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

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.

scholarly journals GENETIC CHARACTERIZATION OF LONGTAIL TUNA Thunnus tonggol (BLEEKER, 1851) BASED ON PARTIAL SEQUENCE OF 16S rRNA MITOCHONDRIAL GENE

2018 ◽  
Vol 24 (2) ◽  
pp. 83
Author(s):  
Achmad Zamroni ◽  
Suwarso Suwarso ◽  
Arif Wibowo
Keyword(s):  
16S Rrna ◽  
Nucleotide Diversity ◽  
Genetic Characterization ◽  
Mitochondrial Gene ◽  
Rrna Gene ◽  
Geographic Scale ◽  
Java Sea ◽  
Mitochondrial 16S Rrna Gene ◽  
Longtail Tuna

Although the Longtail tuna (Thunnus tonggol) is an important fish in Indonesia, the population structure has not been investigated. In this study, the genetic differences in geographic scale are analyzed to provide a clear picture of the structure of T. tonggol populations along a transect stretching from Pemangkat (western Kalimantan) to Pekalongan in the Java Sea. We also analyzed SNPs in the mitochondrial 16S rRNA gene of T. tonggol as potential molecular marker for the identification of the origin within species. In total, three polymorphic sites (all represent singleton dimensions) were identified in the sequence analysis of the 570-bp fragment among a total of 97 T. tonggol individuals from Pekalongan and Pemangkat. Based on these polymorphic sites, four haplotypes were identified. The Pemangkat samples had higher amount of haplotype and nucleotide diversity (h = 0.1556 ± 0.0680 and  = 0.000277 ± 0.000432), meanwhile samples Pekalongan showed lower levels of diversity (h = 0.0400 ± 0.0380 and  = 0.000070 ± 0.000209). The study revealed a single, intermixing population of T. tonggol across the sampled location. No significant structuring was observed between other pairwise comparisons, indicating gene flow between geographically adjacent locations.

scholarly journals Genetic divergence in mitochondrial DNA of Anopheles nuneztovari (Diptera: Culicidae) from Brazil and Colombia

2000 ◽  
Vol 23 (1) ◽  
pp. 71-78 ◽  
Author(s):  
Vera Margarete Scarpassa ◽  
Silvia Geurgas ◽  
Ana Maria L. Azeredo-Espin ◽  
Wanderli Pedro Tadei
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Sequence Divergence ◽  
Brazilian Amazon ◽  
Restriction Endonucleases ◽  
Separate Species ◽  
Geographic Populations

In the present study, we have examined the variability in Anopheles nuneztovari mitochondrial DNA of three populations from the Brazilian Amazon and one from western Colombia (Sitronela), using four restriction endonucleases (BclI, ClaI, HindIII, SstI). The haplotype diversity (h) was slightly elevated in all populations (0.5000 to 0.6765), whereas the nucleotide diversity (pi) was lower in the Sitronela population (0.0029) and higher in populations from the Brazilian Amazon (0.0056 to 0.0098). The degree of sequence divergence (delta) estimated within the Brazilian Amazon and that in Sitronela (0.0329 to 0.0371) suggests that these geographic populations of A. nuneztovari may eventually constitute separate species. The low sequence divergence values among the three Brazilian Amazon populations (0.0012 to 0.0031) indicate that these populations are genetically similar. These results are consistent with those recently reported for allozymes of these same populations.

scholarly journals Genetic Differentiation of Clariid Populations using Microsatellite Markers in Kano State Rivers

2021 ◽  
pp. 35-45
Author(s):  
I. O. Suleiman ◽  
R.O. Okeke ◽  
J. M. Madu ◽  
A. U. Umar ◽  
O.M Akinsola ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Dna Extraction ◽  
Genetic Characterization ◽  
Caudal Peduncle ◽  
Fta Cards ◽  
Fish Samples ◽  
Polymerase Chain ◽  
Outbred Populations

This study aimed to investigate the genetic characterization of strains of Clariid fish species in some river bodies in Kano State using microsatellite markers.One hundred and seventy seven Clariid fish samples (Clariasgariepinus and Heterobranchuslongifilis) were collected from six rivers (Thomas, Ghari, Tiga dam, Duddurun Gaya, Karaye and Bagwai) in Kano state. Blood sample was taken from each fish sample by severing the caudal peduncle and drained into FTA cards for DNA extraction, Polymerase Chain Reaction and electrophoresis to determine genetic variation between the Clariid fish populations.Genealex 6.4 software package was used to analyse the resolve bands from DNA extraction to determine their base pair and genetic variation. Results showed that the Fst values ranged from 0.00 to 0.66, Fit ranged from -0.04 to 0.12, Fis ranged from -0.35 to -0.26. It indicated a large number of gene flow (exchange) among the populations with a range of 0.46 to 0.87. There was an established magnitude of genetic divergence (91.86%) among the populations as shown by the result of the percentage polymorphism which depends on the number of alleles detected per locus and their frequencies. It can be concluded that since there was no inbreeding as shown in the study, none of the population exhibited genetic uniqueness. The populations had a high genetic differentiation between populations but moderate differentiation within populations. The populations were outbred populations; an indication that relatives avoided mating in the population.

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.

scholarly journals Biometry, Distribution and Genetic Characterization of Blue Jack Mackerel Trachurus picturatus (Bowdich, 1825), a Rare Pelagic Fish Species in the Adriatic Sea

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 463
Author(s):  
Barbara Zorica ◽  
Ivana Bušelić ◽  
Vanja Čikeš Keč ◽  
Vedran Vuletin ◽  
Ivana Lepen Pleić ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Fishing Ground ◽  
Jack Mackerel ◽  
Biometrical Analysis ◽  
Meristic Characters ◽  
Positive Allometry ◽  
Northeast Atlantic Ocean ◽  
Published Research

The blue jack mackerel Trachurus picturatus (Bowdich, 1825) specimens (N = 155) were collected during the MEDITS survey, done along the eastern side, precisely, of the Croatian fishing ground in July 2018. Biometrical analysis of ten morphometric and five meristic characters, as well as genetic analysis proved that the collected specimens were blue jack mackerel. The total length (TL) and weight (W) of all observed specimens ranged from 9.2 to 33.7 cm (12.15 ± 2.95 cm) and from 5.79 to 384.94 g (17.64 ± 39.42 g), respectively. All calculated length–length relationships were linear (r > 0.923). Sex was determined only on two larger specimens (28 cm < TL < 32.8 cm), which were females. In the length–weight relationship, positive allometry was established (b = 3.1789). Based on 37 partial cytochrome b sequences, the overall haplotype diversity (h) of 0.812 ± 0.048 and nucleotide diversity (π) of 0.0064 ± 0.0007 indicated high levels of haplotype and low nucleotide diversity. The obtained sequences were compared to previously published research within the Northeast Atlantic Ocean and the Mediterranean Sea, confirming the absence of genetic structure among these populations.

scholarly journals Genetic Characterization of Domesticated F1 Generation in Humpback Grouper (Cromileptes altivelis)

2007 ◽  
Vol 5 (1) ◽  
pp. 87
Author(s):  
Ratu Siti Aliah ◽  
. Wahidah ◽  
K. Sumantadinata ◽  
Estu Nugroho ◽  
O. Carman
Keyword(s):  
First Generation ◽  
Genetic Characterization ◽  
Haplotype Diversity ◽  
Breeding Strategy ◽  
Loop Region ◽  
Pcr Rflp ◽  
D Loop ◽  
F1 Generation ◽  
Mtdna Haplotype

<p>First generation (F1) of hatchery produced humpback grouper (<em>Cromileptes altivelis</em>) has been characterized genetically in order to serve the information of their status in related to their breeding strategy. PCR-RFLP method was used to detect the variation of mtDNA D-loop region of F1 population at BBPBL Lampung and BBAP Situbondo. The result of study showed that reducing of haplotype diversity had been arised from broodstock (0.8548) to F1 generation population (0.7473; 0.7273; and 0.6947, respectively).  Genetic divergence that had found between population BBPBL Lampung and BBAP Situbondo make it possible to do outbreeding in order to get its heterosis's effect.</p> <p>Keywords: mtDNA, haplotype diversity, genetic differentiation, <em>Cromileptes altivelis</em></p> <p> </p> <p>ABSTRAK</p> <p>Ikan kerapu tikus (<em>Cromileptes altivelis</em>) generasi pertama (F1) hasil domestikasi di hatchery telah dikarakterisasi secara genetik untuk menyediakan informasi status sehubungan dengan program pemuliaannya.  Metode PCR-RFLP digunakan untuk mendeteksi variasi sekuens D-loop mtDNA ikan kerapu tikus F1 yang diproduksi di BBPBL Lampung dan BBAP Situbondo.  Hasil penelitian menunjukkan bahwa telah terjadi penurunan keragaman haplotipe dari induk (0,8548) ke populasi generasi F1 (masing-masing 0,7473; 0,7273; dan 0,6947).  Adanya keragaman genetik antara populasi ikan kerapu tikus di BBPBL dan BBAP Situbondo memungkinkan dilakukannya <em>outbreeding</em> untuk mendapatkan efek heterosis.</p> <p>Kata kunci: mtDNA, keragaman haplotipe, diferensiasi genetik, <em>Cromileptes altivelis</em></p>

scholarly journals Genetic characterization and phylogenetic study of Indonesian cuscuses from Maluku and Papua Island based on 16S rRNA gene

2020 ◽  
Vol 13 (11) ◽  
pp. 2319-2325
Author(s):  
Rini Widayanti ◽  
Richo Apriladi Bagas Pradana ◽  
Rony Marsyal Kunda ◽  
Suhendra Pakpahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genetic Characterization ◽  
16S Rrna Gene Sequencing ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Close Relationship ◽  
Rrna Gene Sequencing ◽  
Ethics Guidelines

Background and Aim: Indonesian cuscuses are now becoming scarce because of the reduction of habitat and poaching. Further, molecular characterization of Indonesian cuscuses is still very lacking. This study aimed to determine genetic markers and phylogenetic relationships of Indonesian cuscuses based on 16S rRNA gene sequences. Materials and Methods: This study used 21 cuscuses caught from two provinces and 16 islands: 13 from Maluku and eight from Papua. Cuscus samples were taken by biopsy following ethics guidelines for animals. The genome isolation was done using gSYNC DNA Mini Kit (Geneaid Biotech Ltd., Taiwan). The 16S rRNA gene was amplified by primers (16SKUSAF and 16SKUSAR), and the polymerase chain reaction product obtained was 1875 base pair (bp). The analysis of genetic characterization and the phylogenetic relationship was performed using MEGA version X software (https://www. megasoftware.net/). Results: 16S rRNA gene sequencing attained 1598 bp for all samples. Based on the 16S rRNA nucleotide sequences, cuscuses from Papua and Maluku belong to the genus Phalanger and Spilocuscus. Phalanger spp. and Spilocuscus spp. from Papua can be distinguished from Phalanger and Spilocuscus from Maluku, except Spilocuscus from Ternate has a very close relationship with cuscus from Sentani, Papua. Conclusion: Indonesian cuscuses were derived into two clades based on 16S rRNA gene sequence, one group to genus Phalanger and another group to Spilocuscus.

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