DNA barcoding for identification of some fish species (Carangidae) in Vietnam coastal area

Carangidae family has got about 148 species belonging to 32 genera. In Vietnam, Carangidae is of high commercial value and playing an important role in the ecosystem. In the context Vietnam has received yellow card for seafood since Nov. 2017 by the EU, in which one of the main reasons was related to the restriction of traceability. In this study, DNA barcoding technique of mitochondrial cytochrome oxidase I (COI) gene was used to classify 56 specimens of Carangidae from three coastal areas (Northern, Central and Southern) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 21 species belonging to 16 genera were determined by the COI barcode while 18 species (16 genera) were determined when using morphological method. Seriola quinqueradiata and Trachinotus anak were newly recorded in Vietnam. From 56 sequences with 660 bp of mtDNA (COI), total 27 haplotypes were detected; haplotype diversity (h) and nucleotide diversity (π) were 0.903 ± 0.00060 and 0.14%, respectively. The DNA barcodes of COI gene of 21 species in Carangidae which were developed in this study could be used as a basis for comparison and traceability of their products. In addition, the results showed the high potentiality in using COI barcode to identify Carangidae fish in Vietnam.

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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Conservation Genetics Resources ◽

10.1007/s12686-020-01155-7 ◽

2020 ◽

Vol 12 (4) ◽

pp. 643-658

Author(s):

George N. Ude ◽

David O. Igwe ◽

Chrysten Brown ◽

Myron Jackson ◽

Alusine Bangura ◽

...

Keyword(s):

Dna Barcoding ◽

Fish Species ◽

Phylogenetic Diversity ◽

Nucleotide Diversity ◽

Fishery Management ◽

Haplotype Diversity ◽

Test Statistic ◽

Diversity Assessment ◽

Management And Conservation ◽

Mitochondrial Cytochrome Oxidase

Abstract Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

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Distribution of Two Strains of Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) in the Western Hemisphere: Is L. zonatus a Potential Invasive Species in California?

Insects ◽

10.3390/insects12121094 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1094

Author(s):

Andrea L. Joyce ◽

Hannah Parolini ◽

Harry Brailovsky

Keyword(s):

Nucleotide Diversity ◽

Phylogenetic Analyses ◽

Insect Pest ◽

Haplotype Diversity ◽

Haplotype Network ◽

Western Hemisphere ◽

Coi Gene ◽

Mtdna Coi ◽

New Genotype ◽

Economic Pest

The leaffooted plant bug, Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) is polyphagous and widely distributed in the Western Hemisphere. Although it has been recorded in California since around 1900, it has become a more common pest in almonds in the last decade. Other studies have shown that an established insect can become a pest when a new genotype is introduced. This study investigated the distribution of two lineages (strains) of L. zonatus in the Western Hemisphere. Specimens from the Leptoglossus collection in the national insect collection in Mexico were used to extract DNA and sequence the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene, for use in population genetic and phylogenetic analyses. New sequences from Mexico, Central and South America were combined with those available in GenBank, from California and Brazil. Two lineages (strains) of L. zonatus were uncovered. One lineage occurs in California, Mexico and Ecuador. The second lineage is more widespread and found in California, Mexico, Guatemala, Nicaragua, Bolivia and Brazil. The haplotype number and diversity, and nucleotide diversity, were found for samples from California, Mexico, and Brazil, for the two lineages, and for all 118 sequences combined. All sequences combined produced five haplotypes, and a haplotype diversity of 0.54. California and Brazil had 3 haplotypes each, with one haplotype shared (5 total). Haplotype diversity in California and in Brazil were 0.526 and 0.505, respectively. A haplotype network found that one haplotype was most abundant and widespread. The small number of haplotypes, a range expansion, and economic pest status of L. zonatus in California, all contribute to this insect being a potentially invasive insect pest.

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DNA BARCODING APPLICATION OF MITOCHONDRIAL COI GENE TO IDENTIFY SOME FISH SPECIES OF FAMILY GOBIIDAE IN VIETNAM

Tạp chí Khoa học và Công nghệ Biển ◽

10.15625/1859-3097/18/4/13662 ◽

2019 ◽

Vol 18 (4) ◽

pp. 443-451

Author(s):

Nguyen Manh Linh ◽

Pham The Thu ◽

Nguyen Van Quan ◽

Pham Van Chien ◽

Dao Huong Ly ◽

...

Keyword(s):

Dna Barcoding ◽

Coi Gene ◽

Dna Barcodes ◽

North Central ◽

Coastal Fish ◽

Mitochondrial Coi ◽

Fisheries Resources ◽

Mitochondrial Coi Gene ◽

The Family ◽

Mitochondrial Cytochrome Oxidase

The family Gobiidae is a relatively high abundance family of coastal fish with about 2000 species in 210 genera described. In Vietnam, the study on Gobiidae is very complex due to the large number of species, small size and high morphological variation which makes difficulties in identification and classification. In this study, the DNA barcoding technique has been used through mitochondrial cytochrome oxidase I (COI) gene to classify 30 specimens of Gobiidae from three coastal areas (North, Central and South) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 26 species belonging to 21 genera were determined by the COI barcode while 19 species (17 genera) were determined when using morphological method. Mahidolia mystacina was new recorded in Vietnam. The DNA barcodes of COI gene developed in this study could be useful for estimating phylogenetic diversity as well as other studies of gobiids in terms of conservation, management and utilization of fisheries resources in Vietnam. In addition, the results showed the high potentiality in using COI barcode to identify marine fish.

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Parasitic wasps as natural enemies of aphid populations in the Mashhad region of Iran: New data from DNA barcodes and SEM

Archives of Biological Sciences ◽

10.2298/abs1104225d ◽

2011 ◽

Vol 63 (4) ◽

pp. 1225-1234 ◽

Cited By ~ 1

Author(s):

Reyhaneh Darsouei ◽

Javad Karimi ◽

Mehdi Modarres-Awal

Keyword(s):

Dna Barcoding ◽

Modern Method ◽

Diaeretiella Rapae ◽

Coi Gene ◽

Dna Barcodes ◽

Parasitic Wasps ◽

Pome Fruit ◽

Initial Attempt ◽

Morphometric Characters ◽

Preliminary Identification

DNA barcoding is a modern method for the identification of different species, including insects. Among animals, the major emphasis of DNA barcoding is on insects. Due to this global trend we addressed this approach for surveying a group of insects. The parasitic wasps (including primary and hyperparasitoids) of pome fruit orchard aphids were collected from Iran-Mashhad during 2009-2010. Preliminary identification of this group was performed by using morphological and morphometric characters and SEM. The COI gene in the specimens was amplified and sequenced. In this survey, Aphidius matricariae, Binodoxys angelicae, Diaeretiella rapae, Ephedrus persicae, Lysiphlebus fabarum and Praon volucre parasitoids and Alloxysta sp., Asaphes suspensus, Dendrocerus carpenteri, Pachyneuron aphidis, Syrphophagus aphidivorus hyperparasitoids were studied. Based on intra-interspecies distances and phylogenetic analysis using NJ, all species possess diagnostic barcode sequences. The results of this study show that the COI sequence could be useful in identification study of this group of insects. Here we have provided the first GenBank data for the COI gene of the above-mentioned hyperparasitoids as well as an initial attempt toward preparing DNA barcodes for Iranian parasitoid and hyperparasitoid aphids.

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Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

10.7287/peerj.preprints.26801 ◽

2018 ◽

Author(s):

Kam-Cheng Yeong ◽

Haruo Takizawa ◽

Thor-Seng Liew

Keyword(s):

Dna Barcoding ◽

West Coast ◽

Leaf Beetle ◽

Coi Gene ◽

Beetle Species ◽

Dna Barcodes ◽

The West ◽

Leaf Beetles ◽

Baseline Knowledge ◽

Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

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Description of two new Australian species of Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) and females of two further species with notes on their biogeography

Zootaxa ◽

10.11646/zootaxa.4822.1.3 ◽

2020 ◽

Vol 4822 (1) ◽

pp. 71-93

Author(s):

MICHAEL D. MOORE ◽

ETHAN P. BEAVER ◽

ALEJANDRO VELASCO-CASTRILLÓN ◽

MARK I. STEVENS

Keyword(s):

Arid Regions ◽

Common Ancestor ◽

Species Recognition ◽

Species Distributions ◽

Coi Gene ◽

Dna Barcodes ◽

Coastal Regions ◽

Late Mesozoic ◽

Australian Species ◽

Mtdna Coi

Abantiades cephalocorvus sp. nov. and Abantiades tembyi sp. nov. are described, along with the previously undescribed females of A. macropusinsulariae Simonsen, 2018 and A. pallida Simonsen, 2018. All of these species belong to a triforked Abantiades Herrich-Schäffer clade that is loosely centred around the Nullarbor and other arid regions of Australia. We explore DNA barcodes (mtDNA COI gene) from these and other Abantiades and discuss their significance for species recognition. The species distributions are entirely or largely allopatric and we discuss their origins from a widespread common ancestor that was likely distributed over inland and coastal regions in the mid- to late-Mesozoic before the onset of desertification. Notes on new distributional data for all of the known species in this clade are included.

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Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron

DNA Barcodes ◽

10.1515/dna-2015-0007 ◽

2015 ◽

Vol 3 (1) ◽

Cited By ~ 4

Author(s):

Lauren M. Overdyk ◽

Heather E. Braid ◽

Stephen S. Crawford ◽

Robert H. Hanner

Keyword(s):

Dna Barcoding ◽

Lake Huron ◽

Coi Gene ◽

Sampling Effort ◽

Coregonus Clupeaformis ◽

Dna Barcodes ◽

Lake Whitefish ◽

Life Data ◽

New Perspective ◽

St Lawrence River

AbstractDNA barcoding is a useful tool for both species identification and discovery, but the latter requires denser sampling than typically used in barcode studies. Lake Whitefish (Coregonus clupeaformis) is a valuable species, fished traditionally, commercially, and recreationally in Lake Huron. Based on the natural geographic and bathymetric separation of the three major basins in Lake Huron, the potential separation of Lake Whitefish within these basins, and the variation among life history (early and late spawning), we predicted that Lake Huron might harbour cryptic lineages of Lake Whitefish at the basin level. To test this prediction, DNA barcodes of the mitochondrial 5’ cytochrome c oxidase subunit I (COI) gene sequences were recovered from spawning phase Lake Whitefish (n = 5 per site), which were collected from sites (n = 28) around Lake Huron during Fall 2012. These sequences, combined with other publically available DNA barcodes from the Barcode of Life Data System (BOLD), revealed twelve unique haplotypes across North America, with seven unique to Lake Huron. The dominant haplotype was found throughout Lake Huron and east to the St. Lawrence River. No deep divergences were revealed. This comprehensive lake-wide sampling effort offers a new perspective on C. clupeaformis, and can provide insight for environmental assessments and fisheries management.

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DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries

Zootaxa ◽

10.11646/zootaxa.1839.1.1 ◽

2008 ◽

Vol 1839 (1) ◽

pp. 1 ◽

Cited By ~ 43

Author(s):

MANUEL ELÍAS-GUTIÉRREZ ◽

FERNANDO MARTÍNEZ JERÓNIMO ◽

NATALIA V. IVANOVA ◽

MARTHA VALDEZ-MORENO ◽

PAUL D. N. HEBERT

Keyword(s):

Dna Barcoding ◽

Classification Systems ◽

Coi Gene ◽

Aquatic Environments ◽

Dna Barcodes ◽

Chydorus Sphaericus ◽

Mitochondrial Coi ◽

Mitochondrial Coi Gene ◽

Current Classification ◽

Excellent Tool

DNA barcoding, based on sequence diversity in the mitochondrial COI gene, has proven an excellent tool for identifying species in many animal groups. Here, we report the first barcode studies for freshwater zooplankton from Mexico and Guatemala and discuss the taxonomic and biological implications of this work. Our studies examined 61 species of Cladocera and 21 of Copepoda, about 40% of the known fauna in this region. Sequence divergences among conspecific individuals of cladocerans and copepods averaged 0.82% and 0.79%, respectively, while sequence divergences among congeneric taxa were on average 15-20 times as high. Barcodes were successful in discriminating all species in our study, but sequences for Mexican Daphnia exilis overlapped with those of D. spinulata from Argentina. Our barcode data revealed evidence of many species overlooked by current classification systems —for example, based on COI genotypes the Diapahanosoma birgei group appears to include 5 species, while Ceriodaphnia cf. rigaudi, Moina cf. micrura, Mastigodiaptomus albuquerquensis and Mastigodiaptomus reidae all include 2–3 taxa. The barcode results support recent taxonomic revisions, such as recognition of the genus Leberis, and the presence of several species in the D. birgei and Chydorus sphaericus complexes. The present results indicate that DNA barcoding will provide powerful new insights into both the incidence of cryptic species and a better understanding of zooplankton distributions, aiding evaluation of the factors influencing competitive outcomes, and the colonization of aquatic environments.

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GENETIC CHARACTERIZATION OF KISSING GOURAMI (Helostoma temminckii Cuvier, 1829) IN OGAN RIVER, SOUTH SUMATRA INFERRED FROM 16S rRNA AND COI MITOCHONDRIAL GENES

Indonesian Fisheries Research Journal ◽

10.15578/ifrj.25.1.2019.37-44 ◽

2019 ◽

Vol 25 (1) ◽

pp. 37

Author(s):

Tuty Arisuryanti ◽

Gregorius Altius Pratama ◽

Lukman Hakim ◽

Johan Putra Koentjana ◽

Fitria Kurnia Nazira

Keyword(s):

16S Rrna ◽

Genetic Divergence ◽

Nucleotide Diversity ◽

Genetic Characterization ◽

Haplotype Diversity ◽

Mitochondrial Genes ◽

Coi Gene ◽

Fish Stock ◽

Fish Samples

Genetic characterization data of kissing gourami are important to understand historical lineage thus enhancing sustainability of the species and to establish regulation for sustainable management of the fish stock in their habitat. However, investigation of genetic characterization of kissing gourami, one of native Indonesian freshwater fishes has poorly understood. Therefore, the aim of this study was to examine genetic characterization of the fish species collected from Ogan River, South Sumatra using partial sequences of two mitochondrial genes, 16S rRNA and COI. The results revealed that for the 621 bp determined in 16S rRNA gene of the samples, five sites were variable, of which one was parsimony informative. Concatenate data revealed three haplotypes with an overall haplotype diversity of 0.833±0.222 and nucleotide diversity of 0.003±0.001. The genetic divergence varied from 0-0.49%. Next, sequence analysis of COI gene exhibited 609 bp which can be translated into 203 amino acids. For the 609 bp sequence determined in the fish samples, three haplotypes were revealed with nine variable sites and two parsimony informatives. Haplotype diversity and nucleotide diversity of the fish samples were 0.833±0.22 and 0.00794±0.0025, respectively. The haplotype divergence between the fish samples was also supported by three nonsynonymous codons. In addition, the genetic divergence varied from 0 % to 1.16 %. The results suggest that genetic variation of the kissing gourami has to be monitored and further studies are needed to compare the same species from different location to know the historical lineage and demography.

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