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  • Articles  (7)
  • Nucleotide sequence  (7)
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  • Articles  (7)
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  • 1
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    Molecular study of the populations of Artemia partenogenetica in Iran using PCR-RFLP Method (2018)
    Details
    Publication Date: 2021-05-19
    Description: Considering the importance of genetic studies to manifest inter population differences in species, samples of Artemia partenogenetica were collected from seven inland lakes including Shoor and Inche-Borun lakes in Golestan Province, Hoze-Soltan and Namak lakes in Qom Province, Maharloo and Bakhteghan lakes in Fars Province and Mighan pool in Markazi Province. A total of 210 samples were subjected to DNA extraction by phenol-chloroform method. Primers were designed on a ribosomal fragment (16SrRNA) of the species' mtDNA sequence and the PCR was conducted on the samples. Digestion of the PCR product with approximately 1584bp lengths by 10 restriction endonuclease (AluI, EcoRI, Eco47I, HaeIII, HindIII, HinfI, MboI, MspI, RsaI, TaqI) showed 12 different haplotypes: 4 haplotypes in Shoor and Inche-Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan pool, 1 in Bakhtegan and Maharloo and 3 in Maharloo. Haplotype diversity values within collected samples varied from zero in Hoze-Soltan, Namak and Bakhteghan samples to 0.7425 in Inche-Borun and Shoor while nucleotide diversity varied from zero in Hoze-Soltan, Namak and Bakhteghan, to 0.0077 in Mighan. The minimum nucleotide diversity among samples was zero between Hoze-Soltan vs. Namak and the maximum was 0.1700 between Inche-Borun and Shoor vs. Mighan. Nucleotide divergences among samples were least in Inche-Borun vs. Shoor (%-0.02) and most in Inche-Borun and Shoor vs. Mighan (%16.18), averaging to %3.40. The evolutionary distances between 12 haplotype showed that the maximum value belonged to Mighan haplotypes vs. Inche-Borun and Shoor haplotypes. Regarding the digestive patterns produced by each enzyme in the studied region, Eco47I is introduced as the population-specific marker of A. partenogenetica in Iran. Test of population differentiation based on haplotype frequencies were statistically significant (P~,0.001) with the exception of Hoze-Soltan vs. Namak and Inche-Borun vs. Shoor. We conclude that there are enough evidences in haplotypic level for dividing A. partenogenetica in Iran into five populations: Hoze-Soltan and Namak, Mighan, Maharloo, Bakhtegan, Incheh-Borun and Shoor.
    Description: Published
    Keywords: RNA ; Nucleotide sequence ; Primers ; Nucleotides ; Artemia partenogenetica ; Population Genetics ; Genetics ; DNA ; Enzymes ; Marine
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.53-68
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  • 2
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    Population structure of Acipenser nudiventris in the south coast of Caspian Sea and Ural River using Microsatellite method (2018)
    Details
    Publication Date: 2021-05-19
    Description: Population structure of Ship sturgeon, Acipenser nudiventris, from the south coast of Caspian Sea and Ural River was investigated using Microsatellite method. For this reason, 73 specimens of the sturgeon were collected from five locations in two sampling regions the first consisted of Bandar Anzali, SefidRud River, Babolsar, and Gorgan, and the second was Ural River. Four SSR markers were used in this investigation, of which 5 loci produced DNA band, with three of them being polymorph. One primer showed two loci with one of them being polymorph and another was monomorphic). Average expected and observed heterozygosity was 0.86 and 0.75 respectively. Genetic variation was assessed through analysis of molecular variance (AMOVA) that indicated almost all of the variance in data namely %94 (P less than or equal to 0.03) was within locations.
    Description: Published
    Keywords: Rivers ; Anadromous species ; Nucleotide sequence ; Induced breeding ; Primers ; Ships ; Sampling ; Coasts ; Acipenser ; Acipenser nudiventris ; Brackish ; Population Genetics ; DNA ; Genetic diversity ; Population structure ; Genotypes ; Biopolymorphism ; Aquaculture techniques ; Fish ; Sturgeon ; Populations ; Sexual Reproduction
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.99-108
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  • 3
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    Investigation of population genetic structure of common carp (Cyprinus carpio) in the south Caspian Sea using mtDNA Method (PCR-RFLP) (2018)
    Details
    Publication Date: 2021-05-19
    Description: The population genetic structure of common carp (Cyprinus carpio) was examined on 260 specimens from Tajan and Gorgan Rivers, Gorgan Gulf, Anzali Lagoon and other regions in east, middle and west of south Caspian Sea. DNA was extracted from fin tissue by phenol-chlorophorm method with a concentration of 50-100 nanograms. PCR was performed using ND-3/4 and ND-5/6 genes. The PCR products of samples were digested by 15 restriction endonuclease enzymes. The digested products accompanied with standard marker (50 pb). To measure fragment size, samples were run on a 6% vertical poyacrylamide gel. The fragments were visualized by silver staining of the polyacrylamide gel. Statistical analysis of data was performed by Reap software. We detected 14 and 12 different haplotypes in ND-3/4 and ND-5/6 genes of common carp. The mean values of haplotype diversity among populations were 0.59 and 0.48 and the average nucleotide diversity was 0.06 and 0.03 for ND3/4 and ND5/6 genes. Also, the mean values of nucleotide divergence among populations were 0.05% and 0.02%, respectively. The haplotype distribution was not significantly different between Mazandaran and Guilan coasts, Mazandaran and Golestan coasts, Golestan coast and Gorgan Gulf and Gorgan River (P less than or equal to 0.05), but this divergence was significantly different between Guilan region and Anzali Lagoon, Guilan and Golestan coasts, Tajan and Gorgan Rivers (P less than or equal to 0.05). We found a significant genetic divergence between some of the samples such that three genetic groups of common carp were identified in the southern part of the Caspian Sea.
    Description: Published
    Keywords: Nucleotide sequence ; Polymerase chain reaction ; Coastal lagoons ; Nucleotides ; Rivers ; Data processing ; Statistical analysis ; Computer programs ; Software ; Haplotypes ; Endonuclease ; Cyprinus carpio ; Brackish ; Population genetics ; Genetics ; DNA ; Freshwater fish ; Enzymes ; Lead ; Lagoons ; Mitochondrial DNA ; Coasts
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.89-102
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  • 4
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    Molecular evaluation of the population of Silver Pomfret (Pampus argenteus) in the Persian Gulf and Oman Sea (Iranian &Kuwaiti waters) (2018)
    Details
    Publication Date: 2021-05-19
    Description: A total of 162 specimens of Silver Pomfret (Pampus argenteus) including 38 samples from Kuwait and 124 samples from Iran (24 from Khouzestan, 24 from Chabahar and 38 from Bushehr) were examined for their DNA structure. DNA from all specimens was extracted using the Phenol-chloroform and amplified using PCR method with a pair of primers with ND sub(2) gene sequence. The PCR products were about 1300 (bp) for all samples. For RFLP analysis 16 restriction enzymes Bcl I, Pst I, Acc II, BseN I, Tru I, Dra I, Alw26 I, Hin6 I, Tas I, Alu I, EcoR I ,Hae III, Hinc II, Hind III, Hinf I and Hpa II were used. DNA bands were visualized by Gel electrophoresis (polyacrylamid) and staining with silver nitrate. Out of 16 enzymes, four showed polymorphism that includedg Hinf I, Alu I, Acc II, and Hpa II. Of the total 162 samples, 13 showed polymorphic patterns. Six haplotypes were rare occurring only once, but others which were only four different kinds occurred more than once. The REAP test gave no significant result for the examined regions (P〉0.05). Therefore, our results revealed that the Pampus argenteus stocks in the Persian Gulf and Oman Sea of Iranian and Kuwaiti waters constitute a unique population.
    Description: Published
    Keywords: Electrophoresis ; Nucleotide sequence ; Polymerase chain reaction ; Primers ; Staining ; Pampus argenteus ; Molecular structure ; Population genetics ; DNA ; Enzymes ; Marine ; Biopolymorphism
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.45-56
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  • 5
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    Molecular study of the populations of Artemia partenogenetica in Iran using PCR-RFLP Method (2021)
    In:  http://aquaticcommons.org/id/eprint/23679 | 18721 | 2018-07-18 06:36:39 | 23679 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-15
    Description: Considering the importance of genetic studies to manifest inter population differences in species, samples of Artemia partenogenetica were collected from seven inland lakes including Shoor and Inche-Borun lakes in Golestan Province, Hoze-Soltan and Namak lakes in Qom Province, Maharloo and Bakhteghan lakes in Fars Province and Mighan pool in Markazi Province. A total of 210 samples were subjected to DNA extraction by phenol-chloroform method. Primers were designed on a ribosomal fragment (16SrRNA) of the species' mtDNA sequence and the PCR was conducted on the samples. Digestion of the PCR product with approximately 1584bp lengths by 10 restriction endonuclease (AluI, EcoRI, Eco47I, HaeIII, HindIII, HinfI, MboI, MspI, RsaI, TaqI) showed 12 different haplotypes: 4 haplotypes in Shoor and Inche-Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan pool, 1 in Bakhtegan and Maharloo and 3 in Maharloo. Haplotype diversity values within collected samples varied from zero in Hoze-Soltan, Namak and Bakhteghan samples to 0.7425 in Inche-Borun and Shoor while nucleotide diversity varied from zero in Hoze-Soltan, Namak and Bakhteghan, to 0.0077 in Mighan. The minimum nucleotide diversity among samples was zero between Hoze-Soltan vs. Namak and the maximum was 0.1700 between Inche-Borun and Shoor vs. Mighan. Nucleotide divergences among samples were least in Inche-Borun vs. Shoor (%-0.02) and most in Inche-Borun and Shoor vs. Mighan (%16.18), averaging to %3.40. The evolutionary distances between 12 haplotype showed that the maximum value belonged to Mighan haplotypes vs. Inche-Borun and Shoor haplotypes. Regarding the digestive patterns produced by each enzyme in the studied region, Eco47I is introduced as the population-specific marker of A. partenogenetica in Iran. Test of population differentiation based on haplotype frequencies were statistically significant (P≤0.001) with the exception of Hoze-Soltan vs. Namak and Inche-Borun vs. Shoor. We conclude that there are enough evidences in haplotypic level for dividing A. partenogenetica in Iran into five populations: Hoze-Soltan and Namak, Mighan, Maharloo, Bakhtegan, Incheh-Borun and Shoor.
    Keywords: Biology ; Population Genetics ; Genetics ; DNA ; Enzymes ; Marine ; RNA ; Nucleotide sequence ; Primers ; Nucleotides ; Artemia partenogenetica ; ISW ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 53-68
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  • 6
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    Unknown
    Investigation of population genetic structure of common carp (Cyprinus carpio) in the south Caspian Sea using mtDNA method (PCR-RFLP) (2021)
    In:  http://aquaticcommons.org/id/eprint/23718 | 18721 | 2018-07-20 08:32:13 | 23718 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-15
    Description: The population genetic structure of common carp (Cyprinus carpio) was examined on 260 specimens from Tajan and Gorgan Rivers, Gorgan Gulf, Anzali Lagoon and other regions in east, middle and west of south Caspian Sea. DNA was extracted from fin tissue by phenol-chlorophorm method with a concentration of 50-100 nanograms. PCR was performed using ND-3/4 and ND-5/6 genes. The PCR products of samples were digested by 15 restriction endonuclease enzymes. The digested products accompanied with standard marker (50 pb). To measure fragment size, samples were run on a 6% vertical poyacrylamide gel. The fragments were visualized by silver staining of the polyacrylamide gel. Statistical analysis of data was performed by Reap software. We detected 14 and 12 different haplotypes in ND-3/4 and ND-5/6 genes of common carp. The mean values of haplotype diversity among populations were 0.59 and 0.48 and the average nucleotide diversity was 0.06 and 0.03 for ND3/4 and ND5/6 genes. Also, the mean values of nucleotide divergence among populations were 0.05% and 0.02%, respectively. The haplotype distribution was not significantly different between Mazandaran and Guilan coasts, Mazandaran and Golestan coasts, Golestan coast and Gorgan Gulf and Gorgan River (P〈0.05), but this divergence was significantly different between Guilan region and Anzali Lagoon, Guilan and Golestan coasts, Tajan and Gorgan Rivers (P〈0.05). We found a significant genetic divergence between some of the samples such that three genetic groups of common carp were identified in the southern part of the Caspian Sea.
    Keywords: Biology ; Population genetics ; Genetics ; DNA ; Freshwater fish ; Enzymes ; Lead ; Lagoons ; Mitochondrial DNA ; Coasts ; Nucleotide sequence ; Polymerase chain reaction ; Coastal lagoons ; Nucleotides ; Rivers ; Data processing ; Statistical analysis ; Computer programs ; Software ; Haplotypes ; Endonuclease ; Cyprinus carpio ; Brackish ; Gorgan R. Eurasia ; Caspian Sea ; Mazandaran Province ; Guilan Province ; Anzali Lagoon ; Caspian Sea ISW ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 89-102
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  • 7
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    Population structure of Acipenser nudiventris in the south coast of Caspian Sea and Ural River using microsatellite method (2021)
    In:  http://aquaticcommons.org/id/eprint/23700 | 18721 | 2018-07-18 08:50:22 | 23700 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-15
    Description: Population structure of Ship sturgeon, Acipenser nudiventris, from the south coast of Caspian Sea and Ural River was investigated using Microsatellite method. For this reason, 73 specimens of the sturgeon were collected from five locations in two sampling regions the first consisted of Bandar Anzali, SefidRud River, Babolsar, and Gorgan, and the second was Ural River. Four SSR markers were used in this investigation, of which 5 loci produced DNA band, with three of them being polymorph. One primer showed two loci with one of them being polymorph and another was monomorphic). Average expected and observed heterozygosity was 0.86 and 0.75 respectively. Genetic variation was assessed through analysis of molecular variance (AMOVA) that indicated almost all of the variance in data namely %94 (P less than or equal to 0.03) was within locations.
    Keywords: Biology ; Population Genetics ; DNA ; Genetic diversity ; Population structure ; Genotypes ; Biopolymorphism ; Aquaculture techniques ; Fish ; Sturgeon ; Populations ; Sexual Reproduction ; Rivers ; Anadromous species ; Nucleotide sequence ; Induced breeding ; Primers ; Ships ; Sampling ; Coasts ; Acipenser ; Acipenser nudiventris ; Brackish ; Caspian Sea ; Ural R. Eurasia ; Caspian Sea Eurasia ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 99-108
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