Tilapia is an introduced fish for aquaculture that spreads across Indonesia’s water resources. The study aimed to determine the mitochondrial DNA COI sequence, the genetic distance and phylogenetic of tilapia from Lake Toba, Lake Ranau, and the Balai Riset Pemuliaan Ikan (BRPI) Sukamandi, West Java. Five individuals were collected from each site, either wild and culture tilapia; strains of blue tilapia and red tilapia resulting from genetic development at BRPI. Basic Local Alignment Search Tool nucleotide (BLASTN) indicated that Oreochromis mossambicus and O. niloticus exist in natural water resources and culture in Sumatra and Java; O. aureus exists in natural water resources of Lake Toba and Lake Ranau, however, O. Urolepsis is only present at the research center of BRPI. The phylogenetic tree indicated four different subclusters of O. niloticus, O. mossambicus, O. aureus, and O. urolepsis; however, all are still in the same cluster with a bootstrap value of 88%.

Carob moth, Ectomyelois ceratoniae, is the most important pest of pomegranate in Iran and is one of the most effective threats to the export of this product, but only a few studies have been done on the diversity and genetic structure of its populations. Therefore, in order to increase knowledge about the structure and genetic diversity of this pest populations, infested pomegranates were collected from 12 provinces of the country during 2016 and 2017 and genetic diversity components were investigated using a part of the mitochondrial DNA gene, CYTOCHROME OXIDASE I (COI). Also, the haplotypic network and the phylogenetic tree was drawn using the maximum likelihood method. In the present study, six haplotypes were obtained. The first haplotype (H1) was common in all populations, which can be considered as the ancestral haplotype so that other haplotypes have been evolved from it. This haplotype is connected to other haplotypes with a mutation and forms a star-like shape in the haplotypic network. Results of the grouping populations indicate that the northern part of Iran has the most diversity of haplotypes in comparison to the central and southern parts, which can be related to native cultivars, genetic diversity of cultivars, and natural habitat of Pomegranates in this area. The adaptation of pomegranates to different micro-climates, development of commercial cultivation of traditional varieties, and the role of the human in product transformation lead to high gene flow and genetic differences reduction even at wide geographical distances.

Genetic 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.

Silaginidae family fish from Perciforms, are appropriate candidates for shallow water and coastal aquaculture. At least three species of this family represents in the Persian Gulf. Genetic analysis of Sand whiting Sillago sihama, the most common species of family performed using COI gene. During the present study 10 samples were collected from Bushehr and Hormozgan provinces coastal waters. DNA extracted by modified CTAB method. Polymerase chain reactions were performed using universal primers-FISHF1 and FISHR1-. Sequencing results showed a 627 bp amplified fragment. Performing BLAST supported high identity to Sillago sihama species, hence morphometric identification confirms molecular barcoding. Genetic distance of 0. 02 was calculated between samples of two areas based on Kimura 2-parameter using Mega software. Constructed phylogenetic tree using neighbor joining method whereas the Acanthopagrus latus sequences was used as an outgroup revealed no differentiation between two stations samples. In conclusion based on the results of the present study, the gene flow was high among studied samples and no significant differentiation was observed between Bushehr and Hormozgan samples. In conclusion no discrete populations differentiated based on the results of the present study.

BACKGROUND: Argas persicus has a great importance for health and veterinary, it can transmit many infectious agents such as Borrelia anserina (avian spirochetosis) and Aegyptianella pullorum. Distinguishing Argasidae due to close morphological relationship is difficult. OBJECTIVES: In the present study, we performed molecular analyses based on PCR and sequencing of Amplicon derived from 16S rRNA and COX1 genes of A. persicus specimens in several provinces of Iran. METHODS: Out of seventy Argas persicus collected and confirmed morphologically, eight ticks were chosen from five provinces of Iran for gene analysis. Their DNA were extracted and amplificated using primers derived from 16 S ribosomal RNA and COX1 genes using PCR. Then the amplicons were sequenced and analyzed by Chromas software and sequence alignment program (Clustal W). Phylogenetic analysis was also conducted using MEGA ver. 6. 06 with a maximum-likelihood method. RESULTS: Sequencing results indicated that all eight samples belonged to A. persicus species. Their nucleotide sequencing revealed that the interspecific sequence differences of both genes (16S rRNA genes and COX1) between our isolates were very infrequent. All isolates from different provinces were conserved across regions except for one isolate that exhibited a difference of only 1 nucleotide. Within Phylogenetic tree, A. persicus formed a clade with A. persicus from other regions of the world (South Arica, Italy, China, and South Australia). CONCLUSIONS: Our findings suggested a very close phylogenetic relationship between A. persicus specimens obtained from different regions of Iran.

Background: Bedbugs are blood feeding ectoparasites of humans and several domesticated animals. There are scarcity of information about the bed bugs population throughout Iran and only very limited and local studies are available. The aim of this study is to assess the phylogenetic relationships and nucleotide diversity using partial sequences of CYTOCHROME OXIDASE I gene (COI) among the populations of tropical bed bugs inhabiting Iran. Methods: The bedbugs were collected from cities located in different geographical regions of Iran. After DNA extraction PCR was performed for COI gene using specific primers. Then DNA sequencing was performed on PCR products for the all 15 examined samples. Results: DNA sequencing analysis showed that the all C. hemipterus samples were similar, despite the minor nucleotide variations (within the range of 576 to 697bp) on average between 5 and 10 Single nucleotide polymorphisms (SNPs). Subsequently, the results were compared with the database in gene bank which revealed close similarity and sequence homology with other C. hemipterus from other parts of the world. Conclusion: In conclusion, this study has demonstrated the ability of the COI gene to differentiate between the C. hemipterus populations from a few different locations in Iran. The current research is the first report of phylogenetic and genetic species diversity analysis conducted on C. hemipterus in Iran. These results provided basic information for further studies of molecular epidemiology, public health and pest control operators in Iran.

The black-striped pipefish, Syngnathus abaster, is a species of the Syngnathidae family. This study provides data on the morphometric, meristic and genetic structuring of the Caspian Sea pipefish, Syngnathus abaster. Eight morphometric characteristics based on total length and five morphometric characteristics based on standard length were analyzed.A total of 50 specimens were collected in brackish-water biotopes. The average of total length (LT) and standard length (LS) were 102.37 mm and 98.68 mm, respectively. Also in this study, DNA barcodes were expanded for Caspian Sea Black-striped pipefish, hence 652 base-pair of the CYTOCHROME OXIDASE I (COI) gene was sequenced in accordance with standard DNA barcoding protocols. Since Pipefish (S. abaster) is one of the most endangered fishes in the Caspian Sea, information about its phylogenetic relationships are very rare; therefore, DNA barcoding will give a more accurate picture of the future persistence of Black-striped pipefish populations.

Background: Honey bees, classified within the insect class and widely distributed globally, consist of 26 identified subspecies across five evolutionary lines. Among these, the Iranian honey bee (Apis mellifera meda) is notable for its presence in Iran and neighboring regions. This subspecies exhibits unique biological traits, including a high reproductive capacity and effective propolis collection, distinguishing it from other local bee populations. Understanding genetic diversity within these populations is crucial for conservation and breeding efforts. Objectives: The aim of this study is to determine the phylogenetic relationships and natural variations of the Iranian honey bee in comparison to other bee breeds worldwide using the CYTOCHROME OXIDASE I (COI) region. Methods: The study focuses on the identification of COI gene sequences in honeybees. The mitochondrial COI gene sequences related to the Iranian honey bee and eight populations of other honey bee breeds from around the world (24 ecotypes) were extracted and aligned from the genome database (NCBI). BLAST was used for sequence retrieval, and Clustal W was employed for alignment among species. Phylogenetic analysis was performed using MEGA software, applying the Neighbor Joining method to construct a phylogenetic tree based on the edited sequences. The percentage of nucleotide substitutions and replacements was calculated using the maximum likelihood method. Additionally, molecular diversity indices were computed using DnaSP software to assess genetic variation and conservation parameters among populations. Results: The bioinformatics analysis of biological data revealed that transfer substitution occurred more frequently than crossover substitution. Additionally, the percentage of substitution in pyrimidine bases was higher than in purine bases. The dN/dS substitution ratio in the gene locus sequence across the examined ecotypes was estimated at 0.08, indicating purifying selection during the evolution of this gene locus. Furthermore, examination of the COI region of the mitochondrial genome identified a total of 4 haplotypes, 20 mutations, and 195 polymorphic loci within the entire studied population. The neutrality values, based on Tajima's test, indicated effects related to genetic drift, genetic bottlenecks, or balancing selection during the evolutionary history of the studied population. Phylogenetic analysis revealed nine distinct categories of evolutionary paths for the COI gene in the studied ecotypes. In the phylogenetic tree, the Iranian honey bee was placed in a separate cluster, exhibiting the highest and lowest phylogenetic distances relative to Apis koschevnikovi and Apis mellifera, respectively. Conclusions: This research indicates that the conserved region of the mitochondrial CYTOCHROME OXIDASE gene among various bee species is minimal, highlighting significant polymorphism and susceptibility to mutations. A total of 20 mutations and 195 polymorphic sites were identified, suggesting purifying selection processes that contribute to the gene's biological functions. The study also demonstrates that the COI region can effectively differentiate Iranian honey bee populations from others globally. Overall, these findings enhance our understanding of genetic diversity and evolutionary relationships within bee species, underscoring the importance of continued research for conservation efforts.

Background: Chronic obstructive pulmonary disease (COPD) is characterized by decreased expiratory flow rates, increased pulmonary resistance and hyperinflation. CYTOCHROME C OXIDASE (COX) as a key oxidative enzyme modulates oxygen uptake and catalyzes the oxidation of reduced CYTOCHROME C by molecular oxygen. In vitro studies indicate that the activity of COX can be directly regulated by the presence of molecular oxygen. Thus, a better understanding of the role of COX in patients with COPD can provide an important link between the availability of oxygen to tissues and the regulation of oxygen uptake and energy production in these patients.Materials and Methods: We studied 42 COPD patients (36 males, 6 females) with clinically stable conditions and 50 (42 males, 8 females) healthy sedentary volunteers of similar age. Whole blood was collected by venipuncture in sodium citrate tubes and WBCs were separated by Ficoll according to standard protocol and lysed with microtube pestle homogenizer. The homogenates were centrifuged and the supernatants were used as a cell extract for COX activity determination. Aliquots of this were assayed for total protein content and COX activity. Analysis of COX activity was performed using COX assay kit. Absolute specific COX activity was normalized for total protein. Relative activities were determined by dividing absolute specific COX activity on absolute specific citrate synthase activity. Results: Mitochondrial COX activity and specific activity (absolute and relative) significantly increased in WBCs of patients with COPD in comparison with control samples (p< 0.05). Conclusion: These results indicated that the activity of COX was increased in WBCs of patients with COPD but whether this is a primary or secondary change relevant to hypoxic condition in these patients is not clear and needs further investigation.