Search Results (103)

Background/Objectives: The gene pool of the Apennine wolf is affected by admixture with domestic variants due to anthropogenic hybridisation with dogs. Genetic monitoring at the population level involves assessing the extent of admixture in single individuals, ranging from pure wolves to recent hybrids or wolf backcrosses, through the analysis of nuclear and mitochondrial DNA (mtDNA) markers. Although individually non-diagnostic, mtDNA is nevertheless essential for completing the final diagnosis of genetic admixture. Typically, the identification of wolf mtDNA haplotypes is carried out via sequencing of coding genes and non-coding DNA stretches. Our objective was to develop a fast real-time PCR assay to detect the mtDNA haplotypes that occur exclusively in the Apennine wolf population, as a valuable alternative to the demanding sequence-based typing. Methods: We validated a qualitative duplex real-time PCR that exploits the combined presence of diagnostic point mutations in two mtDNA segments, the NDH-4 gene and the control region, and is performed in a single-tube step through TaqMan-MGB chemistry. The aim was to detect mtDNA multi-fragment haplotypes that are exclusive to the Apennine wolf, bypassing sequencing. Results: Basic validation of 149 field samples, consisting of pure Apennine wolves, dogs, wolf × dog hybrids, and Dinaric wolves, showed that the assay is highly specific and sensitive, with genomic DNA amounts as low as 10⁻⁵ ng still producing positive results. It also proved high repeatability and reproducibility, thereby enabling reliable high-throughput testing. Conclusions: The results indicate that the assay presented here provides a valuable alternative method to the time- and cost-consuming sequencing procedure to reliably diagnose the maternal lineage of the still-threatened Apennine wolf, and it covers a wide range of applications, from scientific research to conservation, diagnostics, and forensics. Full article

Carassius auratus var. suogu, an endemic fish in southern China, is a natural triploid crucian carp mutant. In this study, the characteristics of mitochondrial DNA sequences were analyzed to understand their taxonomic status and genetic background at the gene level. The complete mitochondrial genome of C. auratus var. suogu (length, 16,580 bp) comprises 37 genes (13 protein-coding genes, 22 transfer RNA (tRNAs) genes, and 2 ribosomal RNA (rRNAs) genes) and a non-coding control region. The RSCU of the mtDNA of Carassius was similar. Ka/Ks analyses showed the ND4 gene had the highest evolutionary rate. Moreover, the whole mitogenome sequences and D-loop region were employed to examine phylogenetic relationships among C. auratus var. suogu and other closely related species. The result indicated that Carassius auratus suogu var clustered with Carassius auratus auratus and divided Carassius into four clades, providing new insights and data support for the taxonomic status of Carassius. Full article

Mitochondria are currently of great interest to scientists. The role of mitochondrial DNA (mtDNA) mutations has been proven in the genesis of more than 200 pathologies, which are called mitochondrial disorders. Therefore, the study of mitochondria and mitochondrial DNA is of great interest not only for understanding cell biology but also for the treatment and prevention of many mitochondria-related pathologies. There are two main trends of mitochondrial therapy: mitochondrial replacement therapy (MRT) and mitochondrial transplantation therapy (MTT). Also, there are two main categories of MRT based on the source of mitochondria. The heterologous approach includes the following methods: pronuclear transfer technique (PNT), maternal spindle transfer (MST), Polar body genome transfer (PBT) and germinal vesicle transfer (GVT). An alternative approach is the autologous method. One promising autologous technique was the autologous germline mitochondrial energy transfer (AUGMENT), which involved isolating oogonial precursor cells from the patient, extracting their mitochondria, and then injecting them during ICSI. Transmission of defective mtDNA to the next generation can also be prevented by using these approaches. The development of a healthy child, free from genetic disorders, and the prevention of the occurrence of lethal mitochondrial disorders are the main tasks of this method. However, a number of moral, social, and cultural objections have restricted its exploration, since humanity first encountered the appearance of a three-parent baby. Therefore, this review summarizes the causes of mitochondrial diseases, the various methods involved in MRT and the results of their application. In addition, a new technology, mitochondrial transplantation therapy (MTT), is currently being actively studied. MTT is an innovative approach that involves the introduction of healthy mitochondria into damaged tissues, leading to the replacement of defective mitochondria and the restoration of their function. This technology is being actively studied in animals, but there are also reports of its use in humans. A bibliographic review in PubMed and Web of Science databases and a search for relevant clinical trials and news articles were performed. A total of 81 publications were selected for analysis. Methods of MRT procedures were reviewed, their risks described, and the results of their use presented. Results of animal studies of the MTT procedure and attempts to apply this therapy in humans were reviewed. MRT is an effective way to minimize the risk of transmission of mtDNA-related diseases, but it does not eliminate it completely. There is a need for global legal regulation of MRT. MTT is a new and promising method of treating damaged tissues by injecting the body’s own mitochondria. The considered methods are extremely good in theory, but their clinical application in humans and the success of such therapy remain a question for further study. Full article

The ability to differentiate between different Apis mellifera subspecies can have significant implications for their conservation. In this study, we explored the possibility of obtaining multi-level information that could be useful in assigning a colony to the A. m. ligustica subspecies. This was accomplished by combining (1) standard morphometric characteristics of the honeybees with mitochondrial DNA (mtDNA) sequence data obtained from both the (2) honeybees and (3) honey present in a honeycomb sampled from the same colony. Eighty colonies were sampled in the Emilia-Romagna region (Northern Italy). From these colonies, a total of 413 honeybees were analyzed to obtain sequence information of the tRNALeu-COII mtDNA region. When we combined the results obtained from all three methods, 63.75% of the colonies were found to be compatible with being assigned to A. m. ligustica. For 36.25% of the colonies, morphometric analysis indicated a hybrid origin and mtDNA from honeybees or honey samples indicated the presence of mtDNA haplotypes other than those characteristic for this subspecies. Cohen’s Kappa statistic indicated poor agreement in the classification of the colonies between morphometric analysis and the two DNA-based methods, which, in turn, were in substantial agreement with each other. Although not completely effective, mtDNA analysis of honey samples could serve as an initial and practical compromise to begin initiatives aimed at preserving the genetic integrity of A. m. ligustica in the Emilia-Romagna region, as well as in other regions where it is necessary to preserve the genetic integrity of autochthonous honeybee populations. Full article

The Arabian leopard (Panthera pardus nimr), a critically endangered subspecies endemic to the Arabian Peninsula, faces severe threats from habitat loss, prey depletion, and inbreeding, with fewer than 200 individuals remaining. Genomic resources for this subspecies have been scarce, limiting insights into its evolutionary history and conservation needs. Here, we present the first complete mitochondrial DNA (mtDNA) sequence of P. pardus nimr, derived from a wild-born male sampled at the Oman Wildlife Breeding Centre in 2023. Using PacBio HiFi sequencing, we assembled a 16,781 bp mitogenome (GenBank: PQ283265) comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, with a GC content of 40.94%. Phylogenetic analysis, incorporating 17 Panthera mtDNA sequences, positions P. pardus nimr closest to African leopard populations from South Africa (Panthera pardus), while distinguishing it from Asian subspecies (P. pardus japonensis and P. pardus orientalis). This mitogenome reveals conserved vertebrate mitochondrial structure and provides a critical tool for studying Panthera genus evolution. Moreover, it enhances conservation genetics efforts for P. pardus nimr by enabling population structure analysis and informing breeding strategies to strengthen its survival. Full article

Background: Smilax glabra (S. glabra) and Smilax zeylanica (S. zeylanica), two medicinally important species within the genus Smilax, have been widely used in Traditional Chinese Medicine (TCM) for the treatment of rheumatism, traumatic injuries, and related ailments. Despite their medicinal significance, research on the mitochondrial DNA (mtDNA) of Smilax species remains limited. Methods: We utilized NovaSeq 6000 and PromethION sequencing platforms to assemble the complete mitochondrial genomes of Smilax glabra and Smilax zeylanica, and conducted in-depth comparative genomic and evolutionary analyses. Results: The complete mitochondrial genomes of S. glabra and S. zeylanica were assembled and annotated, with total lengths of 535,215 bp and 471,049 bp, respectively. Both genomes encode 40 unique protein-coding genes (PCGs), composed of 24 core and 16 non-core genes, alongside multiple tRNA and rRNA genes. Repetitive element analysis identified 158 and 403 dispersed repeats in S. glabra and S. zeylanica, respectively, as well as 123 and 139 simple sequence repeats (SSRs). RNA editing site predictions revealed C-to-U conversions in both species. Additionally, chloroplast-to-mitochondrial DNA migration analysis detected 34 homologous fragments in S. glabra and 28 homologous fragments in S. zeylanica. Phylogenetically, S. glabra and S. zeylanica cluster within the Liliales order and Smilacaceae family, closely related to Lilium species. Collinearity analysis indicated numerous syntenic blocks between Smilax and three other Liliopsida species, though gene order was not conserved. Conclusions: This study presents high-quality mitochondrial genome assemblies for S. glabra and S. zeylanica, providing valuable insights into molecular identification and conservation efforts of these traditional medicinal plants. Full article

We report on a sporadic patient suffering Leigh syndrome characterized by bilateral lesions in the lenticular nuclei and spastic dystonia, intellectual disability, sensorineural deafness, hypertrophic cardiomyopathy, exercise intolerance, and retinitis pigmentosa. Complete sequencing of mitochondrial DNA revealed the heteroplasmic nucleotide change m.15635T>C affecting a highly conserved amino acid position (p.Ser297Pro) in the cytochrome b (MT-CYB) gene on a haplogroup K1c1a background, which includes a set of four non-synonymous polymorphisms also present in the same gene. Biochemical studies documented respiratory chain impairment due to complex III defect. This variant fulfils the criteria for being pathogenic and was previously reported in a sporadic case of fatal neonatal polyvisceral failure. Full article

Background: The Balkan Peninsula has served as an important migration corridor between Asia Minor and Europe throughout humankind’s history and a refugium during the Last Glacial Maximum. Past migrations such as the Neolithic expansion, Bronze Age migrations, and the settlement of Slavic tribes in the Early Middle Ages, are well known for their impact on shaping the genetic pool of contemporary Balkan populations. They have contributed to the high genetic diversity of the region, especially in mitochondrial DNA (mtDNA) lineages. Serbia, located in the heart of the Balkans, reflects this complex history in a broad spectrum of mtDNA subhaplogroups. Methods: To explore genetic diversity in Serbia and the wider Balkan region, we analyzed rare mtDNA subclades—R0a, N1a, N1b, I5, W, and X2—using publicly available data. Our dataset included already published sequences from 3499 HVS-I/HVS-II and 1426 complete mitogenomes belonging to West Eurasian and African populations, containing both contemporary and archaeological samples. We assessed the parameters of genetic diversity found in different subclades across the studied regions and constructed detailed phylogeographic trees and haplotype networks to determine phylogenetic relationships. Results: Our analyses revealed the observable geographic structure and identified novel mtDNA subclades, some of which may have originated in the Balkan Peninsula (e.g., R0a1a5, I5a1, W1c2, W3b2, and X2n). Conclusions: The geographic distribution of rare subclades often reveals patterns of past population movements, routes, and gene flows. By tracing the origin and diversity of these subclades, our study provided new insights into the impact of historical migrations on the maternal gene pool of Serbia and the wider Balkan region, contributing to our understanding of the complex genetic history of this important European crossroads. Full article

The Alaska Tribal Health System is increasing colorectal cancer (CRC) screening among Alaska Native (AN) peoples, who experience the highest CRC rate in the world. Through a clinical trial (NCT04336397), AN people living in rural/remote Alaska were offered either the previously unavailable multi-target stool DNA test (mt-sDNA; Cologuard^®) or colonoscopy. From April 2022 to August 2024, 113 (59%) people who completed mt-sDNA testing and 51 (39%) who completed a colonoscopy procedure participated in a survey on factors influencing their screening test choice. The majority of mt-sDNA participants (79%) were aware of the colonoscopy option, while most colonoscopy participants (72%) reported being unaware of the mt-sDNA option. Key mt-sDNA preference themes included not having to travel, less time commitment, childcare and work responsibilities, physical limitations, greater convenience, and the test being less invasive and dangerous than a colonoscopy. In contrast, colonoscopy preference themes included wanting to adhere to screening recommendations, be proactive about preventative health, family history of cancer, awareness of the higher CRC risk among AN peoples, as well as the belief that colonoscopy is more reliable and accurate since it is performed by medical providers. These findings underscore the complex factors influencing CRC screening preferences among rural and remote AN people. Limited access to medical facilities, financial burdens, and personal commitments, along with personal factors, have a substantial bearing on the screening decision-making process. Recognizing and addressing these multifaceted influences can help CRC screening programs better meet community member needs and preferences, ultimately improving screening rates and colorectal health outcomes. Full article

Navicula incerta, a marine benthic diatom, holds promise for human nutrition and health as well as for aquaculture applications. However, the scarcity of organelle genome data within the Navicula clade has impeded a comprehensive understanding and utilization of this group. Our research presents a pioneering exploration into the complete mitochondrial and chloroplast genome sequences of N. incerta CACC 0356, shedding light on its phylogeny and evolutionary history. The mitochondrial genome (mtDNA) spans 61,320 bp with a GC content of 29.87%, comprising one circular DNA molecule that encodes for 34 protein-coding genes, 24 tRNAs, and 34 rRNAs. Whereas, the chloroplast genome (cpDNA) is larger at 129,090 bp, encompassing 127 protein-coding genes, 30 tRNAs, and 7 rRNAs. Notably, the cpDNA of N. incerta is approximately 2.1 times the size of its mtDNA. Our annotation identified four genes that are partially situated in the homologous regions between the mitogenome and chloroplast genome, totaling 372 bp, which represents 0.61% of the entire mitogenome. Comparative analyses revealed that N. incerta CACC 0356 is closely affiliated with Fistulifera saprophila and Fistulifera solaris, both members of the Naviculaceae order. This study significantly expands the mitochondrial and chloroplast genomic resources for algae and lays a foundation for the development of genetic diversity analyses in algae. Full article

Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). Strains without mtDNA (known as rho⁻ mutants or petite mutants) are respiration-deficient and require fermentable carbon sources (such as glucose) for their metabolism. However, they are compromised in many aspects of fitness and competitiveness. Nevertheless, a few research groups have reported that some petite mutants of Candida glabrata and Saccharomyces cerevisiae manifested higher levels of tolerance to the antifungal fluconazole than their wild-type (WT) counterparts. In this study, we show that elevated tolerance to two or three out of four tested antifungals is a generic feature of at least five petite-positive species of yeasts including C. glabrata (higher tolerance of petites to clotrimazole and miconazole), S. bayanus (tolerance to clotrimazole, fluconazole, and miconazole), S. cerevisiae (tolerance to clotrimazole and fluconazole), S. paradoxus (tolerance to clotrimazole, fluconazole, and miconazole), and S. pastorianus (tolerance to clotrimazole and fluconazole). Comparing the levels of tolerance to the antifungals in WT and petite mutants was based on measuring the diameters of the zones of inhibition (ZOIs) using disc diffusion assays. The mode of inhibition in the majority of WT strains by all antifungals was fungicidal; most of the rho⁻ mutants manifested fungistatic inhibition. We observed partial (not complete) inhibition in WT, with four different types of ZOI patterns that were species- and antifungal-specific. The partial inhibition was characterised by the presence of antifungal-tolerant colonies within ZOI areas. The inability of these colonies selected from ZOIs to grow on glycerol, as a single source of carbon, proved that they were rho⁻ mutants spontaneously generated in the WT populations. The results on the elevated tolerance of petite strains to antifungals are discussed in terms of the prospective positive selection of respiratory-deficient mutants and the various implications of such selection. Full article

Southern Brazil is home to a large biodiversity of elasmobranchs from the Brazilian coast. Several genera and species of small sharks of the Triakidae family live in this marine environment. Studies on these shark species are scarce, with few genetic data and little information on animal population structures. The present study aimed to sequence the complete mitochondrial genome (mtDNA) of the endangered species Mustelus schmitti (narrownose smooth-hound shark) and to perform a phylogenetic analysis of the Triakidae family. The mtDNA sequenced here was 16,764 bp long and possessed the usual 13 mitochondrial protein coding genes (PCGs), 22 tRNAs, two rRNAs (12S and 16S) and a large D-loop DNA sequence, presenting an overall organization similar to other species from the genus Mustelus. Phylogenetic analyses were performed using a dataset containing this new mtDNA and 59 other mitochondrial genomes of the Carcharhiniformes species (including 14 from the Triakidae family), using the Maximum Likelihood (ML) method. All the species of the Triakidae family were clustered into a monophyletic topology group. In addition, polyphyly was observed in Galeorhinus galeus, Hemiatrakis japanica, Triakis megalopterus and Triakis semifasciata. In conclusion, this study contributes to a deeper understanding of the genetic diversity of sharks and represents an important step towards the conservation of these endangered animals. Full article

Lineages of the Triops longicaudatus (LeConte, 1846) complex, originally endemic to the Americas, have been able to successfully colonize extreme environments such as temporary aquatic systems through shifts in their reproductive modes. To gain insights into their stress adaptations and species differentiation, we explored the genetic diversity of populations of the T. longicaudatus complex and constructed their haplotype networks. Using maximum likelihood and Bayesian analyses, we analyzed the complete mitogenome sequences of seven Triops species to infer their phylogenetic relationships. To identify the possible role of mtDNA evolution in stress adaptation, the evolutionary rates and molecular signatures of natural selection for all 13 PCGs were investigated using multiple approaches of selection tests. The results showed that signals of relaxed purifying selection and positive selection were found in specific genes of complexes I, IV, and V, indicating that mitogenomes in the T. longicaudatus complex have undergone adaptive evolution. Different patterns of selection in the mitochondrial genes between the hermaphroditic and gonochoric branches imply that functional constraints have played a significant role in the evolution of T. longicaudatus complex mitogenomes, which was essential for survival in extreme environments. Full article

The fauna of Lepidoptera in the Mediterranean is still inadequately documented. As a result, even remotely complete DNA barcode libraries (mt. COI (cytochrome c oxidase 1) gene) are lacking in most areas. This proposed gap is being analyzed for the first time for the fauna of North Cyprus. In the initial phase, 248 morphospecies from 29 families (exclusive Heterocera) were sampled, sequenced and compared with existing DNA reference sequences in the global BOLD database (Barcode of Life Data Systems) via BINs (Barcode Index Numbers). A total of 194 species could be unequivocally assigned to a Linnaean taxon. Additionally, six species previously unidentified in BOLD, as well as fourteen species without reference barcodes, were identified at the species level. Twenty-four of these species were new records for Cyprus. In addition, 25 taxa with new BINs could not be assigned to a valid species due to potential cryptic diversity or the lack of relevant revisions. Furthermore, a few species could not be identified due to barcode sharing and/or potential misidentifications in BOLD. Overall, approximately 20% of the samples could not be identified using the existing DNA barcode libraries, a significant deficit for European standards, which should be addressed as a priority issue in future studies. Full article

The grey-shanked douc langur (Pygathrix cinerea) is a recently described, critically endangered primate, endemic to Vietnam. In this study, we describe the Central Highland species’ complete mitochondrial genome (mitogenome—mtDNA). It is a circular molecule with a length of 16,541 base pairs (bp). The genome consists of 37 genes, consistent with those found in most other vertebrates, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs. A comparison with the mitogenomes of more than 50 primates showed that the mitogenome of Vietnamese Central Highland Pygathrix cinerea has a conservative gene order. We identified 43 nucleotide differences when comparing this genome with a previously published mitogenome of Pygathrix cinerea. It is evident that there are distinct differences between the Pygathrix cinerea we are currently studying and other Pygathrix cinerea specimens. These differences are unlikely to be solely the result of sequencing errors, as the mitogenomes were generated using high-quality methods. The genetic divergence observed between the two Pygathrix cinerea mitogenomes implies the potential existence of at least two distinct lineages or forms of this primate species within its native range in Vietnam. Full article