bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial Gene Pool of Ukrainians in the Context of Variability of Whole Mitogenomes in Slavic Peoples
Authors: Malyarchuk B. A. , Derenko M. V.
Published: April 2024

Data on the variability of nucleotide sequences of whole mitochondrial genomes in Ukrainians were analyzed. A comparative analysis of genetic diversity parameters showed that Ukrainians, like other European populations, are characterized by a high level of mtDNA diversity. However, between-population differences in Europe are very low (FST = 0.36%, p 0.00001). According to the results of the FST-analysis, Ukrainians show the greatest similarity with Slovaks, Russians, Poles, Serbs, and Estonians. On the graph of multidimensional scaling of FST-distances, Ukrainians are located together with Western and Eastern Slavs, occupying a central position among them. The results of the analysis of the dynamics of the effective population size (Ne) showed differences in the long-term dynamics of Ne between populations of the north and south of Eastern Europe. For Ukrainians and the southwestern Russian populations, a period of sharp population growth was recorded in the Neolithic period (approximately 8.2 thousand years ago), while for Estonians and northwestern Russians, population growth was observed much later, in the Bronze Age (approximately 4.3 thousand years ago). An analysis of data on mtDNA variability in Slavic populations showed that the frequency of ethnic specific mtDNA haplotypes varies quite widely in different ethnic groups, from 1.3% in Slovaks to 10.3% in Poles. The proportion of Slavic-specific mtDNA haplotypes also varies: the least number of such haplotypes was found in Czechs and Serbs (less than 10%), and most of all in Ukrainians (23.6%).
Gene–Gene Interactions and Biological Network Analysis of Diseases with Disturbances of Human Cognitive Functions
Authors: Bocharova A. V. , Stepanov V. A.
Published: April 2024

Neurological and mental diseases, such as schizophrenia, Alzheimer’s disease, bipolar disorder, Parkinson’s disease, have complex phenotypes with cognitive impairment. These diseases are socially significant pathologies and serious problems for world health and are distinguished by the multilevel nature of the implementation of genetic information. A number of active genes are involved in the formation of the final phenotype. Thereby, it is necessary to apply the analysis of biological networks aimed at identifying the interacting genes and proteins that lead to the pathogenesis of the disease, in order to understand the molecular mechanisms underlying the studied pathology. In this study, various online resources and databases were used to implement this approach: WebGestalt, Gene Ontology, STRING. The protein-protein interaction network was obtained, where two subnets are distinguished, one of which is involved in the risk of developing schizophrenia, and the other in the risk of developing Alzheimer’s disease.
Mitochondrial DNA Evolution Trends of Baikal Endemic Sponges. I. Mitochondrial Genome of S. khanaevi
Authors: Maikova О. О. , Sherbakov D. Yu.
Published: April 2024

The nucleotide sequence of the mitochondrial genome of a new species of sponge from the Baikal endemic family Lubomirskiidae – Swartschewskia khanaevi was determined, the length of which was 26 638 bp. An increase in the rate of accumulation of nucleotide substitutions in protein-coding genes from 2 to 3 times relative to other species of sponges of the Lubomirskiidae family was revealed. On the phylogenetic tree, the species S. khanaevi clusters with another representative of the genus Swartschewskia. It was shown that all studied mitochondrial genomes of Lubomirskiidae are characterized by the presence of a large number and diversity of inverted repeats in intergenic regions, which distinguishes them from other members of the Demospongiae class.
Symbiogenetics and Symbiogenesis: Molecular and Ecological Bases of Integrative Evolution
Authors: Provorov N. A. , Tikhonovich I. A.
Published: April 2024

Symbiogenetics is presented as a discipline aimed to study the combined genetic systems resulted from co-evolution of unrelated organisms. Their research complements the methodology of genetic analysis with the approaches of “genetic synthesis” aimed at characterizing the molecular and ecological factors of integration of heterologous genomes. Hologenomes and symbiogenomes that arise via integrative evolution (symbiogenesis) are dissected, like prokaryotic pangenomes, into the core and accessory parts. In hologenome, the core part, which is constant in composition, is represented by the host genome (nuclear-cytoplasmic system of heredity), and the variable accessory part composed by metagenome of the microbial community which is associated with the host and performs functions useful for it. Mechanisms of symbiogenesis go beyond the factors of evolution of free-living organisms and include: (a) interspecies altruism associated with the refusal of symbionts from autonomous existence, and upon a deep reduction, from the ability to maintain the genome; (b) inheritance by host of symbionts as of “acquired” genetic determinants (pangenesis). Under the impacts of these factors, symbionts can be transformed into cellular organelles that have lost their genetic individuality and sometimes lack genomes. Symbiogenesis is presented as a multi-stage process, including the emergence of: (i) genome-containing prokaryotic cell; (ii) multi-genomic eukaryotic cell; (iii) multicellular eukaryotes as holobionts composed of host organisms and associated microbial communities. Genome-free organelles that have retained the basic reproductive and metabolic functions can be used as models for reconstructing the early stages of cell evolution, including the emergence of cellular genome.
Long-Term and Seasonal Dynamics of Inversion Polymorphism of the Malaria Mosquito Anopheles messeae Fall. (Diptera: Culicidae) in the Population of the Central Part of the Species Range (Western Siberia, Tomsk Region)
Authors: Sibataev A. K. , Wasserlauf I. E. , Usov K. E. , Alekseeva S. S. , Abylkassymova G. M. , Stegniy V. N.
Published: April 2024

The assessment of the level of genetic variability from 1974 to 2020 in the population of the malaria mosquito Anopheles messeae Fall. in the village of Kolarovo (Tomsk region) was carried out on the basis of cytogenetic analysis of polytene chromosomes. Analysis of the dynamics of inversion polymorphism of the malaria mosquito Anopheles messeae Fall. in the period from 1974 to 2020, according to the frequencies of inversion variants of chromosomes and gametes in the population village Kolarovo showed the replacement of “northern” variants in the period of the 90s of the last century with “southern” variants and the stabilization of these changes until 2020. The correlation of the frequency distribution of chromosomal inversions from 1972 to 2020 was revealed with an annual temperature including a semi-annual average April–September and semi-annual average October–March temperature. The results obtained made it possible to reveal the nature of dynamic processes associated with the modification of a specific ecological niche during a long period due to climate warming. The spatiotemporal stationarity (dynamic stability) of adaptive inversion polymorphism is evidence of high population-genetic (or rather species-specific) homeostasis and the absence of tendencies to speciation.
Su(Hw) Architectural Protein Binding Sites Stimulate Recruitment of PcG/TrxG Epigenetic Regulators to Chromatin: CRISPR/Cas9-Test
Authors: Erokhin M. M. , Gorbenko F. V. , Lomaev D. V. , Chetverina D. A.
Published: April 2024

Polycomb and Trithorax group proteins (PcG and TrxG) are epigenetic factors responsible for the repression and activation of transcription, respectively. In Drosophila, PcG/TrxG proteins are recruited to specialized DNA elements called PRE (Polycomb response elements). Depending on the context, these elements may repress, activate, or be neutral with respect to the promoter of the target gene. Previously, in transgenic studies using PhiC31 site-specific integration system, we have demonstrated that sites for architectural proteins inserted next to PRE can induce the repressive activity of bxdPRE by stimulating the binding of PcG/TrxG factors to this element. However, this effect may depend on additional DNA elements present at the integration site after PhiC31-dependent transgene insertion. In the present study, using an alternative system of integration based on CRISPR/Cas9-catalyzed homology-directed repair, we have proved that the binding sites of the architectural protein Su(Hw) are indeed able to induce the repressive activity of bxdPRE and recruitment of PcG/TrxG proteins, regardless the heterogenous DNA-sequences present at the site of integration after PhiC31-dependent insertion of the transgenes.
Genetic Diversity of Juniperus communis L. in Eurasia and Alaska, Inferred from Nuclear Microsatellites Markers
Authors: Hantemirova E. V. , Bessonova V. A.
Published: April 2024

The structure of genetic variation of the common juniper (Juniperus communis L.), a widespread wind-pollinated golarctic shrub of Cupressaceae was surveyed. We used 7 microsatellite markers including three new to genotype samples from 23 Eurasian populations and one from North America (Alaska). The geographical patterns are interpreted jointly with our previously available chloroplast DNA data. High genetic diversity was revealed with highest values in the same northern populations (Sweden, Estonia, Mezen, Polar Urals, Yamal, Kolyma, as well as in the Alps) as previously identified at cpDNA analysis. Nuclear markers exhibited a lower level interpopulation differentiation (FST = 9.8%) than chloroplast markers (FST = 76%). Bayesian cluster analysis showed that the optimal number of genetic groups (K) was two. All the 24 populations of J. communis were divided into the East group (north-east and Far East of Russia, Alaska and Himalayan) and the West group (Europe, Ural and Siberia). In the Alpine and Mountain Shoria populations, genotypes from different genetic groups are combined.
Analysis of ADCY8 и RYR3 Genes Polymorphism for Identification Wild and Domestic Animal of Species Canis lupus
Authors: Kipen V. N. , Patrin M. M. , Snytkov E. V. , Viarchuk A. N. , Semak A. N.
Published: April 2024

As a result of the study, we confirmed the high differentiating potential of polymorphic variants g.27748425TC (ADCY8 gene) and g.1414373TC (RYR3 gene). A test model of two polymorphisms for the differentiation of a wolf and a domestic dog is proposed, which is distinguished by high values of accuracy (96.2%), specificity (96.3%) and sensitivity (98.9%). Using KASP, a quick and simple approach to differentiation based on the proposed test model has been developed, which is designed to reduce the time and cost of molecular genetic analysis, as well as reduce the risk of cross-contamination, because the process is one-stage (restriction and electrophoresis stages are excluded).
Variability of 27 Autosomal STR Loci for the Population of the Republic of Belarus Based on the Mass Parallel Sequencing Data
Authors: Kotova S. A. , Parfionava N. S. , Zabauskaya T. V. , Rybakova V. I. , Spivak A. A. , Paliavoi S. A. , Lugovnev A. V.
Published: April 2024

Variability of 27 autosomal STR loci of the ForenSeq DNA Signature Prep Kit (Illumina) commercial panel was studied using the technology of mass parallel sequencing (MPS) in 733 unrelated individuals representing the population of the Republic of Belarus as well as a population base of MPS allele frequencies for expert probabilistic calculations in human identification and paternity establishment was evaluated. The agreement between genotypes obtained by MPS and capillary electrophoresis (CE) was 99.96%. The number of MPS alleles increased more than two times for eight loci (D12S391, D21S11, D2S1338, vWA, D3S1358, D8S1179, D13S317, D9S1122). Thirteen alleles detected were not included in the STRSeq BioProject catalog of the international online database STRbase 2.0. The random match probability of 27-locus MPS profiles decreased from 1.43 × 10–31 to 2.89 × 10–35, and the combined paternity index increased from 2.08 × 1010 to 3.25 × 1012 compared to CE data.
Informative Relevance of 11 Microsatellite Loci for Forensic DNA-Identification of Wild and Farm American Minc (Mustela vison) in Belarus
Authors: Lukashkova V. M. , Spivak A. A. , Kotova S. A.
Published: April 2024

American mink is involved in economic activity of the Republic of Belarus since it belongs to resource hunting species as well as breeds for fur production. We propose identification test system consisting of 11 microsatellite DNA loci designed for forensic investigation of cases of illegal hunting and animals stealing for precious furs. Informative relevance of the test system studied using two samples of farm minks and a sample from a wild population of M. vision geographically isolated from fur farms. The significant genetic differences between wild and farmed minks (Fst = 0.04397, P 0.05) showed with random match probabilities of 11-locus genotypes calculated with and without taking into account the Fst value differing by two orders (1.84 × 10–8 and 1.39 × 10–10 respectively). As concerned to forensic DNA analysis, the reference databases should be formed for wild and farm animals separately.
Polymorphism of the rs1815739 Locus of the ACTN3 Gene and rs11227639 cis-eQTL Affecting Its Expression in Populations of Siberia
Authors: Malyarchuk B. A. , Derenko M. V. , Denisova G. A.
Published: April 2024

The polymorphism of the rs1815739 locus of the ACTN3 gene and the rs11227639 cis-eQTL that affects expression of this gene was studied in the populations of the northern (Chukchi, Koryaks, Evens, and Evenks) and southern (Buryats, Altaians, and Tuvinians) parts of Siberia. It was shown that the frequencies of the rs1815739-C allele of the ACTN3 gene (corresponding to the 577R amino acid variant) and the rs11227639-A upregulating ACTN3 allele, which increases the expression level of this gene, are significantly higher in the north than in the south of Siberia. Similarly, in the northern direction, the frequency of the combination of CC/AA genotypes at these loci increases. The revealed pattern of the geographical distribution of alleles and genotypes at the rs1815739 and rs11227639 loci in Siberian populations may be due to adaptation to cold and the processes of thermoregulation of the body when exposed to cold. It is assumed that an increase in the frequency of rs1815739-C and rs11227639-A alleles in the aboriginal populations of the north of Siberia is associated with an increase in the role of shivering thermogenesis during adaptation to cold exposure, and also contributes to an increase in muscle mass in their carriers, which reduces heat loss in the conditions of the North.
A Recombination Suppressed Region of Sunflower (Helianthus annuus L.) Linkage Group 13 Covers Restoration of Fertility (Rf1) and Downy Mildew Resistance (Pl) Gene Clusters
Authors: Anisimova I. N. , Alpatieva N. V. , Voronova O. N. , Gavrilova V. A. , Karabitsina Yu. I. , Kuznetsova E. B. , Radchenko E. E.
Published: April 2024

A number of genes that control valuable for breeding traits introgressed from wild relatives, i.e. pollen fertility restoration, resistance to fungal diseases (downy mildew and rust), are mapped on linkage group 13 of the cultivated sunflower Helianthus annuus L. genome. In sunflower and other plants, the recombination in the chromosome regions containing resistance genes can be suppressed that is favourable for marker assisted selection with applying molecular markers linked to these loci. The joint inheritance of the loci Rf1 (the phenotypic marker is fertility restoration trait) and Pl5/Pl8 conferring resistance to many races of Plasmopara halstedii (Farl) Berl. De Toni (the STS marker Ha-P1) was studied in the F2 generation of hybrids between a sterile line VIR 116A lines and pollen fertility restorers from sunflower VIR collection. In the crossing VIR 116А × VIR 740, the frequency of recombination between the loci Pl5Pl8 and Rf1 constituted 8.61 whereas in the crosses VIR 116А × VIR 195 and VIR 116А × VIR 80 turned out to be twice as high. In all examined F2 populations the absence of phenotypic class of sterile plants possessing paternal Нa-Р1 marker variant was mentioned. It has been shown by the cytological analysis that pollen fertility indices are most probably determined by the plant genotype rather than the male gametophyte allelic constitution. A deficiency of a recombinant F2 class was proposed to be associated with embryonic lethality, i.e. the collapse of zygotes carrying the recessive allele of fertility restoration gene and a specific allele of the resistance (susceptibility) gene obtained from the male parent.
Dynamics of Rye Translocations Frequency in Russian Common Wheat Triticum aestivum L. Cultivars
Authors: Fisenko А. V. , Lyapunova О. А. , Zuev Е. V. , Novoselskaya-Dragovich А. Yu.
Published: April 2024

The widespread using 1RS/1BL and 1RS/1AL translocation cultivars in wheat breeding was due to their high complex resistance provided by genes on 1RS chromosomes. Numerous data on the emergence of new virulent pathogen races that caused the loss of protective properties by genes on 1RS make it relevant to analyse the prospects for using both rye translocations in modern breeding programs. The use of various genetic sources of the 1RS rye chromosome in introgressive hybridization poses the problem of studying the diversity of 1RS linkage groups. We have studied the rye translocations dynamics in 240 genotypes of the wheat cultivars from 3 breeding centers of the Russian Federation. Multiple alleles of storage protein genes specific for 1RS were used to mark 1RS. The effectiveness of 1RS resistance genes to a number of pathogens, in particular to powdery mildew and stem rust, has been established. The grain quality dynamics of the 1RS/1BL cultivars has been traced. A statistically significant grain quality improvement of winter wheat cultivars since the 2000s has been confirmed. The spring cultivars quality does not depend on the presence of rye translocations in the genotypes. Accumulation of cultivars with TR:1RS/1BL observed in all three centers. A high allelic diversity of the secalin coding locus on 1RS chromosome was shown. However, all cultivars with rye translocations, regardless of 1RS origin, carried the same allele. Possible reasons for this uniformity are discussed. Translocation 1RS/1AL was not detected in the studied cultivars. Possible reasons are discussed.
A Robust Test System for DNA Identification of Raccoon Dogs
Authors: Hrebianchuk A. E. , Lukashkova O. N. , Kotava S. A. , Tsybovsky I. S.
Published: April 2024

To establish a system for DNA identification of biological samples of the raccoon dog (Nyctereutes procyonoides), we carried out a study of polymorphism of 39 microsatellite loci and three sex loci specific to various species of the Canidae family. This resulted in the development of the NPlex test system, which includes 14 autosomal STRs and two sex loci. The test system has been validated for use in forensic identification of racoon dogs based on biological traces (such as traces of blood and secretions, fragments of muscle tissue or bones, dermis and hair, etc.) found at crime scenes, as well as for establishing biological relationship of animals of this species. Validation efforts were performed in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods.
The First University School of Russian Genetics
Authors: Inge-Vechtomov S. G. , Golubkova E. V. , Zhouravleva G. A.
Published: April 2024

Professor Yu.A. Filipchenko founded the first department of genetics (then genetics and experimental zoology) in Russia in 1919. The first department of genetics in Russia made its first steps in the context of world science was facilitatedthrough contacts between leading scientists in genetics, who today are recognized as classics of genetics – T.H. Morgan, Yu.A. Filipchenko, N.I. Vavilov, W. Bateson, G.A. Levitsky, G.D. Karpechenko, F.G. Dobzhansky, H.J. Muller, M.E. Lobashev and others. The modern scientific and educational activities of the department are predetermined by its previous history and the staff of the department continues to develop the traditions of the educational and scientific complex. Teaching work is link inextricably with research work within the framework of a common problem – “Mechanisms of the genetic processes integration”. The formulation of a broad problem makes it possible to resist centrifugal tendencies, the cause of which may be the differentiation of interests and specific tasks of researchers, what, in turn, is fraught with the danger of training narrow specialists. The formularization of some unifying problem is traditional for the department and preserves the basis of mutual understanding between different geneticists, and emphasizes that geneticsis one of the most important general biological disciplines.
Eupolyploidy as a Modeinplant Speciation
Authors: Rodionov A. V.
Published: April 2024

When discussing phenomena of the whole genome duplication (WGD), the terms neopolyploid, mesopolyploid, and paleopolyploid are used in their modern “post-genomic” interpretation. In our opinion, in the flow of changing genome states between neopolyploids and paleopolyploids, it makes sense to single out the eupolyploid stage – a state of a polyploid, when its polyploid nature is beyond doubt, but the genome (karyotype) of the eupolyploid, unlike the neopolyploid, is already relatively stable. Most of so-called polyploid plant species are actually eupolyplids, the polyploid nature of the karyotype of which is beyond doubt among researchers – geneticists, karyologists, and florists. Optionally, eupolyploids can enter new rounds of interspecific hybridization with the hybrid maintaining the level of ploidy of the parents or with the emergence of an allopolyploid of a higher level of ploidy. Eupolyploidization of the genome is a radical and rapid method of speciation and genus formation in plants. In this way, tens of thousands of species of modern plants arose. Successful combinations of alleles of eupolyploid subgenomes, large sizes characteristic of high polyploids, frequent transition to asexual reproduction can contribute to the successful development of new areas by eupolyploids, adaptation to extreme conditions of existence at the edge of areas, but not to the acquisition of new aromorphoses – this is speciation, but speciation on already mastered level of evolutionary complexity, a step that does not in itself lead to progressive evolution.
Analysis of Genetic Factors of Sporadic Schizophrenia in Family Trios Using Whole Genome Sequencing
Authors: Andreeva T. V. , Afanasiev Ph. A. , Gusev F. E. , Patrikeev A. D. , Kunizheva S. S. , Rogaev E. I.
Published: April 2024

Schizophrenia is a mental disorder, the hereditary nature of which has been confirmed by numerous studies. Currently, more than a hundred genetic loci associated with schizophrenia have been described, and rare variants in genes and chromosomal rearrangements associated with familial cases of the disease have also been identified. However, it is not always possible to determine the hereditary nature of the pathology, many cases of schizophrenia are sporadic, and the genetic cause of such cases remains unknown. Using whole genome sequencing data for three family trios from Russia with sporadic cases of schizophrenia, we searched for rare potentially pathogenic variants in the coding and regulatory loci of the genome, including de novo and compound mutations. The polygenic risk of schizophrenia was also assessed using common polymorphic markers. As a result of the analysis, the genetic heterogeneity of sporadic forms of schizophrenia was shown, as well as the potential role of rare substitutions in genes associated with the metabolism of glutamate and inositol phosphate in sporadic cases of schizophrenia.
Impact of Chromatin 3D-Organization on Promoter–Superenhancer Interactions in Embryonic Stem vs Cancer Cells
Authors: Eidelman Yu. A. , Andreev S. G.
Published: April 2024

The interaction of enhancers and superenhancers (SE) with promoters is functionally significant for the regulation of gene expression. Pattern of these interactions plays a key role in various processes, such as differentiation, malignant transformation, etc. In order to quantify the relationship between 3D chromatin organization and promoter–SE contacts, a computational analysis of chromatin conformations near the murine Nanog pluripotency gene was performed for normal embryonic stem (mESC) and lymphoma (CH12LX) cells. Using biophysical modeling approach, the following parameters of the promoter–SE interactions were identified: the distribution of distances between the Nanog promoter and the SEs, the frequency of contacts with one and several SEs simultaneously. In normal mESC expressing Nanog, the frequency of contacts of promoters with SEs is higher than in cancer cells, and complex contacts with two or more SEs are more frequent. The modelling reveals a small subpopulation of cancer cells, where the promoter contacts simultaneously three SEs. The predicted subpopulation of cancer cells with multiple promoter–SE contacts may be predisposed to increased stemness and hypothetically be considered as a reservoir for generation of cancer stem cells.
DNA Repair Does Not Trigger Genetic Instability of Yeast Cells
Authors: Evstratova E. S. , Petin V. G. , Geraskin S. A.
Published: April 2024

The dependence of the delayed formation of colonies on the dose of ionizing radiation (gamma rays of 60Co, dose rate 10 Gy/min) was obtained for six strains of wild-type haploid and diploid yeast, capable of recovering from radiation damage and characterized by sigmoidal survival curves as well as for six haploid and diploid radiosensitive mutants defective in reparation and characterized by exponential survival curves. The delay in the formation of colonies by survival cells after irradiation is considered as a genetic instability display. It was shown that for all diploid strains, genetic instability reached 100% with an increase in the dose of ionizing radiation, regardless of the shape of survival curves and the cell ability to recover from radiation damage. Conversely, for all haploid strains, genetic instability was only close to 20%. In contrast to traditional concepts, these data indicate that the late formation of colonies by surviving yeast cells after irradiation is determined mainly by cell ploidy and does not depend on the shape of the dose-response curves and cell radiosensitivity. This means that DNA repair does not trigger genetic instability in yeast cells.
Identification of Hybrid Specimens of Rock Lizards Darevskia armeniaca × Darevskia valentini Based on Microsatellite Genotyping
Authors: Girnyk A. E. , Vergun A. A. , Ryskov A. P.
Published: April 2024

The paper presents the results of microsatellite genotyping of hybrid lizards D. armeniaca × D. valentini from sympatric populations of Armenia. Triploid individuals were identified based on the totality of the Du281 and Du47G loci and their origin was determined. It was shown that the hybrids contain both alleles of the maternal parthenospecies D. armeniaca and alleles of the paternal species D. valentini.
Genetic Variability of MAOA Gene among Aggressive Animals from the Non-Canonical Behavioral Model Neogale vison
Authors: Manakhov A. D. , Dudko N. A. , Gusev F. E. , Andreeva T. V. , Trapezov O. V. , Rogaev E. I.
Published: April 2024

The MAOA gene is widely known regulator of aggressive behavior among human and animals. Here, we analyzed the genetic variability of the MAOA gene and its promoter region in non-canonical behavioral model – American mink (Neogale vison). We didn’t observe any significant genetic variations among animals with aggressive behavior, that suggests the presence of genetic and/or epigenetic variations in other systems involved in regulation of aggression in this model.
Comparative Analysis of Structural Variant Callers on the Short-Read Whole-Genome Sequencing Data
Authors: Mkrtchian A. A. , Grammatikati K. S. , Kazakova P. G. , Mitrofanov S. I. , Zemsky P. U. , Ivashechkin A. A. , Pilipenko M. N. , Svetlichny D. V. , Sergeev A. P. , Snigir E. A. , Frolova L. V. , Shpakova T. A. , Yudin V. S. , Keskinov A. A. , Yudin S. M. , Skvortsova V. I.
Published: April 2024

In this study three structural variant callers (Manta, Smoove, Delly) were analysed on the whole-genome sequencing data using four different alignment algorithms: DRAGEN, GDC DNA-Seq Alignment Workflow, GDC DNA-Seq Alignment Workflow + GDC DNA-Seq Co-Cleaning Workflow, NovoAlign, different lengths of raw reads: 2 × 150 bp and 2 × 250 bp, different mean genome coverage values. Results were compared to etalon results of GIAB team. Structural variants validation was hold also with Sanger sequencing. Structural variants deletions and insertions as it turned out were best determined with Manta tool. We’ve got 89–96% of accuracy and 59–70% of sensitivity for analysed deletions, and also 96–99% of accuracy and 15–36% of sensitivity for insertions. Smoove and Delly showed less accurate and sensitive results (Smoove: 91–95% of accuracy and 8–54% of sensitivity for deletions, Delly: 78–87% of accuracy and 31–66% of sensitivity for deletions, 99–100% of accuracy and 1–13% of sensitivity for insertions). Simultaneous using of two or even three structural variant callers didn’t give a rise of accuracy and sensitivity for deletions. Analysis showed that accuracy and sensitivity of structural variant callers rise with the rising of mean genome coverage value, increasing of reads length from 150 to 250 bp influence in to varying degrees on the accuracy and sensitivity of individual tools. Another inference of this study was that accuracy of structural variants callers vary depends on structural variants size range. For example, Manta finds better deletions in the range from 200 and more bp, Delly – from 1000 to 10 000 bp, Smoove – from 200 to 10 000 bp.
Studying the Genetic Diversity of the Rice Break Cause Pyricularia oryzae Cav. on the Complex of Molecular and Morphological Features
Authors: Nartymov D. V. , Dubina E. V. , Ruban M. G. , Aniskina Yu. V. , Garkusha S. V. , Shilov I. A. , Velishaeva N. S. , Kolobova O. S. , Istomin N. K.
Published: April 2024

On the basis of molecular genetic approaches, the study of the biodiversity of the phytopathogenic fungus Pyricularia oryzae Cav. in the south of Russia and a classification of the morphological and cultural characteristics of the pathogen was carried out. For 2020–2022 monitoring was carried out and 24 strains of the pathogen were isolated from the affected herbarium material collected from the fields of five ecological rice growing zones of the Krasnodar Territory (Krasnoarmeisky, Kalininsky, Abinsky, Slavyansky districts, Krasnodar). Using the multiplex PCR system developed by us based on fragment analysis, five genotypes were identified among the studied Pyricularia oryzae Cav. strains over the entire period of the project, each of which is characterized by a unique genetic profile. Compiled their “DNA passport”. The studied isolates of the causative agent of blast were characterized by morphological and cultural characteristics. Six morphotypes of the pathogen have been identified.
Peculiarities of Transfer of DNA Markers of Wild Allotetraploid Potato Species Solanum stoloniferum to Backcross Progenies Depending on Their Subgenomic Location and Used Schemes of Introgression
Authors: Yermishin A. P. , Levy A. V. , Ageeva A. S. , Voronkova E. V. , Luksha V. I. , Gukasian O. N. , Zharich V. M.
Published: April 2024

Genomic difference between wild allotetraploid potato species Solanum stoloniferum Schltdl et Bouchet (genome AABB) and S. tuberosum L. (AAAA) is one of the factors hampering its use in breeding. However, there is practically no information on valuable genes of this species located in the subgenome B and on the way of their transfer into the genome A of cultivated potatoes. The objectives of this research were to identify subgenomic location of a set of S. stoloniferum genes using an original approach based on a difference of inheritance of DNA markers of the genes in backcross BC1 of chromosome doubled triploid hybrids (6x, AAAABB) to 4х S. tuberosum dependent on belonging to A or B subgenome; to study their inheritance in BC2 and BC3 in the framework of four introgression schemes and marker assisted selection of the gene Rpi-sto1. The markers of late blight (LB) resistance genes Rpi-sto1, R3b, R2, potato virus Y (PVY) resistance genes Rysto, Ryadg were located on the subgenome B and the marker of PVY resistance gene Rychc – on the subgenome A. We observed an appearance of unexpected sporadic hybrids free of markers in BC1 that may be explained by rare cases of homeological recombination of A and B subgenome chromosomes. The segregation of the markers in BC2 (close to 1 : 1) matched in general to that expected in the case of random transfer of the corresponding chromosomes of the subgenome B. Some promising for breeding hybrids have been selected in BC3 having the marker of the gene Rpi-sto1.
Mitochondrial DNA Mutations in Cardiovascular Diseases
Authors: Korepanov V. A. , Rebrova T. Yu. , Batalov R. E. , Afanasiev S. A.
Published: April 2024

Early prevention of development and timely diagnosis of diseases of the cardiovascular system are some of the main tasks of modern cardiology. One of the promising approaches is aimed at identifying associations between the carriage of mitochondrial DNA (mtDNA) mutations and the development of cardiovascular diseases. Mitochondria are the only source of energy accumulation in cardiomyocytes; therefore, failure of their functioning, caused by mtDNA mutations, directly affects the bioenergetics and the work of myocardial cells. The purpose of this review is to describe the current achivements in the study of associations of mutant mtDNA with the development of various pathologies of the cardiovascular system.
Mitochondrial Genetic Diversity of Eurasian Otter (Lutra lutra) from European Part of Russia and Transcaucasian Countries
Authors: Sokolova N. A. , Korablev N. P. , Korablev P. N. , Hernandez-Blanco J. A. , Kaloyan G. A. , Gyonjyan A. A. , Malkhasyan A. H. , Sorokin P. A.
Published: April 2024

In this study we examined mitochondrial DNA diversity of Eurasian otter from European part of Russia and Transcaucasian countries and compared it with other European populations. We used a fragment of mtDNA control region (255 bp) and also included previously detected haplotypes from NCBI. Six haplotypes were found in 75 samples from European part of Russia and Transcaucasian countries. Lut1 was the most common haplotype (62.1% of samples), Lut4 was detected in 17.6% of samples, other 4 haplotypes were newly detected. Haplotype diversity for European part of Russia and Transcaucasian countries were h = 0.56 ± 0.054, nucleotide diversity were π = 0.0016 ± 0.002. When we elongated the fragment of mtDNA (820 bp), haplotype (0.85 ± 0.03) and nucleotide diversity (π = 0.002 ± 0.001) were increased and 14 haplotypes were found. Geographic distribution of haplotypes depends neither on region, nor on river system. Central haplotype was detected throughout European part of Russia and Transcaucasian countries, as well as minor haplotypes, observed in lesser number of regions. Therefore, genetic diversity of Eurasian otters from European part of Russia and Transcaucasian countries is higher than in the rest of Europe. Besides, the population structure repeats European pattern with several regional features.
Reaction of Bifidobacterium longum subsp. infantis Strain ATCC 15697 to Oxidative Stress
Authors: Averina O. V. , Kovtun A. S. , Mavletova D. A. , Ziganshin R. H. , Danilenko V. N.
Published: April 2024

The genus Bifidobacterium is one of the predominant bacterial populations in human gut microbiota. Despite the increasing number of studies on the beneficial functionality of bifidobacteria for human health, knowledge about their antioxidant potential is still insufficient. The role of the antioxidant potential of bifidobacteria in maintaining the homeostasis of the intestinal microbiota of the host organism as a whole is an important task that requires solutions. For the first time, this paper presents the data of genomic, transcriptomic and proteomic analyses of probiotic strains Bifidobacterium longum subsp. infantis ATCC 15697 after the action of oxidative stress. The growing culture of strain was exposed to hydrogen peroxide for 2 hours and oxygen for 2 and 4 hours. Preliminary genome analysis of the strain showed the presence of 18 genes encoding a known protein with antioxidant function, as in other complied genomes of B. longum subsp. infantis strains available in the international database. The complete transcriptome analysis revealed an increase in transcript levels by more than two times for 6 genes with a known antioxidant function. The data of quantitative proteomic analysis showed an increase in protein levels by more than two times for five enzymes with a known antioxidant function. 28 other proteins with increased levels more than twice were identified in the cells of the growing culture in response to the long action of oxygen. These proteins can be involved in the processes of the cell’s response to stress, the amino acids, nucleotides metabolism and transport processes. Six proteins with unknown functions, which may play a significant role in the antioxidant response of anaerobic bifidobacteria, were found to have high levels in the cells after the action of stress. The obtained data are supposed to be used in the selection of B. longum subsp. infantis strains and the creation of pharmacobiotics able to correct the composition of the microbiota.
Genetic Polymorphisms Associated with the Efficiency of Weight Loss: A Systematic Review
Authors: Egorova E. S. , Ahmetov I. I.
Published: April 2024

Interindividual differences are associated not only with body weight but also determine the body’s response to diet and physical activity. This systematic review aimed to identify the genetic markers associated with diet-induced and exercise-induced weight loss. The eligible intervention studies for this systematic review contained all the necessary parameters for genetic polymorphism, diet, exercise, and changes in anthropometric or body composition parameters. In total, 91 articles met the criteria and were included in this systematic review. The vast majority of studies (n = 88) are used of candidate gene approach, and only three studies were performed using hypothesis-free approach (GWAS). A total of 98 genetic variants were found, of which 72 markers are associated with the efficiency of diet therapy, and 26 – with individual response to physical activity. It should be noted that the significance of markers was replicated for only 10 of 98 genetic variants. In the near future, we should expect progress in this area, which will result in the development of a method for individual selection for each patient of the type of diet and exercise for the prevention and treatment of obesity.
The Use of the Genetic Resources of Tetraploid Wheat Triticum aethiopicum on the Developing of Purple-Grain Common Wheat with a High Content of Anthocyanins
Authors: Fisenko А. V. , Dragovich А. Yu.
Published: April 2024

The article considers the results on the developing of purple-grain common wheat and the study of its genetic diversity. Triticum aethiopicum Jakubz. 2n = 28 is the only source of genes for the purple grains color among the wheat species. The trait of purple grain is accompanied by an increase in the content of anthocyanins and micronutrients in the grain. To develop common wheat lines with purple grain, T. aethiopicum k-19068 was first hybridized with the Iranian landrace T. aestivum k-14333. The resulting hybrids were then crossed with the highly productive common wheat cultivar Liza. The developing lines F6 (2n = 42) characterize low diversity on multiple alleles of gliading-coding loci (H = 0.410). They were dominated by alleles inherited from the parent variety Liza. No gliadin alleles that could belong to T. aethiopicum have been identified. Comparison of groups of lines with purple and white grains made it possible to show that they do not significantly differ from each other in terms of yield and elements of its structure. As a result, we have not found a negative correlation between the high content of anthocyanins in grain and grain productivity. This allows us to hope for the possibility of developing high-yielding lines of common wheat with purple grain enriched with anthocyanins.
Genome-Wide Association Study of the Risk of Schizophrenia in the Republic of Bashkortostan
Authors: Gareeva A. E.
Published: April 2024

Genome-wide association studies (GWAS) have proven to be a powerful approach to discovering genes for susceptibility to schizophrenia; their findings are important not only for our understanding of the genetic architecture of a given disease, but also for potential applications in the field of personalized medicine. The aim of this study was to study the genetic risk factors for the development of schizophrenia during a genome-wide association analysis in the Republic of Bashkortostan.
Genetic-Demographic Analysis of Natural Reproduction Parameters and Crow’s Indices in Ethnic Groups of Moscow and St. Petersburg (Based on the 2010 Russia’s Population Census)
Authors: Gracheva A. S. , Udina I. G. , Kurbatova O. L.
Published: April 2024

Based on the analysis of the materials of the 2010 All-Russia’s Population Census and the demographic statistics of Rosstat Agency, the genetic-demographic parameters of temporal and interethnic variability of natural reproduction parameters and selection parameters (Crow indices) were calculated for the most numerous ethnic groups of Moscow and St. Petersburg. A decrease in the selection component due to differential prereproductive mortality was shown to decrease to the minimum possible values (index Im 0.01). In both megacities, interethnic differences were revealed in the parameters of natural reproduction and the selection component due to differential fertility, while the birth rate in both capitals for all ethnic groups, except for Uzbeks in St. Petersburg, is lower than required even for simple reproduction of the population, and hence stable reproduction of the gene pool. This indicates the unfavorable nature of the genetic and demographic processes in all the represented nationalities of the megacities. The If index ranges from 0.2 to 0.5. The temporal dynamics of the average number of offspring and its variance, as well as the If index, traced according to the data on the age cohorts of women born in the 1940s–1960s, is weakly expressed – the tendency to selection relaxation is not observed for all the studied ethnic groups. It is shown that the intensity of intergroup selection, due to interethnic differences in fertility, in the population of St. Petersburg increases from older age cohorts to younger ones, while in the population of Moscow it does not change significantly, while the temporal dynamics of this indicator, calculated on the base of the materials of the 2002 All-Russia’s Population Census for cohorts born in 1930s–1950s has the opposite direction. The genetic-demographic consequences of the revealed tendencies are discussed.
Analysis of Mutations of the Maize Genes of Autonomous Embryo-, Endospermogenesis
Authors: Moiseeva E. M. , Fadeev V. V. , Krasova Yu. V. , Chumakov M. I.
Published: April 2024

The gynogenesis and parthenogenesis genes in Saratov maize lines was evaluated. In particular, the (Zm_Gex2, Zm_Gcs1, Zm_Pla1, Zm_CenH3, Zm_Dmp7) genes in haploid-inducing (ZMS-8, ZMSP) and (Zm_Chr106, Zm_Hdt104 and Zm_Fie1) genes in parthenogenetic (AT-1, AT-3, AT-4) and ordinary (KM, GPL-1) maize lines were sequenced. Using bioinformatic methods, gene sequences were compared in different maize lines and changes in nucleotide sequences were revealed. We suppose that it is possible to use Zm_Pla1, Zm_Gex2, and Zm_Fie1 genes for maize line genotyping.
Genome-Wide Association Study: Analysis of Association of Polymorphic Loci in 4p15.2 and 20q13.31 Regions with Paranoid Schizophrenia
Authors: Gareeva A. E.
Published: April 2024

Over fifteen years, genome-wide association studies (GWAS) have identified several million polymorphic risk markers for schizophrenia, significantly advancing our understanding of the genetic architecture of schizophrenia. The aim of this study was to study genetic risk factors for the development of schizophrenia in a genome-wide association analysis in Russians, Tatars, and Bashkirs from the Republic of Bashkortostan. The studied sample consisted of 816 patients with paranoid schizophrenia and 989 healthy individuals. GWAS genotyping of DNA samples was carried out on the PsychChip, which included 610 000 single nucleotide polymorphic variants (SNPs). As a result of the study, for the first time, an association of SNPs rs73254185 (4p15.2) and rs587778384 of the GNAS gene (20q13.31) with the risk of paranoid schizophrenia in individuals of different ethnicity, Russians, Tatars and Bashkirs living in the Republic of Bashkortostan, was established, which probably may indicate involvement of PI4K2B and GNAS genes localized in these chromosomal regions in the pathogenesis of schizophrenia.
Immunogenetic Factors in the Pathogenesis of Schizophrenia
Authors: Plotnikova M. Yu. , Kunizheva S. S. , Rozhdestvenskikh E. V. , Andreeva T. V.
Published: April 2024

Human predisposition to neurological diseases such as schizophrenia, Alzheimer’s, Parkinson’s and other neuropathologies is associated with genetic and environmental factors. One of the promising directions in the area of molecular neurosciences is the study of the role of immunogenetic mechanisms in different types of pathological processes in brain. This review explores the role of complex histocompatibility genes in the pathogenesis of schizophrenia, evaluating changes in the immune repertoire of T- and B-cell receptors in neuroinflammation.