Study of mtDNA variation of Russian sturgeon population from the south Caspian Sea using RFLP analysis of PCR amplified ND5/6 gene regions

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

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

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

Genetic variation of Barbus capito in the southern Caspian Sea by PCR-RFLP method

In this study 60 samples were collected from the southern Caspian Sea and some rivers of Mazandaran and Guilan provinces. Genetic variation and probable population differentiation of Barbus capito were studied based on the mitochondrial cytochrom-b gene. The mitochondrial DNA was extracted from fish fin using phenol-chlorophorm method. The specific primers were designed for B. capito and the PCR experiments were done on 60 samples. 11 restriction endonuclease enzymes were applied for RFLP analysis (ALuI, AvaI, AvaII, HinfI, DdeI, HincI, HpaII, RsaI, Sau3AI, HaeIII, TaqI). PCR products (1062 pb) and DNA digests were subjected to agarose and polyacrilamid gel electrophoresis to seperate fragments according to their molecular weight. These patterns were identified similar fpr all samples. Regarding to this patterns, it can be seen that polymorphysm phenomena cannot be observed by above mentioned enzymes and cytochrome-b gene, and there is no seperate population of B. capito in the southern Caspian Sea

Identification of different species of squids in Oman Sea (Iranian waters)

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

Short communication: Population genetic structure studies of Liza aurata based on mtDNA control region sequences analyses in the southern coasts of the Caspian Sea

Nowadays many species are endangered as a result of habitat loss. Decreases in population lead to reduced genetic diversity, which can cause survival crisis in a population (Cecconi et al., 1995). Nowadays optimal management of fish stocks needs information on population structure of species that is provided to researchers through genetic science. Bereavement of science about stock composition will lead to the fracture of fisheries management and unsuitable harvest of stocks (Papasotiropoulos et al., 2007). One of the beneficial methods to demonstrate genetic diversity is haplotype analysis of the D-loop region, an index which is very important and determinant for the preservation of species. Significant genetic variation is found in the D-loop region, even among individuals within a given species. Grey mullets are not endemic species of the Caspian Sea. Juveniles of L. aurata, L. saliens and Mugil cephallus were introduced from the Black Sea into the Caspian Sea during the years 1930-1934. But only the introduction of L. aurata and L. saliens was successful and they adapted well to the ecological conditions of the Caspian Sea (Fazli et al., 2008)

Introducing genetic markers for identification and separation of 4 species of Persian Gulf and Oman Sea fishes using PCR- RFLP method

In order to introduce genetic markers of four species of fishes, 80 samples of each species, i.e. Parastromateus niger, Scomberomorus comersoniannus, Trachionotus mookalee and Caranx para were collected. DNA was extracted using phenol- chloroform method. The target gene (cytochrome b) was amplified by Thermal cycle (PCR) and the PCR product size estimated 1105 bp. In this research out of 27 DNAase enzymes which were used for PCR product enzyme digesting 8 enzymes (Bam HI, Alw 261, Rsa I, Mbo I, Alu I, Hinf I, Dpn I, Dde I) have cut side on target DNA and three enzymes of them Alu I, Hinf I and Mbo I showed polymorphism genetic differences while other enzymes displayed similar patterns. Variation of haplotypes from four species are as follows: BAA for P. niger, AAB for T. mookalee, ABA for C. para, and ACA for S. comersonianus. So it is possible to claim that each of the above Haplotypes may be used as genetic markers for each of the species

Molecular population study on Penaeus semisulcatus from the Persian Gulf and Oman Sea using cytochrom oxidase subunit I (COI) gene by RFLP method

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

Investigation of population genetic structure of common carp (Cyprinus carpio) in the south Caspian Sea using mtDNA method (PCR-RFLP)

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

The PCR-RFLP investigation of Clupeonella cultriventris from the south Caspian Sea, Iran

Fifty common kilka (Clupeonella culiriventris) specimens from Guilan Province and fifty others from Mazandaran Province, South Caspian Sea were collected to study genetic variation in the fish using Restricted Fragment Length Polymorphism (RFLP) of the mIDNA. DNA was extracted from fm tissue by phenol-chloroform method. The PCR products were digested using 13 restriction endo-nuclease enzymes. Five out of thirteen restriction enzymes were polymorphic resulting in nine different haplotypes. The haplotype divergence ranged from 0.0073 to 0.0369. The mean value of haplotype and nucleotide diversity among populations was 0.7339±0.0006 and 0.0098±0.0, respectively. The nucleotide divergence among populations was 0.01%. Statistically significant differences in haplotype frequencies among all samples were observed (P<0.01). Therefore, we conclude the populations are different genetically

Population genetic studies of Liza aurata using D-Loop sequencing in the southeast and southwest coasts of the Caspian Sea

Genetic diversity as an important marker of the ecological status of aquatic ecosystems is considered a unique and powerful tool to evaluate biological communities. In order to evaluate the genetic diversity among golden mullet species (Liza aurata) in the southeast and southwest coasts of the Caspian Sea by D-Loop gene sequencing, a total of 23 fin specimens of golden mullet were collected from the Gilan (Anzali area) and Golestan (Gomishan area) provinces. Total DNA from the samples was extracted by ammonium acetate method and the quality and quantity of the extracted DNA were assessed by spectrophotometry and electrophoresis. Polymerase Chain Reaction (PCR) was conducted on the target DNA and then DNA sequencing was carried out. D-loop region in mitochondrial DNA (mtDNA) of golden mullet contained 900 base pairs (bp). Phylogenetic relationships among golden mullet were calculated by MEGA software version 5.05 and divergence time was estimated using Tahjima's test. The results obtained from this study revealed that there were high genetic differences among two regions in the Gilan and Golestan provinces. Kimura 2-parameter was used for genetic distance analysis and the genetic distance recorded between Gilan and Golestan Provinces was calculated at 0.259. The high levels of FsT were observed between Gilan and Golestan Provinces which indicates that genetic differences exist among present populations (p≤.05). Based on the results obtained from the south Caspian Sea, probably two different populations of Liza aurata are living in the Gilan and Golestan Provinces