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  • Biology  (24)
  • 1
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    Genetic relationships of Iranian coastline ship sturgeon (Acipenser nudiventris) samples and Ural population based on microsatellite DNA (2021)
    In:  http://aquaticcommons.org/id/eprint/22458 | 18721 | 2018-04-09 17:47:06 | 22458 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-05
    Description: Genetic relationships among 96 specimens of ship sturgeon, Acipenser nudiventris, collected from six locations along the Iranian coastline as well as 8 specimens from northern population (Ural River) were analysed by the restricted maximum likelihood method, as well as two distance analysis method (Nei's and Cavalli-Sforza's distance) of gene frequencies. We have used four SSR markers that produced three polymorphic and two monomorphic loci. Overall results showed that Iranian coastline samples form a monophyletic group (clade) which was different from the northern (Ural) samples. Iranian coastline samples are divided into two groups (clades): Anzali-Kiashahr clade and Sefidrud-Babolsar-Noushahr-Gorgan clade. Bootstrapping test showed monophyleticity of Sefidrud, Babolsar, Noushahr, Gorgan with high (Bootstrap support=93) and Anzali-Kiashahr with middle (Bootstrap support=65) confirmation. Topology of reconstructed trees was in correspondence with geographical distributions of samples.
    Keywords: Biology ; Fisheries ; Ship sturgeon ; Acipenser nudiventris ; Genetic relationships ; Microsatellite DNA ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 229-240
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  • 2
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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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  • 3
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    Identification and extraction of streptococcusis gene from streptococcus iniae and recording in Gene Bank (2021)
    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25458 | 18721 | 2018-09-26 09:47:40 | 25458 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-16
    Description: S. iniae is an important pathogen in both marin animals and humans, causing systemic infections in these hosts. The symptoms of infections are very similar to symptoms of infections caused by human¬specific streptococcal pathogens. The enzyme phosphoglucomutase (PGM) has recently been discovered to play an important role in polysaccharide capsule production and virulence in s. iniae. We aim to isolate S. iniae and cloning phosphoglucomutase gene. S. iniae grew on sheep blood agar as mucoid and beta- hemolytic colonies after 24 h of incubation at 37C. Then confirmed it by sensitive and rapid method of PCR. The pgm gene was amplified successfully and cloned in pTZ57R cloning vector.The recombinant plasmid was sub cloned into pETDuet-l expression vector by rectriction enzymes and confirmed by PCR. Although S. iniae is a pathogen of economic importance, relatively little is known regarding mechanisms of its pathogenesis and few specific virulence determinants have been established. These include the enzyme phosphoglucomutase which contributes to cell wall integrity and resistance to antimicrobial peptides. Thus, this enzyme is the best choice to product the vaccine and more investigations.
    Keywords: Biology ; Iran ; Streptococcusis ; Gene ; Streptococcus iniae ; Gene Bank ; S. iniae ; Pathogen ; Enzyme ; Phosphoglucomutase ; PCR
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 33
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  • 4
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    Comprehensive study on assessment of sturgeons population genetic structure in the Caspian Sea (2021)
    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25174 | 18721 | 2018-09-03 17:15:43 | 25174 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-16
    Description: The population genetic structure of five Caspian Sea sturgeon species was investigated. Totally 1121 samples of caudal and unault's fin tissue of the sturgeons (Acipenser persicus, A. gueldenstaedtii, A. stellatus, A. nudiventris and Huso huso) were collected from the Volga River (Russia), Ural River (Kazakhstan), Kura River (Azerbaijan), Sepidrud River and the coastline of the south Caspian in the Iranian waters as well as from the sampling stations selected for the marine survey for sturgeon stock assessment in the Caspian Sea. All samples were stored in 96% ethyl alcohol and transferred to the genetic laboratory of the International Sturgeon Research Institute. Genomic DNA was extracted using phenol-chloroform method. The quality and quantity of DNA was assessed by Agarose gel (1%) electrophoresis and spectrophotometry. The population genetic structure of Ship and Persian sturgeon was studied using both PCR-RFLP (D-loop and ND5/6 gene) and microsatellite technique and that of H. huso, A. stellatus and A. persicus were studied using microsatellite technique. After amplification of genes using PCR, the RFLP technique was used to digest mtDNA using restriction enzyme. The PCR products were electrophoresed on 6% sequencing polyacrylamide gels followed by silver nitrate staining. Data for PCR-RFLP were analyzed using REAP program and those from microsatellite technique were analyzed using Gene Alex. Population genetic parameters including allele frequency, expected and observed heterozygosity, effective allele, Shannon's index were determined. Genetic identity and distance were calculated following Nei criteria and Hardy Weinberg equilibrium was tested based on X2 and analysis of molecular variance (AMOVA) using Reap and Gen Alex at 99% confidence limit. Phylogenetic relationship was determined and drawn using TFPGA program. The population genetic structure and genetic diversity of the 1121 sturgeon specimens were determined. Three independent populations were identified for Acipenser persicus (two populations in the south Caspian in the Iranian waters and one in the north Caspian). Three independent populations were identified for A. gueldenstaedtii (Volga, Ural and South Caspian populations) using the microsatellite technique. Population genetic structure using PCR-RFLP revealed no genetic differentiation among the A. gueldenstaedtii specimens studied from the different regions using ND5/6 gene, while two populations (Ural and south Caspian populations) were detected for this species with the same technique using D-loop genes. Four independent populations (Volga, Ural, Kura and Sepidrud populations) were reported for A. stellatus using the microsatellite technique and four more populations which most probably belong to the autumn and spring races of the above mentioned independent populations were identified for this species. The present study also identified two populations for H. huso; The North Caspian population (in Volga and Ural Rivers) and The South Caspian population (in Golestan and Guilan regions) which were significantly different from each other (P〈0.01). The genetic population structure of A. nudiventris was studied using the microsatellite and PCR-RFLP techniques which revealed two populations for this species one in the Ural River and the other in the Sepidrud River (South Caspian). Comparison of the ND5/6 and D-loop genes studies in Russian sturgeon revealed that the D-loop gene is better than the ND5/6 genes in population's differentiation and is therefore strongly recommended for population genetic studies on sturgeons in the Caspian Sea. Genetic diversity studied using microsatellite technique was higher and more accurate as compared to that using RFLP. Nevertheless the RFLP technique was able to introduce molecular markers for the population’s species pacific identification. On developing suitable primers these studies can be speeded up and the cost of such studies can be cut down. However the drawback in using microsatellite technique for population genetic studies is that it cannot introduce a molecular marker for the identification of populations. The present study was able to introduce molecular markers to differentiate the ship sturgeon population in the south Caspian from that in the Ural River using the PCR-RFLP technique Based on the results obtained it is strongly recommended that all activities related to restocking and rehabilitation of sturgeon stocks in Iran be conducted on the basis of genetic principles. Also serious and immediate measures should be taken for the restoration and conservation of rare population of native species of Iran particularly in the Sepidrud region using genetic markers before they are become extinct.
    Keywords: Biology ; Iran ; Caspian Sea ; Guilan Province ; Golestan province ; Sepidrud River ; Assessment ; Sturgeons ; Population ; Genetic ; PCR-RFLP ; Microsatellite ; Species ; Samples ; Tissue ; Acipenser persicus ; A. gueldenstaedtii ; A. stellatus ; A. nudiventris ; Huso huso ; Survey
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 329
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  • 5
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    Polymerase Chain Reaction (PCR) and direct sequencing of mtDNA from the ND5/6 gene region in Persian sturgeon Acipenser persicus from the southern Caspian Sea (2021)
    In:  http://aquaticcommons.org/id/eprint/22213 | 18721 | 2018-02-27 12:20:44 | 22213 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-06-30
    Description: A partial sequence of the mtDNA ND5 gene region was used for population study in Persian sturgeon (west and east areas of southern Caspian Sea). The result showed that although this approach was informative for phylogenetic study in sturgeon, it was less informative for population study in Persian sturgeon.
    Keywords: Biology ; Fisheries ; Polymerarase Chain Reaction ; mtDNA ; Sturgeon ; Caspian Sea ; Iran
    Repository Name: AquaDocs
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    Format: application/pdf
    Format: application/pdf
    Format: 23-34
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  • 6
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    Study of mtDNA variation of Russian sturgeon population from the south Caspian Sea using RFLP analysis of PCR amplified ND5/6 gene regions (2021)
    In:  http://aquaticcommons.org/id/eprint/22225 | 18721 | 2018-02-24 15:32:00 | 22225 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-06-30
    Description: PCR-based mtDNA analysis (RFLP) was used for the study of population differentiation in the Russian sturgeon (Acipenser gueldenstaedti). The mtDNA ND5/6 gene regions were amplified using PCR techniques followed by RFLP analysis. 39 different composite haplotypes were detected among 62 specimens. 29 haplotypes were rare occuring only once in two regions (west and east areas of the Southern Caspian Sea). The average nucleotide and haplotype diversity within populations were estimated to be 0.028727 0.00 and 0.9645 00042 respectively and divergence between populations to be 0.052%. A highly significant differences were observed in the distribution of haplotypes between the west and east areas.
    Keywords: Biology ; Fisheries ; mtDNA ; Russian sturgeon ; South Caspian Sea ; RFLP analysis ; PCR ; ND5/6 ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 13-36
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  • 7
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    Identification of different species of squids in Oman Sea (Iranian waters) (2021)
    In:  http://aquaticcommons.org/id/eprint/22252 | 18721 | 2018-03-06 08:09:01 | 22252 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-01
    Description: Identification of different species of oceanic and neritic squids in Iranian waters of Oman Sea was carried out from December 1996 to February 1997. The trawl surveys were conducted during a 12-months period. Fishing was also undertaken by Mid-water and bottom trawl for species confirmation purposes in deep (200-350m) and shallow (0-100m) waters to collect enough specimens that could be used for later species identification. The RN Ferdows-I was used for sampling with an approximate hauling speed of 3.0 knots. Three oegopsid species including Ancistrocheirus lesueuri, Liocranchia reinhardti, Sthenoteuthis oualaniensis and neritic squid, Loligo duvauceli were identified. Another loliginid squid different from Loligo duvauceli was also observed. A. lesueuri (Enoploteuthidae Family) and Liocranchia reinhardti (Cranchiidae Family) are here reported from this area for the first time. Neither was any report about these two families of oegopsid squids in Oman Sea nor Persian Gulf.
    Keywords: Biology ; Fisheries ; Squid ; Oceanic ; Neritic ; Oman Sea ; Iran
    Repository Name: AquaDocs
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    Format: 63-72
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  • 8
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    Investigation on genetic structure of cobia (Rachycentron canadum) using microsatellite markers (2021)
    In:  http://aquaticcommons.org/id/eprint/23801 | 18721 | 2018-07-27 15:05:49 | 23801 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-15
    Description: The genetic diversity of Cobia, Rachycentron canadum populations in the Persian Gulf and Oman Sea were assessed using microsatellite technique. We removed about 3-5g of pectoral and dorsal fin tissue from 184 samples in winter 2006 and spring 2007, and stored it in pure ethylic alcohol (96%). Polymerase chain reactions (PCR) were conducted on the target DNA using 10 paired microsatellite primers. The dendrogram was constructed and drawn using MEGA software package version 4. Based on the analysis of molecular variance, the highest Fst (0.063) was observed when comparing specimens from Dayer Port and Pozm zones. Significant differences (P〈0.01) were not observed between R5t recorded for the specimens studied in the same region but were observed between RSA recorded for different regions. The dendrogram of genetic distance showed two major clusters: the Bushehr and Dayer populations were in one cluster, and the remaining four populations in the other. The second cluster was further separated into two sub-clusters: the Lengeh and Bandar Abbas populations composed one cluster and the Pozm and the Beris populations were in the other cluster. The present study showed that at least three different populations of R. canadum are living in the Persian Gulf and Oman Sea. The populations include Bushehr, Bandar Abbas and Chabahar populations.
    Keywords: Biology ; Rachycentron canadum ; Microsatellite ; Hormozgan province ; Oman Sea ; Persian Gulf ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
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    Format: 67-78
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  • 9
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    Investigation of genetic structure in populations of Mnemiopsis leidyi from north and south of Caspian Sea using RAPE method (2021)
    In:  http://aquaticcommons.org/id/eprint/23877 | 18721 | 2018-08-01 06:30:09 | 23877 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-15
    Description: The molecular structure in populations of Mnemiopsis leidyi were examined for 200 samples from the south (Guilan, Mazandaran and Golestan provinces) and north of the Caspian Sea. DNA was extracted from M leiydi tissue by phenol-chiorophorm method and its concentration was found at 50 to 10Ong. We used the PCR method using 19 random primers (10bp). The PCR products of samples were accompanied with standard marker (50bp DNA). To measure fragment size, samples were run on a 1% agarose gel. Ten of the ninteen primers showed polymorphism. Statistical analysis of data was performed using POPGENE software. The avarage genetic variation was 0.189 in total samples and the maximum variation was found in samples from north of the Caspian Sea. Also, the maximume genetic distance was between north of the Sea and Golestan coasts in the south (0.089). The minimum genetic distance was between Mazandaran and Guilan coasts (0.001). The UOGMA dendogram showed two clusters. The samples of Mazandaran, Guilan and Golestan coasts were placed in one cluster and samples of the north area in another. The genetic diversity was significantly different between samples of the north area and Golestan coasts (P〈0.05). We found a significant genetic divergence between some samples and therefore suggested at least two genetic groups of Mnemiopsis leidyi in the Caspian Sea.
    Keywords: Biology ; Genetic diversity ; RAPD ; Mnemiopsis leidyi ; Golestan Province ; Mazandaran province ; Caspian Sea ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
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    Format: 119-126
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  • 10
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    Molecular population study on Penaeus semisulcatus from the Persian Gulf and Oman Sea using cytochrom oxidase subunit I (COI) gene by RFLP method (2021)
    In:  http://aquaticcommons.org/id/eprint/24025 | 18721 | 2018-08-03 06:42:51 | 24025 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-15
    Description: The objective of this investigation was molecular population study on Penaeus semisulcatus stocks from the Persian Gulf and Oman Sea. Samples were collected using trawling method from Hormuz (40 individuals) and Bushehr (35 individuals) regions. The DNA of samples were extracted using phenol and chloroform method and then were simplified using a pair premier of Cytochrom Oxidase Subunit I (COI) gene sequence by a thermal cycler. Nine restriction enzyme were Used to digest the larger gene region that five of them (Alu I, Hinf I, Hinc I I, Hpa I I and Rca I) appeared Polymorphic patterns. Reap software and X^2 test were used to analyses the RFLP data. The average nucleotide diversity arid haplotype diversity among the population were 0.0345720 ± 0.0011952 and 0.28590±0.08174 and nucleotide divergence among population, being studied, is supposed to be 8.5%. Considering the result dispersion of haplotypes in two region showed a significant difference and this is an evidence for proving the variety of the stocks.
    Keywords: Biology ; Penaeus semisulcatus ; Cytochrom ; COI ; RFLP ; Persian Gulf ; Oman Sea ; Hormuz ; Bushehr province ; Iran
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 15-30
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