Regions Of Mitochondrial Genome Research Articles

A multiplex DNA probe-based method for simultaneous identification of adulteration in meat samples

Meat adulteration and admixing are prevalent malpractices observed in processed and raw meat samples, where the consumption of adulterated meat has been associated with food allergies, financial losses, and consumer distrust. Meat authentication is pivotal to address these concerns. The meat authenticity can be determined through genetic, protein, and immunological markers and advanced detection methods. However, these methods often target a single species and lack the specificity to distinguish closely related species. Here, in the present study, we have developed a multiplex detection method based on the species-specific primers and probes, that can target four meat species in one reaction. The developed method amplifies the mitochondrial genomic regions of chicken, pork, sheep and goat using TaqMan multiplex probe-based RT-qPCR assay. Unique pairs of species-specific primers and probes that target specific mitochondrial DNA (mtDNA) regions of each species were designed and screened for specificity and sensitivity. The detection limit for species identification using the designed primers in real-time qPCR assays was 0.1 picogram per microliter (pg/μL) DNA detected in singleplex reaction and facilitates the simultaneous detection of closely related species, such as goat and sheep. Further, DNA-based probes were utilized in a multiplex real-time qPCR assay to identify chicken, pork, sheep and goat DNA in a single tube reaction. The multiplex assay was validated for raw and processed meat products, demonstrating its applications in ensuring the quality of meat products and safeguarding consumer interests.

Genetic diversity and phylogeography of Phlebotomus argentipes (Diptera: Psychodidae, Phlebotominae), using COI and ND4 mitochondrial gene sequences.

Phlebotomus argentipes complex is the primary vector for cutaneous leishmaniasis, a burgeoning health concern in contemporary Sri Lanka, where effective vector control is important for proper disease management. Understanding the genetic diversity of the P. argentipes population in Sri Lanka is vital before implementing a successful vector control program. Various studies have indicated that genetic divergence, caused by genetic drift or selection, can significantly influence the vector capacity of arthropod species. To devise innovative control strategies for P. argentipes, exploring genetic diversity and phylogeography can offer valuable insights into vector competence, key genetic trait transfer, and impact on disease epidemiology. The primary objective is to analyze the genetic diversity and phylogeography of the P. argentipes complex in Sri Lanka, based on two mitochondrial genomic regions in modern representatives of P. argentipes populations. A total of 159 P. argentipes specimens were collected from five endemic areas of cutaneous leishmaniasis and identified morphologically. Two mitochondrial regions (Cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) were amplified using the total DNA and subsequently sequenced. Partial sequences of those mitochondrial genes were utilized to analyze genetic diversity indices and to explore phylogenetic and phylogeographic relationships. Among five sampling locations, the highest genetic diversity for COI and ND4 was observed in Hambantota (Hd-0.749, π-0.00417) and Medirigiriya (Hd-0.977, π-0.01055), respectively. Phylogeographic analyses conducted using COI sequences and GenBank retrieved sequences demonstrated a significant divergence of P. argentipes haplotypes found in Sri Lanka. Results revealed that they have evolved from the Indian ancestral haplotype due to historical- geographical connections of the Indian subcontinent with Sri Lanka. Utilizing high-mutation-rate mitochondrial genes, such as ND4, can enhance the accuracy of genetic variability analysis in P. argentipes populations in Sri Lanka. The phylogeographical analysis of COI gene markers in this study provides insights into the historical geographical relationship between India and P. argentipes in Sri Lanka. Both COI and ND4 genes exhibited consistent genetic homogeneity in P. argentipes in Sri Lanka, suggesting minimal impact on gene flow. This homogeneity also implies the potential for horizontal gene transfer across populations, facilitating the transmission of genes associated with traits like insecticide resistance. This dynamic undermines disease control efforts reliant on vector control strategies.

Variants in the Control Region of Mitochondrial Genome Associated with type 2 Diabetes in a Cohort of Mexican Mestizos

According to the International Diabetes Federation, Mexico is seventh place in the prevalence of type 2 diabetes (T2D) worldwide. Mitochondrial DNA variant association studies in multifactorial diseases like T2D are scarce in Mexican populations. The objective of this study was to analyze the association between 18 variants in the mtDNA control region and T2D and related metabolic traits in a Mexican mestizo population from Mexico City. This study included 1001 participants divided into 477 cases with T2D and 524 healthy controls aged between 42 and 62 years and 18 mtDNA variants with frequencies >15%. Association analyses matched by age and sex showed differences in the distribution between cases and controls for variants m.315_316insC (p = 1.18 × 10-6), m.489T>C (p = 0.009), m.16362T>C (p = 0.001), and m.16519T>C (p = 0.004). The associations between T2D and variants m.315_316ins (OR = 6.13, CI = 3.42-10.97, p = 1.97 × 10-6), m.489T>C (OR = 1.45, CI = 1.00-2.11, p = 0.006), m.16362T>C (OR = 2.17, CI = 1.57-3.00, p = 0.001), and m.16519T>C (OR = 1.69, CI = 1.23-2.33, p = 0.006) were significant after performing logistic regression models adjusted for age, sex, and diastolic blood pressure. Metabolic traits in the control group through linear regressions, adjusted for age, sex and BMI, and corrected for multiple comparisons showed nominal association between glucose and variants m.263A>G (p <0.050), m.16183A>C (p <0.010), m.16189T>C (p <0.020), and m.16223C>T (p <0.024); triglycerides, and cholesterol and variant m.309_310insC (p <0.010 and p <0.050 respectively); urea, and creatinine, and variant m.315_316insC (p <0.007, and p <0.004 respectively); diastolic blood pressure and variants m.235A>G (p <0.016), m.263A>G (p <0.013), m.315_316insC (p <0.043), and m.16111C>T (p <0.022). These results demonstrate a strong association between variant m.315_316insC and T2D and a nominal association with T2D traits.

Mature Red Blood Cells Contain Long DNA Fragments and Could Acquire DNA from Lung Cancer Tissue.

Red blood cells (RBC) are commonly known as cells with no nucleus or mitochondria and are assumed to be a transportation vehicle. This study confirms that RBC contain long DNA fragments inside with stain by both microscope and flow cytometry, which covers most nuclear and mitochondrial genome regions by next-generation sequencing (NGS). Such characteristics demonstrate a significant difference compared with A549 cell line or paired peripheral blood mononuclear cell as nucleated cells. To further explore the characteristics of RNA DNA, DNA from 20 RBC samples is sequenced by NGS. Interestingly, several gaps and multiple regions with copy number variation are observed significantly different between different samples, which could be used to distinguish samples with different health status accurately. Using an in vitro co-culture system, it is shown that RBC could absorb DNA-bearing tumorigenic mutations from cancer cell lines but requires cell-to-cell contact. Finally, based on a small scale clinical trial, it is confirmed that common genetic mutations of cancer tissues could be detected in RBC from patients with early-stage non-small-cell lung cancer. This study highlights a new biological phenomenon involving RBC and its translational potential as a novel liquid biopsy technology platform for early cancer screening and diagnosis of malignancy.

Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae.

Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.

Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae).

The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth’s history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.

G-quadruplexes in the mitochondrial genome - a cause for instability.

Accumulation of mutations such as deletions in mitochondrial DNA is associated with ageing, cancer and human genetic disorders. These deletions are often flanked by GC-skewed sequence motifs that can potentially fold into secondary non-B DNA conformations. G-quadruplexes are emerging as key initiators of mitochondrial genomic instability. In this issue, Dahal etal provide an insilico analysis of sequence motifs that can fold into altered DNA structures in mitochondrial genomic regions that contain frequent deletions. They show the formation of five G-quadruplexes near such frequent breakpoints using biochemical and biophysical approaches invitro and more importantly inside mammalian cells. Comment on: https://doi.org/10.1111/febs.16113.

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.

Structural variation and phylogenetic relationship of Geospiza magnirostris based on mitochondrial control region

The control region of mitochondrial genome is the main non-coding region. There is no details about Geospiza magnirostris’s control region, who is the only species of Geospiza in Darwin finches whose mitochondrial genome has been sequenced. In this study, the control region mitochondrial genome of G. magnirostris was analyzed. Compare research for 15 Passerine species, belonging to 4 families (Darwin ground finch, Thraupidae, Icteridae, Emberizidae), was also been done. The result showed the length was 1202 bp and it could been divided into three parts, domainI, domainII and domainIII. Genetic distances showed average divergence of different family ranged from 0.36% (Darwin ground finch) to 9.20% (Emberizidae), indicated that the Darwin ground finch may be a very conservative single-source species. Some specific sequence fragments such as conservative sequence box, boxes C, D, F and E, HSP/LSP, CSB-1, TAS-1 were also found in the control region of G. magnirostris, while B-box, CSB-2 and CSB-3 were not found in it. The F-box was detected in all selected 15 species and was 29 bp in length with no variant sites. In the E-box, 20 of the 21 nucleotide positions were identical as conserved among the selected species. There are two variant sites in the D-box, and five variant sites in the C-box. Basing the phylogenetic tree, it can be clearly seen that the relationship of G. magnirostris and family Thraupidae is the closest in all selected family. Through this study, the structure characteristics of G. magnirostris control region were explored and understood. This study provided more basic information for in-depth research of G. magnirostris. It’s also reminded us that we should pay more attention to explore the characteristics of the control region of Darwin’s finches.

RADseq as a valuable tool for plants with large genomes-A case study in cycads.

Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60Gbp. Restriction site-associated DNA sequencing (RADseq) offers an approach to find genome-wide informative markers and has proven to be effective with both model and nonmodel organisms. We tested the application of RADseq using ezRAD across all 10 genera of the Cycadales including an example data set of Cycas calcicola representing 72 samples from natural populations. Using previously available plastid and mitochondrial genomes as references, reads were mapped recovering plastid and mitochondrial genome regions and nuclear markers for all of the genera. De novo assembly generated up to 138,407 high-depth clusters and up to 1,705 phylogenetically informative loci for the genera, and 4,421 loci for the example assembly of C. calcicola. The number of loci recovered by de novo assembly was lower than previous RADseq studies, yet still sufficient for downstream analysis. However, the number of markers could be increased by relaxing our assembly parameters, especially for the C. calcicola data set. Our results demonstrate the successful application of RADseq across the Cycadales to generate a large number of markers for all genomic compartments, despite the large number of plastids present in a typical plant cell. Our modified protocol was adapted to be applied to cycads and other organisms with large genomes to yield many informative genome-wide markers.

A novel variant m.641A>T in the mitochondrial MT-TF gene is associated with epileptic encephalopathy in adolescent

We present a 14-year-old girl with loss of motor functions, tetraplegia, epilepsy and nystagmus, caused by a novel heteroplasmic m.641A>T transition in an evolutionary conserved region of mitochondrial genome, affecting the aminoacyl stem of mitochondrial tRNA-Phe. In silico prediction, respirometry, Western blot and enzymatic analyses in skin fibroblasts support the pathogenicity of the m.641A>T substitution.This is the 18th MT-TF point mutation associated with a mitochondrial disorder. The onset and the severity of the disease, however, is unique in this case and broadens the clinical picture related to mutations of mitochondrial tRNA-Phe.

Development of mitochondrial 12S rRNA gene for identification of dog and rat in beef using multiplex PCR

The 12S rRNA gene is one of unique regions in mitochondrial genome usually used for phylogenetic studies and species identification. The objective of present study was to develop species specific primers from mitochondrial 12S rRNA gene for identification of dog and rat in beef by using multiplex PCR assay. Three primer pairs of mitochondrial 12S rRNA gene specific for bovine, dog and rat were designed and selected to evaluate their specificity and fidelity. Moreover, a total of twelve DNA samples extracted from meat tissue were also prepared to test those primers using simplex and multiplex PCR. The PCR products were then visualized using 2% of agarose gel under the UV light and three of them were sequenced. In addition, sequence data were analyzed using Clustal Omega software and BLAST. The result showed that simplex PCR assay successfully amplified DNA targets which are respectively indicated by 155 bp (bovine), 244 bp (dog), and 491 bp (rat) of DNA bands. Furthermore, DNA sample sequences were identically similar to reference sequence used in this study. Multiplex and simplex PCR analyses also indicated that these primer pairs specifically amplified DNA target for each species in the samples containing various species. The results suggested that designed primers in this study could be used to identify dog and rat in raw beef containing these species meat. Further experiment should be conducted using meat-processed products and commercial meat products as samples.

Novel cell line derived from natural host Apodemus Peninsulae for in-vitro studies of tick-borne encephalitis virus

Purpose: The purpose of the research was to develop a natural host-derived cell line for the study of the host specificity of tick-borne encephaitis virus and evalute the reproduction of virus in this cell line. Methods & Materials: The cell line was established from trypsinized homogenates of kidneys of female Apodemus peninsulae (Korean field mouse). Cell line was characterized by cariotyping and by nucleotide sequence analysis of the cytochrome B gene and the D-loop region of mitochondrial genome. Cells were infected with the tick-borne encephalitis virus (TBEV) isolate 92 M belonging to Siberian subtype. Tissue cultures were sampled at 0, 4, 8, 12, 16, 20 and 24 hours (hpi) as well as after 4 and 7 days post infection (dpi). TBEV reproduction dymamics was evaluated by plaque titration of supernatant medium from infected cells. Replication of intracellular RNA was measured by quantitative PCR. Production of TBEV antigen was evaluated using ELISA test. Porcine embryo kidney cell line SPEV was used in parallel as reference. All experiments were performed in triplicates. Results: The adhesive diploid cell line was obtained by serial passages of primary culture and designated as ApnK. Sequencing confirmed the species origin of the cells. This cell line was used for experiments at passage 30. The growth of TBEV infectivity started at 12 hpi and concentration of infectious virus gradually increased up to 4 dpi. Afterwards it stabilized with titres of 7 lg PFU/ml. The synthesis of intracellular genomic RNA was firstly confirmed at 8 hpi and the dynamics was similar to the infectivity growth reaching the plateau at 4 dpi with concentration of 8 lg copies/mkl. TBEV antigen was detected in cell supernatants at 20 hpi and the dynamics corresponded to those of infectivity growth and RNA replication. In all experiments the reproduction of TBEV in ApnK cells was slowly than in SPEV cells up to 4 dpi when they equilibrated. Conclusion: The stabile cell line of natural host of TBEV, A. peninsulae, was established. This cell line susceptible for TBEV infection, however the reproduction of the virus is restricted in comparison to convenient in vitro model, porcine embryo kidney cell line SPEV

Alterations and Interchange of Morphometric Characters in Different Life Cycle Stages with Reference to Genomic Variations of Anopheles subpictus (Diptera; Culicidae) Sibling Species Complex in Sri Lanka.

The species complex of the mosquito Anopheles subpictus is designated by the sibling species A–D, depending on morphological characters of life cycle stages and variations in polytene chromosomes. However, morphological aberrations in the life cycle stages make the identification of sibling species uncertain and imprecise. The objective of the present study is to determine the suitability of morphological variations of sibling species and their genomic variations to identify the sibling species status of an An. subpictus population in Sri Lanka. Life cycle stages of larvae, pupal exuviae, and adults were examined for previously reported distinctive morphological features. Five nuclear and mitochondrial genome regions, including the Internal transcribed spacer 2 (ITS2) region, D3 region, white gene, cytochrome c oxidase I (COI), and Cytochrome b (Cyt-b), were sequenced and analyzed for variations. The eggs changed their distinct sibling morphological characters during metamorphosis (89.33%). The larvae, pupal exuviae, and adult stages showed deviation from their sibling characters by 26.10%, 19.71%, and 15.87%, respectively. However, all the species from the analysis shared two distinct sequence types for all regions, regardless of the morphological variations. In conclusion, the An. subpictus sibling species complex in Sri Lanka is not identifiable using morphological characters due to variations, and the genomic variations are independent from the morphological variations.

Detection of threshold heteroplasmy level of mtDNA in lypofibrous plaques of human aortic intima

Objectives: The aim of the present study was the analysis of the threshold heteroplasmy level of 11 mitochondrial mutations of DNA samples, extracted from all the lipofibrous plaques and segments of normal intima of several aortas. 11 mutations 652delG, A1555G, C3256T, T3336C, 652insG, C5178A, G12315A, G13513A, G14459A, G14846A and G15059A localized in coding region of mitochondrial genome were investigated.

Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patellaspp.) from non-destructive sampling

Accurate discrimination of two morphologically similar species ofPatellalimpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

Haplotype and meristic variations of Oreochromis niloticus and its hybrids present in selected reservoirs in Sri Lanka

The Nile tilapia, Oreochromis niloticus was introduced from Africa’s to Sri Lanka in the 1970s. Since then tilapia has dominated in most of the reservoir fisheries in Sri Lanka. The genetic and meristic variation of the domesticated tilapia was studied using polymorphisms in mitochondrial DNA (mt-DNA) and by analysis of morphometric and meristic characters. Ninety seven fish from three locations, namely Kurunegala, Anuradhapura, Polonnaruwa and ten control samples from the brood stock of the Udawalwe Tilapia Breeding Centre were collected. The genetic analysis targeted 16Sr region of mitochondrial genome. The Meristic analysis included fourteen meristic counts, which were subjected to discriminant analysis and cluster analysis. The PCR- SSCP procedure of the mt-DNA resolved eight haplotypes that overlapped between the four locations. The meristic and the genetic composition were common within the three domesticated fish populations collected from Kurunegala, Anuradhapura, Polonnaruwa and the brood stock of the Udawalwe Tilapia Breeding Centre. The results of this study will significantly contribute towards new inferences regarding management of the brood stocks and the wild stocks of tilapia aquaculture. Tropical Agricultural Research and Extension 16(4): 2013: page 114-122

Insulin resistance is associated with epigenetic and genetic regulation of mitochondrial DNA in obese humans.

BackgroundMitochondrial alterations have been observed in subjects with metabolic disorders such as obesity and diabetes. Studies on animal models and cell cultures suggest aberrant glucose and lipid levels, and impaired insulin signaling might lead to mitochondrial changes. However, the molecular mechanism underlying mitochondrial aberrance remains largely unexplored in human subjects.ResultsHere we show that the mitochondrial DNA copy number (mtDNAn) was significantly reduced (6.9-fold lower, p < 0.001) in the leukocytes from obese humans (BMI >30). The reduction of mtDNAn was strongly associated with insulin resistance (HOMA-IR: −0.703, p < 0.05; fasting insulin level: −0.015, p < 0.05); by contrast, the correlation between fasting glucose or lipid levels and mtDNAn was not significant. Epigenetic study of the displacement loop (D-loop) region of mitochondrial genome, which controls the replication and transcription of the mitochondrial DNA as well as organization of the mitochondrial nucleoid, revealed a dramatic increase of DNA methylation in obese (5.2-fold higher vs. lean subjects, p < 0.05) and insulin-resistant (4.6-fold higher vs. insulin-sensitive subjects, p < 0.05) individuals.ConclusionsThe reduction of mtDNAn in obese human subjects is associated with insulin resistance and may arise from increased D-loop methylation, suggesting an insulin signaling-epigenetic-genetic axis in mitochondrial regulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0093-1) contains supplementary material, which is available to authorized users.

Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.

Genetic analysis of ND4 and ND4L regions of mitochondrial genome in Khorasan native chickens

Preserving genetic diversity of Iranian native chickens is significant in order to perform breeding programs and improved production. Genetic diversity among close populations can be determined by investigating their phylogenetic relations. Different approaches have been applied to determine the phylogenic relations from which genomic sequencing has been considered the most functional approach. In this project, we aimed to evaluate the phylogeny and genetic nucleotide sequences of ND4, ND4L regions in mitochondrial genome of Khorasan native chickens. Blood samples were collected from randomly 6 Khorasan native chicken populations and DNA were extracted. ND4L, ND4 regions were amplified using specific primers of 913 and 802 bp length, respectively. Sequencing was don according to Sanger method based on automated system. In comparison with other breeds (data extracted from NCBI), phylogeny trees and matrices regarding their genetic diversity with Khorasan native chickens for ND4, ND4L were drawn. Results showed that there is no haplotype difference between the studied samples. Lowest genetic distance was observed between Khorasan native chicken and other Asian chickens i.e. Jiangbian, Lvenwv and Red jungle fowl for the ND4, ND4L genes indicating their close relationship.