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Open Access Article
1 - Molecular Identification and Phylogeny of16Species of Bivalvia on Shores of the Persian Gulf(Hengam Island,Larak Island,Geshm Island,Lenge Island)
Shohreh Masaeli Pargol Ghavam Mostafavi Homauon Hosseinzadeh Sahafi Saeid Tamadoni Abdolreza Nabinejad Vahid NoamanInroduction & Objective:Bivalvia are one of the least studied orders in the Persian Gulf .A survey and molecular analysis was conducted to determine bivalvia species diversity in the Persian Gulf.Phylogenetic relationships among all described species of the bivalvia ,we MoreInroduction & Objective:Bivalvia are one of the least studied orders in the Persian Gulf .A survey and molecular analysis was conducted to determine bivalvia species diversity in the Persian Gulf.Phylogenetic relationships among all described species of the bivalvia ,were examined with nucleotide sequence data from portions of mitochondrial gene 16srRNA We provide 16s barcode sequences of commertial bivalvia of Persian Gulf ,Iran.Industrial activities , ecologic consideration , and goals of the bivalvia mollecular Identification campaign make it crucial that species of the south costal be identified. The reconstruction of evolut phylogeny of these species are crucial for revealing stock identity that can be used for the management of fisheries industries in Iran. Mitochondrial DNA sequences were used to reconstruct the phylogeny of the bivalvia species .Material and Methods:: For the purpose , DNA was extracted using Isoamyl alcohl phenol chloroform method. The evolutionary relationships among 16 species of the bivalvia were examined using 550 bp of mitochondrial DNA from the 16s rRNA gene.Results: Finally the cladograms were compared and the resulted phylogenetic trees confirmed that the Iran ′s species origin is Indo west pacific species .some of Iran′s species , which were grouped with the other bivalvia taxa seem to always form a sister clade with Indo-west pacific species with strong bootstrap .Conclusion: The result completely agrees with the previously defined species using morphological characters. However , we still lack any comprehensive and clear understanding of phylogenetic relationship in this group. Manuscript profile -
Open Access Article
2 - Molecular Phylogeny of King soldier bream (Argyrops spinifer) in the Persian Gulf and Oman Sea (Bandar Boushehr, Bandar Abbas , Bandar Chabahar)
shirin valipour Pargol Ghavam Mostafavi Mohammadhassan Shahhosseiny Farhad KaymaramInroduction & Objective: King soldier bream is one of the species of family Sparidae, which is commercially and ecologically very important in the Iranian waters of the Persian Gulf and Oman Sea. The species of this family are morphologically very similar to each ot MoreInroduction & Objective: King soldier bream is one of the species of family Sparidae, which is commercially and ecologically very important in the Iranian waters of the Persian Gulf and Oman Sea. The species of this family are morphologically very similar to each other and they may be mistakenly known as another species. Therefore, molecular identification of them has to be considered. Materials and Methods: In this study, the phylogenetic relationship of king soldier bream fish based on mitochondrial region(CO1) was investigated using DNA sequencing method. For this purpose, 90 samples were collected from the soft tissue of the caudal fin using Ammonium acetate, and its quantity and quality were determined by Spectrophotometry and Electrophoresis. Optimal DNA samples for Polymerase Chain Reaction (PCR) and sequencing were examined. After gene amplification and sequencing, Bio Edit version 7.0.1, BLAST, MEGA 7.0.2 and DnaSP 5.10.01 software were used to draw phylogenetic trees. Results: Based on the phylogenetic tree obtained from the sequences, king soldier bream was divided into two main branches in Bandar Abbas, Bandar Bushehr and Bandar Chabahar areas. All samples of the first branch showed a sister relationship with the second branch and all the samples of branches one and two showed sisterhood with samples KJ012292 and kJ012291 from the Gene Bank in Italy with 82, 67 and 86% accuracy. Conclusion: The results can provide useful information on the conservation and management programs, for the preservation, revitalization, and resource of the population this valuable species. Manuscript profile -
Open Access Article
3 - Phylogenetic comparison of Coat Protein nucleotide and amino acid sequence of Cucumber green mottle mosaic virus from Khorasan province with other isolates of the world
Zohreh Moradi Behrooz JafarpourCucumber green mottle mosaic virus (CGMMV) infects many cucurbit species in the world and causing mottle and systemic mosaic symptoms on cucurbitaceous plant leaves. During a survey, Out of 198 samples of cucurbit plants that were collected from the different fields and MoreCucumber green mottle mosaic virus (CGMMV) infects many cucurbit species in the world and causing mottle and systemic mosaic symptoms on cucurbitaceous plant leaves. During a survey, Out of 198 samples of cucurbit plants that were collected from the different fields and cucumber greenhouses in khorasan province, 39 samples were infected by CGMMV in DAS-ELISA using specific polyclonal antibody (The rate of infection was 19.7%). Using specific primers which were designed based on the CGMMV coat protein (CP) gene sequence; a fragment with 486bp length was amplified by reverse transcription polymerase chain reaction (RT-PCR). The CP gene was cloned, sequenced and compared with the sequence of homologous gene of other CGMMV isolates recorded in GeneBank. Phylogenetic analysis using 486 nucleotide long sequences of coat protein gene showed that all CGMMV sequences can be placed into two groups: I and II. Members of group I were divided into two subgroups: A, B. Iranian isolate (kalat) was classified in the group IA. The result showed it had high homology with the other isolates (the highest homology could reach 97.9% in nucleic acid level). As well, phylogenetic tree based on CP amino acid sequences was established and the highest amino acid homology was 98.1%. This is the first report of CP sequence of CGMMV Iranian isolate, determination of its phylogenetic relationship and comparison of its nucleotide and amino acid sequences with those of the other isolates of CGMMV obtained from GenBank. Manuscript profile -
Open Access Article
4 - Wolbachia grouping study, in major Trichogramma wasps in Iran
R. Darsouei J. Karimi V. JahanbakhshThe intracellular symbiont bacterium, Wolbachia is known as a reproductive parasite in different species of Trichogramma. Regard to importance of this symbiont in biological control programms, the present study addressed the efficiency of wsp gene to typing this symbion MoreThe intracellular symbiont bacterium, Wolbachia is known as a reproductive parasite in different species of Trichogramma. Regard to importance of this symbiont in biological control programms, the present study addressed the efficiency of wsp gene to typing this symbiont from some populations of Trichogramma and also its prevalence. In this study which conducted through 2009 to 2010, 19 populations of Trichogramma were screened for Wolbachia infection. Among these, seven populations were determined as infected by Wolbachia. Eight strains of the bacterium were characterized which six strains belonged to subgroup Kue from A supergroup. The two remained strains were related to B supergroup and Sib subgroup. The double infection and superinfection were observed in Trichogramma populations. Among three species, T. embryophagum, T. brassicae and T. evanescens, the highest prevalence of Wolbachia was observed in T. brassicae with 57 % of samples populations. The most infection rate belonged to populations of Mazandaran province. Despite the separation of different strains of Wolbachia on the basis of wsp gene, recombination analysis indicated a doubt about the grouping results of this symbiont inferring from this gene. This analysis indicated existence of some genetic exchangesbetween different strains of Wolbachia in wsp gene. The new approach called Multilocus Sequence Typing (MLST system) could be effective solution in more accurate characterization of these endosymbionts. Manuscript profile -
Open Access Article
5 - Investigation of Genetic Diversity of Lactobacilli Isolated From Cow Milk Samples by RAPD-PCR
Hakime GhaleKhani Masoumeh Hajirezaei Artadokht TavakoliThe use of lactobacilli in the production of fermented foods has several thousand years old due to their ability to make the desired changes in the taste and texture of the food, as well as their importance in the human health. Different dairy products can be a source o MoreThe use of lactobacilli in the production of fermented foods has several thousand years old due to their ability to make the desired changes in the taste and texture of the food, as well as their importance in the human health. Different dairy products can be a source of new strains of Lactobacillus. Therefore, molecular identification and their genetic variation can be an effective step in identifying native lactobacilli reserves with specific functional characteristics and applying them to industrial dairy products. The purpose of this study is to isolate lactobacilli from flora in cow's milk of Narmeshir city and study their genetic diversity. For this purpose, 21 milk samples were collected from different regions of the city, and Lactobacilli wereisolated by the conventional phenotypic and biochemical methods. In order to screen and investigate the genetic diversity of isolated lactobacilli, five RAPD primers were randomly selected. After doing PCR, the analyses of genetic and phylogenetic diversity were performed using Pyelph software and phylogeny trees were drawn. Cluster analysis of molecular data was able to divide the isolates into seven distinct groups at a genetic distance of 10. K3 and K4 isolates were in group 1 and isolates K21, K13, and K11were in group 4. The remaining isolates were placed in separate groups. Since K3 and K4 isolates were from a region and K21 and K13 isolates were also collected from a region, their placement seems to be logical in a group. Manuscript profile -
Open Access Article
6 - Phylogenetic analysis of Afshari sheep population based on HVR and cytB regions of mitochondrial DNA
Kian Pahlevan AfshariBackground and objectives: Sheep as a domestic animal have played a key role in food resources of Iranian plateau people and this area is known as the origin of this spice. Among the genetic markers mtDNA sequencing is one of the most useful and common methods employed MoreBackground and objectives: Sheep as a domestic animal have played a key role in food resources of Iranian plateau people and this area is known as the origin of this spice. Among the genetic markers mtDNA sequencing is one of the most useful and common methods employed for inferring phylogenetic relationship among closely related species and population and conservation of species. Materials and Methods: For this study 40 blood samples from unrelated Afshari sheep were collected. The DNA was extracted and the HVR1 and cytB regions of mtDNA were amplified with specific primers using PCR. Results: The HVR1 and cytB of mtDNA of Afshari breed were sequenced, alingned and compared with other breeds from all over the world. Results showed 3 and 5 haplotype respectively. In addition both loci were high polymorphicConclusion: Sequencing of mitochondrial genome can showed genetic variation and genetic relationship between oviane in the world. For this reason it is powerful and applicable tool to determine the level of genetic diversity. Manuscript profile -
Open Access Article
7 - Detection of coliform bacteria, determination of phylogenetic typing and antibiotic resistance profile of Escherichia coli in qanats and springs of East-Azerbaijan province
N. Shabani Lokarani J. Shayegh J. Sadeghi Z. MousaviEscherichia coli as a fecal contamination and is considered as an index in water. The aim of this study was to determine the phenotypic and genotypic characteristics of E. coli and antibiotic resistance of the isolates collected from qanats and springs in East-Azerbaija MoreEscherichia coli as a fecal contamination and is considered as an index in water. The aim of this study was to determine the phenotypic and genotypic characteristics of E. coli and antibiotic resistance of the isolates collected from qanats and springs in East-Azerbaijan province. For this purpose, 118 samples were selected from above mentioned area and examined by MPN method. The positive coliform samples were identified by phenotypic and genotypic methods. Afterwards, to determine the genetic diversity of E. coli isolates, phylogenetic typing we conducted by means of multiplex PCR. To determine the antibiotic resistance profile, antibiotic discs of Nalidixic Acid, Co-trimoxazol, Amoxicillin, Gentamaicin Ciprofloxacin, Chloramphenicol, Imipenem, Cefotaxime and Ceftazidime antibiogram were used. Based on results, 48% of the samples were evaluated as positive for coliform including 40% for E. coli and 19% for Klebsiella. Amongst 23 isolates confirmed as E. coli by PCR. Phylogenetic typing revealed that 44% of E. coli strains belonged to type D and B2 and 56% belonged to A and B1 phylotypes. Antimicrobial susceptibility pattern showed that 92% of E. coli isolates were resistant to Amoxicillin. All E. coli isolates were sensitive to Imipenem. It was concluded that presence of pathogenic E. coli with high rate of antibacterial resistance in waters source could be considered as a human health hazard. Manuscript profile -
Open Access Article
8 - Phylogenetic survey of chloroplast matK sequences in some medicinal plant species of Mentheae tribe (Lamiaceae) with emphasis on Zhumeria majdae Rech. & Wendelbo.
Hamed Khodayari Elham Khalili fourogh Sanjarian Yunes AsriThe aim of this research is elucidation of molecular taxonomic and phylogenetic relationship between Zhumeria and other genera of Mentheae tribe using sequencing of chloroplastic matk gene. The aim of this research is taxonomic and phylogenetic status of Mentheae tribe MoreThe aim of this research is elucidation of molecular taxonomic and phylogenetic relationship between Zhumeria and other genera of Mentheae tribe using sequencing of chloroplastic matk gene. The aim of this research is taxonomic and phylogenetic status of Mentheae tribe with emphasis Zhumeria majdae Resh. f. & Wendelbo. (Moorkhosh) belonged to Lamiaceae family that endemic of Hormozgan province, Iran and it have not been reported in elsewhere, using sequencing of chloroplastic gene matK. Zhumeria majdae has long been used in traditional medicine as antispasmodic, antimicrobial, carminative especially in infants and for dysmenorrheal. The therapeutic benefits of medicinal plants are often attributed to their antioxidant properties. It is used for treatment of the stomach ulcer, headache, reduce pain, cold and healing of wounds. The methods are as follow: Extraction of DNA, amplification of a part of matk by specific primers, DNA sequencing, and sequence analysis by FINTCH TV software, drawing phylogenetic tree by PAUP software. The heuristic search of the Cladogram analysis resulted in 10000 shortest trees, 3 tree with lengh of 20 steps and statistic coefficient (Retention index = 0.963) and Consistencies index=0.950. In the trees resulting from maximum parsimony and maximum likelihood methods, Mentheae tribe was monophyletic and composed of three distinct monophyletic clades (subtribes Menthinae, Salviinae and Nepetinae). The The tree derived from the combined data matrix, including in-group and out-group taxa, has a total of 74 sequences. results of this study showed that Zhumeria majdae grouped with Salvia clad. Our results comfirm previous studies done by morphological, trnL-F, psbA-trnH and ribosomal DNA phylogeny. Manuscript profile -
Open Access Article
9 - A review on phylogeny of Damask Rose (Rosa × damascena)
Mehrnoush PanahiDamask rose (Rosa × damascena) is one of the most significant species of Rosaceae family scattered in mountain regions of Iran from west lands to central and eastern hills of the country. R. × damascena has considerable applications in pharmaceuticals and pe MoreDamask rose (Rosa × damascena) is one of the most significant species of Rosaceae family scattered in mountain regions of Iran from west lands to central and eastern hills of the country. R. × damascena has considerable applications in pharmaceuticals and perfumeries and has been the subject of vast research. Extensive studies on genotypes of R. × damascena in Iran have shown considerable diversity in this species, and this could represent Iran as a potential hub for genetic diversification and improvement of its cultivars. The species seems to be the most important direct ancestor of North West cultivars in Europe in sect. Rosa, genus Rosa which is thought to be a hybrid with three parents of wild Rosa species, and R. moschata species is its Asian female parent. Based on the evidence from fossils of the genus Rosa, it has been suggested that Asia is the ancestral area for Rosa genus, and the Synstylae lineage in Europe is probably the oldest group that has expanded from Asia about 30 million years ago. The phylogeny of this difficult genus shows presentation of an evolutionary framework requires more in-depth studies. Manuscript profile -
Open Access Article
10 - The Complete Mitochondrial Genome from Iraqi Meriz Goats and the Maternal Lineage Using Whole Genome Sequencing Data
S.I. Mustafa J.S. Heslop-Harrison T. Schwarzacher -
Open Access Article
11 - Genetic Analysis of Three Structural Proteins in Iranian Infectious Bronchitis Virus Isolate
M. Nosrati M. Tahmorespoor M.R. Nassiry -
Open Access Article
12 - Genetic diversity of Arum L. based on plastid marker
leila Joudi Ghezeljeh Meidan Mostafa Assadi -
Open Access Article
13 - Revision on western Crataegus spp. using morphological characters and molecular marker
ّFarahnaz Nooraei Fariba Sharifnia Fahimeh Salimpour Seyed Mohammad MasoumiThe genus L. Crataegus belongs Rosaceae family. It has economic importance due to its widespread use in traditional medicine and landscaping. This genus has a lot of complexities from a taxonomic point of view and so far many plans have been presented to classify the sp MoreThe genus L. Crataegus belongs Rosaceae family. It has economic importance due to its widespread use in traditional medicine and landscaping. This genus has a lot of complexities from a taxonomic point of view and so far many plans have been presented to classify the species of this genus into sections or subgenera. In this study, morphological traits along with ribosomal DNA (ITS) region sequences were used to study the progeny relationships as well as to determine the species boundary in this genus. In morphological studies, 43 traits (14 quantitative traits and 29 qualitative traits) of vegetative and reproductive organs of 14 species of this genus were studied and the obtained data were statistically analyzed by specialized software such as PAST and SPSS. . In phylogenetic studies, the nuclear genomes of 14 species were extracted by DNA Extraction Kit (MBST) and their DNA sequences along with ITS sequences of 19 non-Iranian species of this genus were extracted from NCBI site and then analyzed by PAUP and Figtree softwares were analyzed based on Maximum Parsimony (MP) method. Although the classification of species based on The maximum Parsimony method was consistent with the monograph presented by Christensen, but these results did not confirm the proposed schemes for classifying species in the flora of Iran. Manuscript profile -
Open Access Article
14 - FLORICAULA (FLO) insilico analysis in Saintpaulia ionantha H.Wendl
mina kazemian elham mohajel kazemi Maryam Kolahi valiolah ghasemiThe transition from vegetative to reproductive stage in Saintpaulia ionantha H.Wendl is controlled by factors such as FLORICAULA (FLO). The process of determining the fate of the flower meristem and its formation pattern is determined by the FLO and the induction of hom MoreThe transition from vegetative to reproductive stage in Saintpaulia ionantha H.Wendl is controlled by factors such as FLORICAULA (FLO). The process of determining the fate of the flower meristem and its formation pattern is determined by the FLO and the induction of homeotic regulators. In this research, FLO sequencing, protein characteristics, secondary structure, intracellular position and phylogenetic tree have been evaluated by bioinformatics tools for the first time in African violet. The results showed that the intracellular location of this protein is predicted in the nucleus. This protein (FLO) belongs to the FLO/LFY family. The secondary structure of the protein consists of 53% alpha helix and 4% beta sheets. Examining the phylogeny tree, species related to one family were placed in one branch. Also, protein sequence alignment has shown that the sequence is highly conserved in plants of the same family. Identifying the characteristics of FLO protein can be important as the main factor in planning the function of the tissue and then controlling the function of this protein. Manuscript profile -
Open Access Article
15 - Biosystematic study of Cotonaster Medikus species in Iran( Hyrcanian province)
Zeynab Lotfi fahimeh salimpoor Fariba Sharifnia Maryam PeyvandiThe genus Cotoneaster L. belongs to the genus Rosaceae. In the study, 17 plant samples were examined based on morphological studies and the nucleus sequence of ITS nrDNA. The results showed that there was a significant difference between all quantitative morphological t MoreThe genus Cotoneaster L. belongs to the genus Rosaceae. In the study, 17 plant samples were examined based on morphological studies and the nucleus sequence of ITS nrDNA. The results showed that there was a significant difference between all quantitative morphological traits. The studied species were classified into five groups. The pattern of species analysis based on morphological traits and molecular sequencing are very similar. There are similarities and differences between the studied species in terms of the studied traits. Molecular cladogram showed that the genus of Cotoneaster with consistency index (CI) is 0.68. Among some species of this genus such as C. pseudodiscolor and C. discolor, morphological similarity of traits such as leaf shape, density of lower surface hairs, and hairs on the fruit is observed, If it is genomically different and because it is not morphologically consistent with the description of the identified species of milk thistle in Iran and neighboring countries. Therefore, we consider it as a new species for Iran and define it as C. pseudodiscolor. In addition, the species C. morrisonesis and C. franchetti are a new record of this genus and have a separate cluster in their phenogram. , the present study is the first study in the field of genetic diversity in Iran (Hyrcanian province) using nuclear markers (ITS) in accurate species identification Is the first step in breeding this valuable taxon, which will be addressed in the present study. Manuscript profile -
Open Access Article
16 - The genetic diversity and ecology of the rumen anaerobic fungi of ruminant animals: past, present and future
Ali Khodaei Mehdi Arzanloo Asadollah Babai Ahari Mohammad Hossein Afsarian Hamid BadaliBackground and Objectives: In 1910 scientist notified the existence of fungi in rumen. Based on chitin content in their cell wall, they were classified as true fungi referred to as Neocallimastix frontalis. Based on morphological characters such as number of flagellates MoreBackground and Objectives: In 1910 scientist notified the existence of fungi in rumen. Based on chitin content in their cell wall, they were classified as true fungi referred to as Neocallimastix frontalis. Based on morphological characters such as number of flagellates in zoospore, rhizomycelium, shape of sporangium, ultra structural of zoospore and nucleotide sequences data, these fungi are recently classified into two monocentric and polycentric groups, consisting of six genera. Materials and Methods: In the present study, literature search was performed based on search of MeSH keywords, such as phylogeny, monophyletic, Neocallimastigomycota, rumen fungi, in several online research tools, such as Pubmed Medline, Scopus, Google scholar, Elsevier databases, Irandoc, Iranmedex, Magiran, SID and MEDLIB limited to the articles published between 1992 to 2013. Results: Different characterises of these fungi such as life cycle, reproductive structures, vegetative thallus and molecular data revealed phytogenic relationship of rumen fungi to the members of Chytridiomycota. Phylogenetic analysis of these fungi and their relatives with other eukaryotes using 18S rDNA sequence data, analyses of structural data and the G+C content showed that this fungi are monophyletic organisms. Conclusion: The investigations on inhibitors and their roles in the interactions between fungi and bacteria can be useful to understand the microbial ecosystem of the rumen. Detection of these factors can be used to determine new ecologic relationships in the rumen. Furthermore, detection of the inhibitors of bacterial activity in the rumen can be used to increase the activity of fungi on plant fibres in this ecologic community. Manuscript profile -
Open Access Article
17 - Bioinformatics Study of the Important Medicinal Plant: Salvia Genus
ELMIRA ZIYA MOTALEBIPOUR AKBAR PIRESTANI PIRESTANI -
Open Access Article
18 - The Study on the Phylogeny of Five Species of Caspian Sea Cyprinids Inferred from Mitochondrial Cytochrome b Gene
مهتاب قریب خانی محمد پورکاظمی لیلا عزیززاده فریبا فلاح باقری مصطفی تاتیناThe family Cyprinidae is the biggest family of freshwater fishes in the world. Previous systematic studies on the genus and species of Cyprinidae were mainly based on morphological characters. But nowadays molecular data are used for these purposes extensively. The main MoreThe family Cyprinidae is the biggest family of freshwater fishes in the world. Previous systematic studies on the genus and species of Cyprinidae were mainly based on morphological characters. But nowadays molecular data are used for these purposes extensively. The main objective of this study is determining phylogenetic relationships of 5 species of Caspian Sea Cyprinids including: Vimba vimba persa, Rutilus frisii kutum, Barbus capito, Rutilus rutilus caspicus andCyprinus carpio inferred from mitochondrial cytochrome b gene sequencing. For this purpose 3 adult fish of each species were from Anzali wetland. 2 g of each specimenand#39;s dorsal fin was removed and stored in 96% ethyl alcohol. Genomic DNA was extracted and Polymerase Chain Reaction (PCR) was conducted on them using one pairs of cytochrome b primers. After electrophoresis, PCR product and primers were sent to Genfanavaran Corp. for sequencing. The phylogenic relationships were assessed with Mega 4. The results of this study showed that both Cyprinus carpio and Rutilus rutilus caspicus are located in the same cluster and evolutionary distance of these two species is very low. Rutilus frisii kutum with a little more evolutionary distance was located in a distinct cluster. Vimba vimba persa and Barbus capito also were located in other distinct clusters. On the other hand, all these five species were located in a separate cluster from Sander lucioperca which confirm the common ancestor for these five species. As a conclusion the results of this study showed that sequencing mitochondrial cytochrome b gene is a reliable method to investigate phylogenetic relationships among Iranian cyprinids. Manuscript profile -
Open Access Article
19 - Intraspecific Variation among Populations of Trapelus lessonea in Iran, Using Sequences of the Mitochondrial Gene ND2
اسرا بانی مهجور اسکندر رستگارپویانی ویدا حجتیThe agamid species Trapelus lessonae (Rastegar Pouyani 2000) is one of the widespread species of the family Agamidae in Iran. It is active in day time and particularly can be seen during first and last hoers of day in summer time. In Iran, it is distributed from northwe MoreThe agamid species Trapelus lessonae (Rastegar Pouyani 2000) is one of the widespread species of the family Agamidae in Iran. It is active in day time and particularly can be seen during first and last hoers of day in summer time. In Iran, it is distributed from northwest towards southeast of the country on the foot hills, open planes and alpines along the Zagros mountain chain. In order to evaluate phylogenetic relationships among different population of this taxon in its range in Iran, several populations of this species were collected within its range from Azerbayejan, Kurdistan, Kermanshah, Hamadan, Ilam, Markazi and Isfehan provinces since mid May to early September 2012. Total genomic DNA was extracted from 33 samples, the mitochondrial gene ND2 were amplified and sequenced in all the specimens. Phylogenetic relationships among different populations were reconstructed using variety of methods (e.g Maximum Parsimony, Maximum Likelihood, Bayesian Inference) and programs (e.g Mega, Mr. Bayes and Paup). The reconstructed phylogeny showed the distinct position of all populations in the tree with relatively high resolution. Considering the branch pattern of the phylogenetic tree and the amounts of genetic distances among populations, it is clear that the populations of Azerbayejan, Kurdistan, Kermanshah and Ilam are closely related and all can be attributed to the same taxon in species level. However, the populations of Isfehan and Hamadan are relatively far from the western populations so that they probably can be considered as a distinct species. Manuscript profile -
Open Access Article
20 - Phylogenetic Relationship of Yellowtail Scad (Atule mate) in the Persian Gulf and Oman Sea Using Cytochrome Oxidase I Gene
Mahzad Shakouri Pargol Ghavam Mostafavi Mohammad Pourkazemi Seyyed Mohammadreza FatemiGenetic analysis of fish populations is essential for conserving biodiversity and increasing knowledge about the survival of species, and finding the factors threatening or contributing to the survival of these populations. The present study is aimed at investigating ph MoreGenetic analysis of fish populations is essential for conserving biodiversity and increasing knowledge about the survival of species, and finding the factors threatening or contributing to the survival of these populations. The present study is aimed at investigating phylogenetic relationship of Yellowtail Scad in the northern Persian Gulf and Oman Sea by sequencing mitochondrial Cytochrome Oxidase I gene. Ninety yellow tail Scad have been collected from Bandar Abbas, Bushehr, and Chabahar port. Genomic DNA was extracted using Ammonium acetate method. After electrophoresis on 1% agarose gel, Cytochrome Oxidase I (COI) gene was amplified by Polymerase Chain Reaction (PCR), using pair of primers. After sequencing of PCR product, the phylogenetic tree was drawn by MEGA7 software with different methods (Maximum Likelihood, Maximum Parsimony, and Bayesian) using (Esox lucius) as an extraspecific group. All samples from Bandar Abbas, Bushehr, and three samples from Chabahar port were located in the same clade. Chabahar sample with a little more distance was located in separate clade and due to high supportive degree (bootstrap) showed sister group relationship. Moreover, these two clades were located with more evolutionary distance from extraspecific group. Consequently, COI gene sequencing was an appropriate and reliable method for phylogenetic relationship of Yellowtail Scad, providing useful information about protection and management of this valuable species. Manuscript profile -
Open Access Article
21 - Molecular Analysis of Najdi Goat Population Using HVR1 Sequence of Mitochondrial Genome
Rouhollah Khademi Seyedeh Ommolbanin Ghasemian Hamid Reza Seyyed Abadi amin kazemizadehThis study was conducted to determine the sequence of the HVR1 region of the mitochondrial genome of the Najdi goat. To conduct this study, 30 blood samples of both gender were collected from unrelated goats. After DNA extraction, the desired region was amplified by spe MoreThis study was conducted to determine the sequence of the HVR1 region of the mitochondrial genome of the Najdi goat. To conduct this study, 30 blood samples of both gender were collected from unrelated goats. After DNA extraction, the desired region was amplified by specific primers by PCR technique, and the sequence was determined. For comparison, the phylogeny of the HVR1 region sequence obtained from Najdi goat was drawn with other breeds worldwide to determine the haplotype group. The phylogenetic tree drawn for the samples showed that they all originated from the same population and the number of 5 different haplotypes was determined based on 20 nucleotide polymorphisms (SNP) for the HVR1 region in the sequences. Also, the sequence of the HVR1 region of the studied sample with 11 sequences recorded from 6 haplotype groups from different countries in the NCBI database showed that the Najdi goat belongs to haplotype group A. Comparing the sequence of the HVR1 region with the sequences in the gene bank can contribute to our information about the Najdi goat breeds and open the ground for their better use in breeding programs. According to the obtained results, the genetic diversity of the Najdi goat has increased over many years, and this increase in genetic diversity can be due to the mixing of this breed with other breeds, which can lead to the extinction of the Najdi goat in the future, which requires more attention to this issue. Manuscript profile -
Open Access Article
22 - Evaluating the Function of Melting Point Temperature of Phylogenetic Genes for Detecting the Taxons of Snakes
Leila Moradi Jaferi Sakineh Kazemi Noureini Eskandar Rastegar PouyaniDeoxyribonucleic acid (DNA) is the molecule encoding the genetic instructions used in the growth and functioning of all living organisms and is very appropriate for biological information storage. Todays, the DNA sequences are regarded as sources for detecting the speci MoreDeoxyribonucleic acid (DNA) is the molecule encoding the genetic instructions used in the growth and functioning of all living organisms and is very appropriate for biological information storage. Todays, the DNA sequences are regarded as sources for detecting the species and their phylogenetic relationships. Despite the modern technologies including the next generation sequencing and DNA barcoding, there is still a need for a fast, cheap, and reliable method for identifying species particularly in ambiguous morphologically-defined organisms. This study evaluated to see if some biophysical chemistry properties of PCR products like melting point can be used before sequencing to identify the samples of interest. Determining the melting temperature of PCR products is available in most available measurements in molecular biology labs. The present study focused on the potential use of melting temperature related to PCR products of 16S and Cyt b (highly used genes in phylogenetic studies) using a real-time PCR machine to identify different species of snakes from Iran. The preliminary results of these two genes are promising although extra steps are required to improve its sensitivity. The development of this method can be used in a rapid evaluation of species. Manuscript profile
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