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

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.

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

2020 ◽  
Vol 19 (4) ◽  
pp. 527-536
Author(s):  
Pham The Thu ◽  
Nguyen Manh Linh ◽  
Nguyen Van Quan ◽  
Pham Van Chien ◽  
Dao Huong Ly ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Yellow Card ◽  
Mtdna Coi ◽  
Seriola Quinqueradiata ◽  
Mitochondrial Cytochrome Oxidase ◽  
The Eu

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.

Molecular epidemiology ofSchistosoma mansoniin Uganda: DNA barcoding reveals substantial genetic diversity within Lake Albert and Lake Victoria populations

Parasitology ◽  
2009 ◽  
Vol 136 (13) ◽  
pp. 1813-1824 ◽  
Author(s):  
J. R. STOTHARD ◽  
B. L. WEBSTER ◽  
T. WEBER ◽  
S. NYAKAANA ◽  
J. P. WEBSTER ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Nucleotide Diversity ◽  
Lake Victoria ◽  
Population Diversity ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Statistical Parsimony ◽  
Mitochondrial Cytochrome Oxidase ◽  
Representative Samples

SUMMARYRepresentative samples of UgandanSchistosoma mansonifrom Lake Albert and Lake Victoria were examined using DNA barcoding, sequence analysis of two partially overlapping regions – ASMIT (396 bp) & MORGAN (617 bp) – of the mitochondrial cytochrome oxidase subunit I (cox1). The Victorian sample exhibited greater nucleotide diversity, 1·4%vs. 1·0%, and a significant population partition appeared as barcodes did not cross-over between lakes. With one exception, Lake Albert populations were more mixed by sampled location, while those from Lake Victoria appeared more secluded. Using statistical parsimony, barcode ASMIT 1 was putatively ancestral to all others and analysis of MORGAN cox1 confirmed population diversity. All samples fell into two of five well-resolved lineages; sub-lineages therein broadly partitioning by lake. It seems that barcode ASMIT 1 (and close variants) was likely widely dispersed throughout the Nilotic environment but later diversifiedin situ, and in parallel, within Lake Albert and Lake Victoria. The genetic uniformity of UgandanS. mansonican no longer be assumed, which might better explain known epidemiological heterogeneities. While it appears plausible that locally evolved heritable traits could spread through most of the Lake Albert populations, it seems unlikely they could quickly homogenise into Lake Victoria or amongst populations therein.

scholarly journals Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia

2017 ◽  
Vol 18 (4) ◽  
pp. 1358-1366
Author(s):  
MOHD LUTFI ABDULLAH ◽  
SITI AZIZAH MOHD NOR ◽  
DARLINA MD. NAIM
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Incomplete Lineage Sorting ◽  
Molecular Taxonomy ◽  
Dna Barcode ◽  
Coi Gene ◽  
Lineage Sorting ◽  
Taxonomic Studies ◽  
Mitochondrial Cytochrome Oxidase ◽  
Blast Result

Abdullah ML, Nor SAM, Naim DMd. 2017. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas 18: 1358-1366. The genus Ariidae contains many valuable fish species threatened by overfishing, but knowledge on distribution and threats is still limited due to taxonomic ambiguities. The aim of this study was to apply DNA barcoding techniques to establish a resource of DNA for identification of Ariidae species in Malaysia. A 621 bp of mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to resolve phylogenetic relationships and molecular taxonomy of eight presumed Malaysian Ariid species. We found the monophyly of most species was well established with a mean Kimura-2 parameter (K2P) interspecies distance of 9.6% except for two species, Arius venosus, and Nemapteryx caelata that have very low interspecies genetic distance. The BLAST result shows only two species matched the presumably eight identified fish species. Such discrepancies could arise as a result of misidentifications or errors in GenBank database input, hybridization or incomplete lineage sorting. We suggest the use of DNA barcoding is integrated into the workflow during taxonomic studies as it could significantly increase knowledge about species distributions.

scholarly journals Extremely low genetic variability within and among locations of the greenfish holothurianStichopus chloronotusBrandt, 1835 in Okinawa, Japan

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2410 ◽  
Author(s):  
Taha Soliman ◽  
Okuto Takama ◽  
Iria Fernandez-Silva ◽  
James D. Reimer
Keyword(s):  
Sea Cucumber ◽  
Nucleotide Diversity ◽  
East Coast ◽  
Histone H3 ◽  
Haplotype Diversity ◽  
Conservation Policies ◽  
16S Ribosomal Dna ◽  
Southern Japan ◽  
Stichopus Chloronotus ◽  
Management And Conservation

The greenfish sea cucumberStichopus chloronotusis an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction.Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies ofS. chloronotusin southern Japan.

scholarly journals Genetic Polymorphism Study on Aedes albopictus of Different Geographical Regions Based on DNA Barcoding

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Yiliang Fang ◽  
Jianqing Zhang ◽  
Rongquan Wu ◽  
Baohai Xue ◽  
Qianqian Qian ◽  
...  
Keyword(s):  
Genetic Polymorphism ◽  
Dna Barcoding ◽  
Aedes Albopictus ◽  
Nucleotide Diversity ◽  
Parallel Evolution ◽  
Haplotype Diversity ◽  
Mitochondrial Coi ◽  
Geographical Regions ◽  
Different Populations ◽  
Hypervariable Loci

Aedes albopictus is a very important vector for pathogens of many infectious diseases including dengue fever. In this study, we explored the genetic polymorphism of Aedes albopictus strains in different geographical regions using DNA barcoding of mitochondrial COI (MT-COI) gene. We collected MT-COI sequence of 106 Aedes albopictus mosquitos from 6 provinces in China including Fujian, Guangdong, Hainan, Yunnan, and Taiwan. The length of the sequences is 709bp with the content of A+T (67.7%) greater than that of G+C (32.3%). We identified mutations in 90 (13.68%) loci, of which 57 (63.33%) are transitions, 28 (31.11%) are transversions, and 5 (5.56%) are hypervariable loci. In addition, we obtained 42 haplotypes, 4 (9.52%) of which are shared among different populations. The haplotype diversity of Aedes albopictus is 0.882 and nucleotide diversity is 0.01017. Moreover, the pedigree network diagram shows that most haplotypes are under parallel evolution, suggesting a local expansion of Aedes albopictus in history. Finally, the Neighbor-Joining tree of MT-COI haplotypes reveals a certain correlation between haplotype clusters and geographical distribution, and there are differences among Aedes albopictus in different geographical regions. In conclusion, DNA barcoding of MT-COI gene is an effective method to study the genetic structure of Aedes albopictus.

scholarly journals The Analysis of Morphological and Genetic Characteristics of Yellowstripe Scad from Muara Baru Modern Fish Market in North Jakarta

2020 ◽  
Vol 12 (2) ◽  
pp. 308
Author(s):  
Rahmat Sawalman ◽  
Hawis Madduppa
Keyword(s):  
Dna Barcoding ◽  
Molecular Analysis ◽  
Fish Species ◽  
Morphological Analysis ◽  
Coi Gene ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Fish Market ◽  
Commercially Important ◽  
Mitochondrial Cytochrome Oxidase

HighlightIdentification and morphological analysis of Selaroides leptolepis fish.Molecular analysis using the DNA Barcoding method with the COI gene (mitochondrial cytochrome oxidase subunit I).The number of base pairs in S. leptolepis from the sequencing results was 675bp.The morphological and molecular similarities of Selaroides leptolepis fishAbstractYellowstripe scad is one of the commercially important fish from the Carangidae family, which is marketed at Muara Baru Modern Fish Market, North Jakarta. In- formation regarding the presence of Selaroides leptolepis fish in the waters allows for effective conservation, and management of marine resources. A morphological identification of fish species is still considered inaccurate, so the molecular anal- ysis is necessary. This study aims to identify commercially important fish species deriving from Muara Baru Modern Fish Market, North Jakarta, employing mor- phological, and molecular analysis. A total of 30 specimens were collected from the field. The morphological analysis utilized a visual identification method, and morphometric measurement, while molecular analysis with DNA barcoding em- ployed the mitochondrial cytochrome oxidase subunit I (COI) gene. The results of the morphological analysis indicated that the fish species were yellowstripe scad (S. leptolepis). It also followed the results of molecular analysis of DNA barcoding that the fish was a S. leptolepis species. Therefore, the combination of morphological and genetic analysis has succeeded in identifying the fish species of S. leptolepis.

Efficacy of DNA barcoding for the identification of larval fish species in the Upper and Middle Ing River, Thailand

Gene Reports ◽  
2021 ◽  
Vol 23 ◽  
pp. 101057
Author(s):  
Dutrudi Panprommin ◽  
Kanyanat Soontornprasit ◽  
Siriluck Tuncharoen ◽  
Niti Iamchuen
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Larval Fish

scholarly journals Objective determination of the sea age of Atlantic salmon from the sizes and dates of capture of individual fish

2010 ◽  
Vol 68 (1) ◽  
pp. 130-143 ◽  
Author(s):  
Philip J. Bacon ◽  
William S. C. Gurney ◽  
Eddie McKenzie ◽  
Bryce Whyte ◽  
Ronald Campbell ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Fishery Management ◽  
East Coast ◽  
Probability Distributions ◽  
Age Classes ◽  
Individual Fish ◽  
Bivariate Probability ◽  
Management And Conservation ◽  
Objective Determination

Abstract Bacon, P. J., Gurney, W. S. C., McKenzie, E., Whyte, B., Campbell, R., Laughton, R., Smith, G., and MacLean, J. 2011. Objective determination of the sea age of Atlantic salmon from the sizes and dates of capture of individual fish. – ICES Journal of Marine Science, 68: 130–143. The sea ages of Atlantic salmon indicate crucial differences between oceanic feeding zones that have important implications for conservation and management. Historical fishery-catch records go back more than 100 years, but the reliability with which they discriminate between sea-age classes is uncertain. Research data from some 188 000 scale-aged Scottish salmon that included size (length, weight) and seasonal date of capture on return to the coast were investigated to devise a means of assigning sea age to individual fish objectively. Two simple bivariate probability distributions are described that discriminate between 1SW and 2SW fish with 97% reliability, and between 2SW and 3SW fish with 70% confidence. The same two probability distributions achieve this accuracy across five major east coast Scottish rivers and five decades. They also achieve the same exactitude for a smaller recent dataset from the Scottish west coast, from the River Tweed a century ago (1894/1895), and for salmon caught by rod near the estuary. More surprisingly, they also achieve the same success for rod-caught salmon taken at beats remote from the estuary and including capture dates when some fish could have been in the river for a few months. The implications of these findings for fishery management and conservation are discussed.

scholarly journals Phylogeography of Bulinus truncatus (Audouin, 1827) (Gastropoda: Planorbidae) in Selected African Countries

2018 ◽  
Vol 3 (4) ◽  
pp. 127 ◽  
Author(s):  
Eniola Abe ◽  
Yun-Hai Guo ◽  
Haimo Shen ◽  
Masceline Mutsaka-Makuvaza ◽  
Mohamed Habib ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Haplotype Diversity ◽  
Snail Host ◽  
Snail Species ◽  
African Countries ◽  
Urinary Schistosomiasis ◽  
Bulinus Truncatus ◽  
High Haplotype Diversity ◽  
Gene Coi ◽  
Mitochondrial Cytochrome Oxidase

The transmission of some schistosome parasites is dependent on the planorbid snail hosts. Bulinus truncatus is important in urinary schistosomiasis epidemiology in Africa. Hence, there is a need to define the snails’ phylogeography. This study assessed the population genetic structure of B. truncatus from Giza and Sharkia (Egypt), Barakat (Sudan) and Madziwa, Shamva District (Zimbabwe) using mitochondrial cytochrome oxidase subunit 1 gene (COI) and internal transcribed spacer 1 (ITS 1) markers. COI was sequenced from 94 B. truncatus samples including 38 (Egypt), 36 (Sudan) and 20 (Zimbabwe). However, only 51 ITS 1 sequences were identified from Egypt (28) and Sudan (23) (because of failure in either amplification or sequencing). The unique COI haplotypes of B. truncatus sequences observed were 6, 11, and 6 for Egypt, Sudan, and Zimbabwe, respectively. Also, 3 and 2 unique ITS 1 haplotypes were observed in sequences from Egypt and Sudan respectively. Mitochondrial DNA sequences from Sudan and Zimbabwe indicated high haplotype diversity with 0.768 and 0.784, respectively, while relatively low haplotype diversity was also observed for sequences from Egypt (0.334). The location of populations from Egypt and Sudan on the B. truncatus clade agrees with the location of both countries geographically. The clustering of the Zimbabwe sequences on different locations on the clade can be attributed to individuals with different genotypes within the population. No significant variation was observed within B. truncatus populations from Egypt and Sudan as indicated by the ITS 1 tree. This study investigated the genetic diversity of B. truncatus from Giza and Sharkia (Egypt), Barakat area (Sudan), and Madziwa (Zimbabwe), which is necessary for snail host surveillance in the study areas and also provided genomic data of this important snail species from the sampled countries.

scholarly journals Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
ABDUL BASITH ◽  
Abinawanto Abinawanto ◽  
ENI KUSRINI ◽  
YASMAN YASMAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Phylogenetic Reconstruction ◽  
Partial Sequence ◽  
Diversity Analysis ◽  
Epinephelus Coioides ◽  
Substitution Model ◽  
Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

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