is one of the key areas of biodiversity in the world. It is a hotspot for speciation and biological invasions. In the current work, a pilot, random sampling trial was carried out to characterize some species in the landings reaching the fish market in Suez city, which is one of the largest fish markets in the Northern Red Sea. Samples of different fish species were subjected to the standard procedures of DNA barcoding, applying the sequencing of the cytochrome oxidase subunit 1 mitochondrial gene (COI). DNA barcoding could successfully identify all the targeted fishes to the species-level (>98%). The results exhibited a taxonomically-versatile commercial trends in this market, being the collected species belonging to 7 different fish families and 3 orders. These species were Coris aygula, Papilloculiceps longiceps, Priacanthus sagittarious, Gerres longirostris, Alepes djedaba, Psettodes erumei Cheilinus trilobatus, Calotomus viridescens, and Pardachirus marmoratus. Haplotype diversities in the first six species were moderate. However, their nucleotide diversities were low. This may have resulted from fishing from bottlenecked populations, or from areas that do not hinder the genetic flow. Also, possible cryptic speciation could be detected in P. sagittarius, P. erumei and G. longirostris. Applying the DNA barcoding for species identification in Suez city fish market could then detect various aspects of fish species diversity. More works using the applied analyses can be strongly recommended to aid proper conservation and management of economic fisheries in the Red Sea.

scholarly journals Finding a suitable DNA barcode for Mesoamerican orchids

Lankesteriana ◽  
2015 ◽  
Vol 7 (1-2) ◽  
Author(s):  
Guillaume Gigot ◽  
Jonathan Van Alphen-Stahl ◽  
Diego Bogarín ◽  
Jorge Warner ◽  
Mark Chase ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Molecular Technique ◽  
Biodiversity Inventories

Recently, DNA barcoding has emerged as an effec- tive tool for species identification. This has the poten- tial for many useful applications in conservation, such as biodiversity inventories, forensics and trade sur- veillance. It is being developed as an inexpensive and rapid molecular technique using short and standard- ized DNA sequences for species identification.  

DNA BARCODING FOR IDENTIFICATION OF PROCESSED TUNA FISH IN INDONESIAN MARKET

2016 ◽  
Vol 78 (4-2) ◽  
Author(s):  
Mala Nurilmala ◽  
Utut Widyastuti ◽  
Wisnu Ananta Kusuma ◽  
Nurjanaha Nurjanaha ◽  
Nuring Wulansari ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Cytochrome B ◽  
Mitochondrial Gene ◽  
Free Trade Area ◽  
Accurate Method ◽  
Molecular Technique ◽  
Direct Sequence ◽  
Tuna Fish ◽  
Trade Area ◽  
Canned Tuna

DNA barcoding is a molecular technique to characterize species organism using a short DNA sequence. Recently, it becomes useful tool to detect seafood mislabeling and species substitution. Cytochrome b is one of the mitochondrial gene used in DNA barcoding. In order to face the regulation of AFTA (ASEAN Free Trade Area), the accurate method to detect the fish species and its products is needed in order to avoid the fraudulent in Indonesia. Thus, an attempt was carried out to identify authentication for tuna’s products (sushi, fish ball, meat floss, and canned tuna). The samples were collected from, Bogor, West Java, Indonesia. DNA was isolated according to the manufacturer’s protocol. The amplification of DNA by PCR was carried out, then the direct sequence was performed. In the present study, DNA barcoding of tuna’s product using cytochrome b were elucidated. The amplification of DNA by PCR was successfully obtained from tuna’s sample except one of canned tuna (K3). It showed that one of the canned tuna as in the label did not contain tuna. It indicated that there was an economic fraud for one of canned tuna.

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 Microcoding: the second step in DNA barcoding

2005 ◽  
Vol 360 (1462) ◽  
pp. 1897-1903 ◽  
Author(s):  
R.C Summerbell ◽  
C.A Lévesque ◽  
K.A Seifert ◽  
M Bovers ◽  
J.W Fell ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Rapid Identification ◽  
Second Step ◽  
Base Pairs ◽  
Software Analysis ◽  
Fungal Identification

After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable, detection. Through appropriate software analysis of typical full-length barcodes (generally over 500 base pairs long), uniquely distinctive oligonucleotide ‘microcodes’ of less than 25 bp can be found that allow rapid identification of circa 100–200 species on various array-like platforms. Microarrays can in principle fulfill the function of microcode-based species identification but, because of their high cost and low level of reusability, they tend to be less cost-effective. Two alternative platforms in current use in fungal identification are reusable nylon-based macroarrays and the Luminex system of specific, colour-coded DNA detection beads analysed by means of a flow cytometer. When the most efficient means of rapid barcode-based species identification is sought, a choice can be made either for one of these methodologies or for basic high-throughput sequencing, depending on the strategic outlook of the investigator and on current costs. Arrays and functionally similar platforms may have a particular advantage when a biologically complex material such as soil or a human respiratory secretion sample is analysed to give a census of relevant species present.

scholarly journals DNA barcoding: A practical tool for the taxonomy and species identification of entomofauna

2019 ◽  
Vol 80 (3) ◽  
pp. 227-232
Author(s):  
Iwona Szyp-Borowska ◽  
Katarzyna Sikora
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Interspecific Variation ◽  
Coi Gene ◽  
Innovative System ◽  
Group A ◽  
Specialist Knowledge ◽  
Practical Tool ◽  
Cryptic Taxa ◽  
Major Target

AbstractDNA barcoding is an innovative system designed to provide rapid, accurate, and automatable species identification by using short, standardized gene regions as internal species codes. The mitochondrial cytochrome C oxidase I (COI) gene was proposed by Paul Hebert as an official marker for animals, because of its small intraspecific but large interspecific variation. Since the launch of the project Barcode of Life, this simple technique has caught the interest of taxonomists, ecologists and plant-quarantine officers charged with the control of pests and invasive species.The great diversity of insects and their importance have made this group a major target for DNA barcoding. In most cases, the identification of insect species by traditional methods based on morphological features requires specialist knowledge and is labor-intensive. DNA barcoding aims at meeting the challenge of monitoring and documenting the biodiversity of insects. The utility of DNA barcoding for identifying small insects, cryptic taxa or rare species, as well as many species of forest entomofauna that are impossible to discriminate morphologically throughout all of their life stages, is a subject discussed in this review. Due to its usefulness, also in Poland in the Forestry Research Institute, a method for identifying selected species of saproxylic beetles based on the sequence of the COI region was developed. In the future, this method will be used to assess the state of biodiversity and the naturalness of forest ecosystems. Therefore, this and other future implications of this promising new technique are also discussed here.

scholarly journals Genetic landscape clustering of a large DNA barcoding dataset reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin

2020 ◽  
Author(s):  
Yvan Papa ◽  
Pierre Yves Le Bail ◽  
Raphael Covain
Keyword(s):  
Freshwater Fish ◽  
Dna Barcoding ◽  
Fish Species ◽  
Genetic Divergence ◽  
River Mouth ◽  
Freshwater Fishes ◽  
Morphological Identification ◽  
The North ◽  
The Status ◽  
Genetic Landscape

The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomical references exist for both the Surinamese and Guyanese parts of the basin, these lists were mainly based on morphological identification and there are still taxonomical uncertainties concerning the status of several fish species. Here we present a barcode dataset of 1,284 COI sequences from 199 freshwater fish species (68.86% of the total number of strictly freshwater fishes from the basin) from 124 genera, 36 families, and 8 orders. DNA barcoding allowed for fast and efficient identification of all specimens studied as well as unveiling a consequent cryptic diversity, with the detection of 20 putative cryptic species and 5 species flagged for re-identification. In order to explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese south-west (Tapanahony and Paloemeu), the Guianese south-east (Marouini, Litany, Tampok, Lawa…), and the river mouth in the north. This could be explained either by lower levels of connectivity between these three main parts or by the exchange of individuals with the surrounding basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogenous species across the basin were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.

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