scholarly journals Features of Picea abies (L.) Karst. population structure formation on the territory of Belarus

2021 ◽  
pp. 78-91
Author(s):  
Vladimir E. Padutov
Keyword(s):  
Mitochondrial Dna ◽  
Spatial Distribution ◽  
Picea Abies ◽  
Chloroplast Dna ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Spruce Forest ◽  
Allelic Variants ◽  
Regional Features ◽  
Migration Flows

One of the main forest forming tree species in Belarus is the European spruce (Picea abies (L.) Karst.). The formation of European spruce forest population genetic structure took place under the influence of migration flows from different refugia during the postglacial period. For the genogeographic study of P. abies 25 isozyme genes (Aat-1, Aat-2, Adh, Gdh, Idh-1, Idh-2, Mdh-1, Mdh-2, Mdh-3, Skdh, 6-Pgd-1, 6-Pgd-2, 6-Pgd-3, Lap-1, Lap-2, Sdh, Gpi, Hk, Me, Dia-1, Dia-2, Dia-4, Pgm-1, Pgm-2, Fl-Est) of nuclear DNA (analysis was carried out in 10 populations), 3 microsatellite loci (Pt63718, Pt26081, Pt71936) of chloroplast DNA (57 populations were considered) and 1 microsatellite locus (mt15-D02) of mitochondrial DNA (56 populations were studied) were used. As a result, 82 allelic variants of isozyme genes, 19 allelic variants of chloroplast DNA loci and 2 allelic variants of mitochondrial DNA locus were found. The spatial distribution of the alleles was defined and the regional features of the genogeographic differentiation of the spruce forest were considered. The presence of two migration flows representatives (southern and northern) in Belarus was confirmed. It was shown that the highest concentration of P. abies trees with southern (Carpathian) origin is observed in the southwest of the country. Clinal variability was revealed for a number of markers in the directions from south to north and from west to east. In general the data obtained are consistent with the results of studies based on the analysis of the spatial distribution of the cone scales traits.

scholarly journals Genogeography of norway spruce (Picea abies (L.) Karst.) according to the analysis of cytoplasmic DNA

2021 ◽  
Vol 65 (4) ◽  
pp. 439-447
Author(s):  
V. E. Padutov ◽  
D. I. Kagan ◽  
S. I. Ivanovskaya ◽  
O. Yu. Baranov ◽  
T. S. Markevich
Keyword(s):  
Mitochondrial Dna ◽  
Picea Abies ◽  
Norway Spruce ◽  
Continuous Distribution ◽  
Distribution Area ◽  
Spruce Forest ◽  
The South ◽  
Allelic Variants ◽  
Regional Features ◽  
Ssr Loci

Norway spruce (Picea abies (L.) Karst.) is one of the main forest-forming species in Belarus. It plays important economic, ecological and social roles. The spruce forest of the region is characterized by a complex history of the formation of its population genetic structure. The aim of this study was the genogeographic analysis of P. abies populations and the description of regional features of its gene pool in Belarus. Molecular genetic analysis of microsatellite (SSR) loci of chloroplast DNA and mt15-D02 locus of mitochondrial DNA of Norway spruce was carried out for samples from 57 naturally originated forest stands. We identified 19 allelic variants of the Pt63718, Pt26081, Pt71936 cpDNA loci and two allelic variants of mt15-D02 mtDNA. The geographical distribution of the alleles has been described and the regional features of the genogeographic differentiation of the spruce forests have been considered. The southern border of the continuous distribution area of P. abies and its island localities lie in the south of Belarus (Brest and Gomel regions). The frequency of occurrence of individual allelic variants of cpDNA SSR loci has the most pronounced deviations from the average values for the whole country in those regions. Analysis of cpDNA showed the presence of certain regional features of the genogeographic structure of the spruce forest in the “south-north” and “west-east” directions. According to mitochondrial DNA analysis higher concentration of P. abies trees of southern (Carpathian) origin is observed in the southwest of Belarus. On the contrary northern (Boreal) origin dominates in the rest of the country. The results of performed genogeographic analysis of Norway spruce populations can serve as a basis for improving the forest seed zoning of the tree species.

scholarly journals Genetic variability of farmed fur animals of the Canidae family assessed by nuclear and mitochondrial DNA analysis

2016 ◽  
Vol 72 (8) ◽  
pp. 505-510 ◽  
Author(s):  
Sylwia Nisztuk-Pacek
Keyword(s):  
Mitochondrial Dna ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Mitochondrial Gene ◽  
Genetic Material ◽  
Cox1 Gene ◽  
Phylogenetic Distance ◽  
Raccoon Dog ◽  
Study Results ◽  
Fur Animals

The aim of the study was to assess the biodiversity of farmed fur animals from the Canidae family (common fox, polar fox, and raccoon dog) using nuclear and mitochondrial markers. The study involved 434 animals. The biological material included whole peripheral blood or skin tissue. The isolated genetic material was subjected to qualitative and quantitative analyses. Mitochondrial DNA (mtDNA) gene fragments (COX1, COX2, CYTB) and nuclear DNA (nDNA) gene fragments (MSTN1, MSTN2, MSTN3, IGF1, GHR) were amplified with the PCR (polymerase chain reaction) technique. The amplicons obtained were sequenced or subjected to PCR-RFLP (restriction fragment length polymorphism) reaction, and bioinformatics analyses were performed. The interspecific analysis of the nDNA sequences revealed a total of 25 polymorphisms. On the other hand, the interspecific analysis of the mtDNA gene fragments identified 277 polymorphisms. The COX1 gene fragment exhibited the greatest variability. It was shown that the frequency of polymorphisms within the mitochondrial genome was almost 20-fold higher than that in the nuclear genome of the raccoon dog. It was found that the genetic distances revealed by the analysis of the mitochondrial gene fragments were similar to the results obtained by the nDNA analysis. The genetic distance between the raccoon and common fox was the greatest. The smallest phylogenetic distance was revealed between the two fox species. The study results indicate mitochondrial and nuclear genes may be alternatively used for determining the phylogenetic relationships between fur animals from the Canidae family.

scholarly journals Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 433 ◽  
Author(s):  
Maxime Merheb ◽  
Rachel Matar ◽  
Rawad Hodeify ◽  
Shoib Sarwar Siddiqui ◽  
Cijo George Vazhappilly ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Genetic Material ◽  
Modern Science ◽  
Criminal Cases ◽  
Trade Routes ◽  
Ancient Trade ◽  
Degraded Samples ◽  
Mtdna Sequence

Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.

scholarly journals Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

ZooKeys ◽  
2018 ◽  
Vol 763 ◽  
pp. 1-111 ◽  
Author(s):  
Tricia C. Goulding ◽  
Munawar Khalil ◽  
Shau Hwai Tan ◽  
Benoît Dayrat
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Comparative Anatomy ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
The Philippines ◽  
Coral Triangle ◽  
Yellow Orange

A new genus of onchidiid slugs,WallaconchisGoulding & Dayrat,gen. n., is described, including ten species. Five species were previously described but known only from the type material:Wallaconchisater(Lesson, 1830),W.graniferum(Semper, 1880),W.nangkauriense(Plate, 1893),W.buetschlii(Stantschinsky, 1907), andW.gracile(Stantschinsky, 1907), all of which were originally classified inOnchidiumBuchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new:WallaconchisachleitneriGoulding,sp. n.,W.comendadoriGoulding & Dayrat,sp. n.,W.melanesiensisGoulding & Dayrat,sp. n.,W.sinanuiGoulding & Dayrat,sp. n., andW.uncinusGoulding & Dayrat,sp. n.Nine of the tenWallaconchisspecies are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia).Wallaconchisis distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify allWallaconchisspecies. The copulatory organs ofWallaconchisspecies are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed,nomina dubiaare discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

scholarly journals Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii

2020 ◽  
Author(s):  
Waleed M. M. El-Sayed ◽  
Alli L. Gombolay ◽  
Penghao Xu ◽  
Taehwan Yang ◽  
Youngkyu Jeon ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Chloroplast Dna ◽  
Chlamydomonas Reinhardtii ◽  
Green Alga ◽  
Genomic Dna ◽  
Nuclear Dna ◽  
Whole Genome ◽  
Human Mitochondrial Dna ◽  
Atp Level ◽  
Unicellular Green Alga

SummaryRibonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genomic DNA of cells. The distribution of rNMPs in DNA has been studied only in limited genomes, such as yeast nuclear and mitochondrial DNA, as well as human mitochondrial DNA. In this study, we used the ribose-seq protocol and the Ribose-Map bioinformatics toolkit to reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. The study presents the discovery of a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the nucleotide content of these C. reinhardtii genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. In addition, we reveal specific rNMP biases and patterns in the mitochondrial, chloroplast and nuclear DNA of C. reinhardtii.

scholarly journals Changes in circulating cell-free nuclear DNA and mitochondrial DNA of patients with adolescent idiopathic scoliosis

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiong Li ◽  
Longjie Wang ◽  
Guanteng Yang ◽  
Yunjia Wang ◽  
Chaofeng Guo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Adolescent Idiopathic Scoliosis ◽  
Idiopathic Scoliosis ◽  
Sensitivity And Specificity ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Predictive Accuracy ◽  
Lower Sensitivity ◽  
Mt Dna ◽  
Potential Biomarker

Abstract Background Adolescent idiopathic scoliosis (AIS) which characterized by complex three-dimensional deformity of spine has been difficult to cure because of the unknown etiopathology and uncertainty of progression. Nowadays, circulating cell-free (ccf) DNA was found to be a potential biomarker for several benign and malignant diseases. However, whether ccf DNA can be a biomarker for AIS has not been reported yet. In this study, we investigate the circulating cell-free nuclear DNA (ccf n-DNA) and mitochondrial DNA (ccf mt-DNA) concentrations in the plasma of patients with AIS and controls (CT), and the changed plasma ccf n-DNA and ccf mt-DNA levels and their association with clinical parameters were assessed. Methods The plasma of peripheral blood from 69 AIS patients and 21 age-matched CT was collected for ccf DNA analysis. Quantitative PCR was used to detect ccf n-DNA and ccf mt-DNA levels, and correlation analyses between the ccf n-DNA and ccf mt-DNA levels and clinical characteristics were conducted. Receiver operator curves (ROC) were used to analyze the sensitivity and specificity of ccf n-DNA and ccf mt-DNA levels to different characteristics. Results The plasma ccf n-DNA levels of both GAPDH and ACTB were significantly decreased in AIS patients compared with those in controls, while the plasma ccf mt-DNA levels did not changed. According to sex-related analyses, the ccf n-DNA levels in male CT-M was higher than that in female CT and male AIS, but the ccf n-DNA levels in female AIS was not significantly changed when compared with male AIS or female CT. However, the concentration of ccf mt-DNA in female AIS increased significantly when compared with male AIS. Surprisingly, Lenke type-related analyses suggested that Lenke type 1 patients had lower ccf n-DNA levels, whereas Lenke type 5 patients had higher ccf mt-DNA levels compared with those of controls. However, a lower sensitivity and specificity of AIS predicted by ccf n-DNA or ccf mt-DNA levels was observed, whether in total, by sex, or by Lenke type. Conclusion Although with no/little predictive accuracy of AIS/progressed AIS by ccf DNA levels, significantly changed plasma ccf DNA levels were observed in AIS patients compared with those in controls.

Leber Hereditary Optic Neuropathy - Idebenone, Hope of Treatment

2020 ◽  
Vol 70 (12) ◽  
pp. 4244-4247
Keyword(s):  
Mitochondrial Dna ◽  
Visual Field ◽  
Optic Neuropathy ◽  
Mitochondrial Function ◽  
Dna Analysis ◽  
Central Vision ◽  
Leber Hereditary Optic Neuropathy ◽  
Mitochondrial Dna Analysis ◽  
Hereditary Optic Neuropathy

Leber hereditary optical neuropathy (LHON) is part of the class of optic neuropathies in which the mitochondrial function is impaired and is characterized by a painless, subacute, bilateral decrease of the central vision. We shall present the case of two brothers AM aged 31 and AT aged 40 who were diagnosed with LHON and whom we initiated treatment with idebenone 900 mg / day with monitoring at one month and 6 months. The mitochondrial DNA analysis demonstrated the existence of mutations 11778G>A for the mtND4 gene in both patients. Idebenone is a synthetic benzoquinone, analogue of ubiquinone. We found a slight but significant improvement in the visual field in patient AM at one month of treatment. We have not found another case in the literature with an improvement in vision so fast after this treatment, and this has led us to write this article. Keywords: Leber hereditary optical neuropathy (LHON), idebenone, mutations 11778G>A, mtND4 gene

scholarly journals The Role of Mitochondria in Carcinogenesis

2021 ◽  
Vol 22 (10) ◽  
pp. 5100
Author(s):  
Paulina Kozakiewicz ◽  
Ludmiła Grzybowska-Szatkowska ◽  
Marzanna Ciesielka ◽  
Jolanta Rzymowska
Keyword(s):  
Prostate Cancer ◽  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Dna Polymorphisms ◽  
Gene Encoding ◽  
Dna Mutations ◽  
Nadh Ubiquinone Oxidoreductase ◽  
Gene Coi ◽  
The Impact

The mitochondria are essential for normal cell functioning. Changes in mitochondrial DNA (mtDNA) may affect the occurrence of some chronic diseases and cancer. This process is complex and not entirely understood. The assignment to a particular mitochondrial haplogroup may be a factor that either contributes to cancer development or reduces its likelihood. Mutations in mtDNA occurring via an increase in reactive oxygen species may favour the occurrence of further changes both in mitochondrial and nuclear DNA. Mitochondrial DNA mutations in postmitotic cells are not inherited, but may play a role both in initiation and progression of cancer. One of the first discovered polymorphisms associated with cancer was in the gene NADH-ubiquinone oxidoreductase chain 3 (mt-ND3) and it was typical of haplogroup N. In prostate cancer, these mutations and polymorphisms involve a gene encoding subunit I of respiratory complex IV cytochrome c oxidase subunit 1 gene (COI). At present, a growing number of studies also address the impact of mtDNA polymorphisms on prognosis in cancer patients. Some of the mitochondrial DNA polymorphisms occur in both chronic disease and cancer, for instance polymorphism G5913A characteristic of prostate cancer and hypertension.

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