Vavilovskii Zhurnal Genetiki i Selektsii最新文献

{"title":"Variability of organelle genomes in a collection of early maturing soybean varieties.","authors":"V V Aleksandrovich, M G Siniauskaya, A P Shatarnov, O G Davydenko","doi":"10.18699/vjgb-26-23","DOIUrl":"https://doi.org/10.18699/vjgb-26-23","url":null,"abstract":"<p><p>Variability of the genomes of cellular organelles (chloroplast and mitochondria) is an important component of the overall variability of the plant genome. A large amount of data has already been obtained on the comparative characteristics of the organization of organelle DNA sequences for different groups of plants. This paper presents new original data on the variability of mitochondrial and chloroplast genomes in soybean (Glycine max (L.) Merr.), a crop of great economic importance widely cultivated in Central Europe, including the Republic of Belarus. Initially, we supposed that the peculiarities of soybean organelle DNA sequence or organization promote certain soybean cultivars to be the best maternal and others, alternatively, the best paternal forms. As a result of the study, new complete nucleotide sequences of chloroplast and mitochondrial genomes of 46 soybean samples were obtained by the next generation sequencing method (NGS) on the Illumina platform. A comprehensive bioinformatic comparative study of intraspecific organelle genome variability in 46 soybean varieties of diverse geographical origin was conducted. Polymorphic loci of genomes were discovered. Data on DNA variability were verified by Sanger sequencing. The spectrum of organelle DNA variability of cultivated soybean was represented by three chloroplast DNA haplotypes (C1-C3) and five mitochondrial DNA haplotypes (M1-M5). A comparatively low level of intraspecific variability of organelle genomes in G. max was revealed. The soybean chloroplast genome had a lower level of sequence variability than the mitochondrial genome. A set of DNA markers for polymorphic loci of organelle genomes was developed, allowing the differentiation of varieties of the studied group into plasmatypes. Additionally, 90 soybean samples from the collection were studied using PCR followed by Sanger sequencing. The low level of intraspecific variability of organelle genomes in G. max was confirmed on the extended group of samples. The majority of cultivars were represented by three plasmatypes - C1/M1, C2/ M2 and C1/M3. 46 complete chloroplast DNA sequences have been deposited in NCBI GenBank. The hypothesis that organelle DNA influences the combining ability of different varieties has not yet been confirmed. A more detailed study of the mechanisms of nuclear-cytoplasmic interaction is required, as well as a search for nuclear markers that affect the expression of organelle genes.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"205-211"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alembic: a framework for converting disparate biological data into structured resources.","authors":"I V Bezdvornykh, K I Yuditskiy, N A Cherkasov, A A Samsonova, A A Kanapin","doi":"10.18699/vjgb-26-33","DOIUrl":"https://doi.org/10.18699/vjgb-26-33","url":null,"abstract":"<p><p>The imperative to re-analyze existing public sequencing data is central to modern biology, driven by new hypotheses and advanced analytical methods. However, this effort is critically hampered by the profound heterogeneity of repository data, particularly the non-standardized, free-text descriptions of biological experiments. This lack of structural and semantic homogeneity prevents systematic search, integration, and comparative analysis, effectively locking away the full potential of accumulated datasets. Advances in Natural Language Processing (NLP) offer a pivotal pathway to overcome this bottleneck by transforming unstructured text into computable, homogeneous information. The integrated Entrez database system, maintained by the National Center for Biotechnology Information (NCBI), provides sophisticated programmatic access via an API to primary sequencing data and its associated metadata, including detailed experimental descriptions. This interface enables researchers to identify and retrieve relevant data through keyword searches, including those based on gene names, and to apply modern NLP techniques to transform textual metadata into structured information. The output is formatted data ready for integration into local databases, accompanied by a systematic list of links for downloading primary files. The Alembic software package offers a comprehensive and automated solution for the entire workflow. Designed as a locally deployable client-server system, Alembic incorporates state-of-the-art transformer-based AI algorithms for analyzing the biomedical text that accompanies sequencing data. Its core utilizes the openly available AIONER platform, which is built upon the PubMedBERT model trained on the PubMed repository, to ensure efficient and accurate recognition of biomedical named entities (e. g., genes, diseases). This provides users with structured and meaningful keyword search results. By delivering a curated list of datasets, Alembic streamlines the path from search to analysis. Researchers can efficiently identify high-value targets and obtain a complete package of metadata and primary data to construct a tailored local repository. This positions Alembic as a universal solution that overcomes the fragmented approach of existing tools, offering an integrated workflow for diverse public sequencing data.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"293-298"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeography and taxonomic status of the Formica picea complex (Hymenoptera: Formicidae).","authors":"Z A Zhigulskaya, S V Shekhovtsov, S V Chesnokova, A P Burnasheva, A A Gurina, R Yu Dudko, T V Poluboyarova, S V Reshetnikov, Yu N Sundukov, D I Berman","doi":"10.18699/vjgb-26-31","DOIUrl":"https://doi.org/10.18699/vjgb-26-31","url":null,"abstract":"<p><p>The black bog ant Formica picea complex is widespread from the Atlantic to the Pacific coasts of Eurasia. This complex was earlier believed to consist of one or two species (F. picea and F. candida). However, molecular analysis suggested that it includes three cryptic species. One is F. picea from Europe, another, F. candida, is currently known exclusively from Kyrgyzstan, while the third one, temporarily designated here as Formica sp., inhabits the easternmost part of Eurasia from China to Kamchatka. It is unknown how F. picea and Formica sp. are distributed in Siberia and whether their ranges intersect. Here we studied a sample of this complex from Siberia using mtDNA and found that their ranges overlap. The distribution of Formica sp. extends from the south of West Siberia, including Altai, to China, and the Russian Far East. No phylogeographic structure was detected, suggesting their recent dispersal from a single source. F. picea was found as far as East Siberia, but was relatively rare. While the European and West Siberian populations were genetically closely related, the specimens from Zabaykalsky Krai differed, suggesting a putative East Siberian refugium. We also determined that ecologically F. picea inhabits peat bogs in lowland areas and grassy communities above the tree line in the European mountains; in Altai, it is found in mountain steppes, while in Transbaikalia, in waterlogged areas along riverbanks. Formica sp. thrives in dry steppes and low riverbanks, but avoids bogs. Thus, F. picea and Formica sp. differ genetically, and have different distribution ranges, as well as habitat preferences. This supports the opinion that Formica sp. should be recognized as a distinct species.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"274-283"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13150739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of explant type and selective agent application in the initial transformation rate of Lens culinaris Medik.","authors":"T V Dyubenko, K V Smirnov, V E Tvorogova","doi":"10.18699/vjgb-26-26","DOIUrl":"https://doi.org/10.18699/vjgb-26-26","url":null,"abstract":"<p><p>Lens culinaris Medik. (lentil) is an agronomically important leguminous species, but its genome modification is rarely used for obtaining new varieties, probably due to a low efficiency of transformation protocols. Development of universal, genotype-independent protocols for obtaining transgenic plants usually relies, among other factors, on the possibility of obtaining a substantial number of transgenic cells in vitro. This study aimed to adapt a previously developed Agrobacterium-mediated transformation protocol, used for a related legume, for the production of transgenic callus tissue in L. culinaris. We used two different markers of transgenic tissue, beta-glucuronidase and green fluorescent protein, to find an optimal type of explant for obtaining transgenic tissue in lentil. We also evaluated the impact of hygromycin, a common selective agent, on the amount of transgenic tissue in developing transformed explants of L. culinaris. According to our results, the transformation protocol commonly used for Medicago truncatula Gaertn. leaf explants can also be applied for obtaining transgenic calli from L. culinaris shoot apices. Explants from shoot apices demonstrated higher initial transformation rate in comparison with explants from roots, stems and leaves. Moreover, explants of different types, which were cultivated on medium without hygromycin, developed significantly fewer calli expressing reporter genes than those grown on hygromycin-containing medium, confirming that hygromycin may be used as an effective selection agent for lentil. During our analysis, we noticed GUS-like staining in calli which didn't contain plasmids for GUS gene expression. This can be explained with so-called intrinsic GUS-like activity, which was described in previous research. These data can be used for further development of effective and universal L. culinaris transformation and genome editing protocols.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"233-240"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13150737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selecting stable rice mutants with linear mixed models (LMM) and stability indexes.","authors":"P Sharifi, A A Ebadi, M T Hallajian, H Aminpanah","doi":"10.18699/vjgb-26-25","DOIUrl":"https://doi.org/10.18699/vjgb-26-25","url":null,"abstract":"<p><p>Mutation serves as a pivotal source of diversity in plant breeding. This study focused on identifying stable rice mutant lines. Fourteen rice mutant lines, along with four conventional cultivars, were evaluated in a randomized complete block design with three replicates across three Iranian locations (Rasht, ChaparSar, and Fars province) during two growing seasons (2015, 2016). All statistical analyses were performed using the 'metan' (multi-environment trial analysis) R package. Single-environment ANOVA indicated significant genotypic effects for all traits. Likelihood ratio tests (LRTs) confirmed significant environment and genotype-by-environment interaction (GEI) effects for all traits. The first three principal components (PCs) captured 68.13, 14.46, and 9.76 % of the GEI variation, respectively. Heatmap visualization of yield performance and WAASB (weighted average of absolute scores based on best linear unbiased prediction, BLUP) highlighted genotypes G3, G9, G6, G12, and G5 as both high-yielding and stable. Multi-trait stability index (MTSI) analysis, designed to reveal genotypic strengths and weaknesses, selected only genotypes G7, G5, and G1. The top five genotypes based on the harmonic mean of the relative performance of genotypic values (HMRPGV) were G5, G12, G7, G2, and G1. The superior performance of certain mutants demonstrates that mutation has effectively generated significant genetic diversity. Notably, genotypes G12, G5, and G9 exhibited a clear advantage over the other genotypes and warrant consideration for selection or cultivar release; however, only G5 was selected based on all traits in the MTSI index and could therefore undergo selection or cultivar introduction processes.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"222-232"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and validation of the PipeSeq program for RNA-seq data analysis in the Chlamydomonas reinhardtii as a model.","authors":"A M Nerezenko, P A Virolainen, S A Tupitsyna, E M Chekunova","doi":"10.18699/vjgb-26-34","DOIUrl":"https://doi.org/10.18699/vjgb-26-34","url":null,"abstract":"<p><p>RNA sequencing (RNA-seq) is a highly sensitive method for transcriptome analysis that allows simultaneous assessment of expression of thousands of genes and identification of expression patterns under various conditions. The existing variety of RNA-seq data formats, normalization methods, and approaches to statistical processing of results complicates comparison of data from different studies and reduces reproducibility of the analysis. This study presents an automated pipeline PipeSeq that combines standard steps of RNA-seq data processing: loading (SRA Toolkit), read alignment to the reference genome (HISAT2), transcript assembly (StringTie), transcript counting (FeatureCounts) and statistical analysis of differential gene expression under various experimental conditions (DESeq2). PipeSeq has a simple visual interface, supports multithreading, and generates ready-to-analyze gene expression heat maps, tables and graphs. The functionality of the pipeline is demonstrated on three sets of raw RNA-seq data from the green alga Chlamydomonas reinhardtii cells available in the NCBI SRA database. The data from these experiments were used to analyze the differential expression of C. reinhardtii genes encoding the GATA family transcription factors under different light cultivation conditions. The data obtained by in silico methods were verified by real-time reverse transcription polymerase chain reaction (RT-qPCR) for 12 GATA genes, which allowed us to hypothesize their functions and evaluate the correlation between the bulk (RNA-seq) and targeted (RT-qPCR) approaches. Our results showed that RNA-seq and RT-qPCR methods reveal similar directions of gene expression changes, but demonstrate differences in the effect size and sensitivity, which emphasizes the need for a combined use of the two approaches. Thus, the PipeSeq program is a tool for conducting a full cycle of bioinformatic analysis of RNA-seq data, additionally providing the opportunity to process RT-qPCR data and perform a comparative statistical analysis of the results obtained.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"299-310"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13150742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel regulatory SNPs that can be activated due to metformin treatment may orchestrate liver gluconeogenesis and add to the variability in AMPK-dependent mechanisms of metformin response.","authors":"E E Korbolina, I S Damarov, T I Merkulova","doi":"10.18699/vjgb-26-29","DOIUrl":"https://doi.org/10.18699/vjgb-26-29","url":null,"abstract":"<p><p>Metformin is a first-line therapy for type 2 diabetes, yet individual response varies significantly, with over 30 % of patients failing to achieve optimal glycemic control. The specific regulatory mechanisms of this phenomenon remain poorly understood and genetic variants involved are mainly undiscovered. There are multiple lines of evidence that the leading role in determining the variance in phenotypic outcome belongs to regulatory SNPs (rSNPs) as they directly modify gene expression. Therefore, the genome-wide search for such functional variants and deciphering associated phenotypes stands as a fundamental challenge. Previously, based on the results of bioinformatics analysis of allele-specific expression and binding landscape in human peripheral blood mononuclear cells, we have established an original panel of 14 796 rSNPs within promotors of 5132 genes. Aiming to pinpoint functional variants most likely linked to metformin hepatic response and impacts on liver gluconeogenesis, we analyzed the relevant open-access data as well as rSNPs from our panel and the corresponding genes. 1196 genes reported to be regulated by metformin in human hepatocytes and 115 genes involved in gluconeogenesis and/or its regulation via Gene Ontology annotations were intersected. Free R software and STRING v.11 tools were used for functional annotation. A number of genes harboring rSNPs within promotor regions were found to be particularly implicated in the mechanisms of metformin's action. Functional enrichment analyses revealed enrichment in critical pathways including FoxO, TNF-α and TGF-β signaling, also implicated in diabetes complications. Among these, six genes (ARPP19, ATF4, NR3C1, PFKFB3, TCF7L2, and WDR5) were strongly associated with regulation of gluconeogenesis, and may be modulated by metformin in the liver. We conclude that metformin therapy response may be influenced by the newly identified functional SNPs including rSNPs within the promotors of genes for gluconeogenic enzymes and transcription regulators.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"259-266"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Naïve human iPSCs obtained by culturing the ICGi022-A cell line with primed pluripotency in HENSM medium efficiently differentiate into endothelial derivatives.","authors":"M A Arssan, A I Shevchenko, S M Zakian, I S Zakharova","doi":"10.18699/vjgb-26-19","DOIUrl":"https://doi.org/10.18699/vjgb-26-19","url":null,"abstract":"<p><p>Naïve human pluripotent stem cells (PSCs) are a promising new tool in biomedical research. They provide access to the early embryonic development programmes and offer breakthrough solutions in regenerative medicine. However, the current inability to obtain long-term cultures of genetically and epigenetically stable naïve human PSC lines poses a challenge to their effective application in biomedicine. The recently proposed HENSM culture medium is claimed to enable the obtaining and long-term maintenance of naïve PSC lines. In this study, the potential of the HENSM medium for obtaining stable naïve human PSC lines was investigated. We successfully reset the primed induced pluripotent stem cell (iPSC) line ICGi022-A (K7-4Lf), derived from a healthy donor, to a naïve state using the HENSM medium. Naïve iPSCs grow in the form of dome-shaped colonies, both with and without a feeder layer of cells. The resulting cells retained expression of the key pluripotency factors and activated the naïve PSC transcriptional programme, including expression of endogenous retroviral elements, early epiblast marker genes and genes associated with totipotency. The naïve iPSC line was capable of differentiating into derivatives of the three primary germ layers, as well as producing trophoblast derivatives. Culturing naïve iPSCs in low-adhesion conditions resulted in the spontaneous formation of three-dimensional structures (blastoids) resembling early human blastocysts. The X chromosome, which was in an eroded inactive state in the original cell line, was reactivated in the naïve cells, but returned to its normal inactive state when the naïve cells were re-primed. Notably, naïve iPSCs demonstrated limited ability to directly differentiate into endothelial cells. However, their competence to give rise to mature endothelial derivatives was restored upon returning to the primed state, achieving comparable efficiency to the original primed iPSCs. Thus, the resulting naïve iPSC line has significant potential for studying the early stages of embryogenesis and for other biomedical applications, including disease modelling. However, the naïve ICGi022-A line proved to be karyotypically unstable during long-term cultivation using HENSM medium. As there is a risk of karyotypic aberrations during the maintenance of naïve PSCs, further improvement of the culture conditions is necessary to obtain reliable, karyotypically stable lines of naïve pluripotent cells.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"181-193"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13150740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pleiotropic genes underlying genetic correlations across human diseases.","authors":"I V Zorkoltseva, N M Belonogova, A V Kirichenko, Y A Tsepilov, T I Axenovich","doi":"10.18699/vjgb-26-28","DOIUrl":"https://doi.org/10.18699/vjgb-26-28","url":null,"abstract":"<p><p>Genetic correlation is a key characteristic of the global genetic similarity of human traits. Its primary underlying mechanism is pleiotropy, which operates at various biological levels. Gene-level pleiotropy is of particular interest, as genes are the fundamental functional units of the genome. Using publicly available results from genome-wide association studies for 324 diseases, we selected a set of 45 diseases in which every pair exhibited a significant genetic correlation. These diseases belonged to 10 nosological categories. The search for genes with pleiotropic effects was carried out using three approaches: (1) gene-based association analysis, (2) selection of single nucleotide polymorphisms (SNP) within gene coding regions significantly associated with at least two diseases, and (3) a cross-trait meta-analysis of SNP association signals followed by the identification of independent loci and gene prioritization within those loci. A comprehensive bioinformatic analysis was performed on all genes identified through these methods. We identified 167 pleiotropic genes implicated in 39 diseases. The most pleiotropic genes in our study were LPA, TCF7L2, SLC22A3, FES, CDKN2B, and APOE, which were associated with 7 to 9 diseases each. Bioinformatic analysis revealed that the pleiotropic genes identified for these 39 diseases are also involved in the genetic architecture of 501 other diseases and traits. This indicates a high degree of pleiotropy, facilitated by the involvement of these genes in diverse biological processes - including homeostasis, cell-cell signaling, regulation of cell proliferation, transport, and catalytic activity - and various molecular functions, such as signaling receptor binding. Thus, we demonstrated that 87% of diseases within a fully connected correlation network share associated genes with at least one other disease. This finding strongly suggests that genetic correlations between human diseases are largely driven by the pleiotropic effects of shared genes.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"250-258"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Concept of natural genome reconstruction. Part 4. Integration of extracellular double-stranded DNA fragments into the genome of hematopoietic stem cells and the formation of extrachromosomal intermediates.","authors":"S G Oshikhmina, V S Ruzanova, G S Ritter, E V Dolgova, S S Kirikovich, E V Levites, Y R Efremov, T V Karamysheva, A S Molodtseva, Y V Raitsina, O S Taranov, S V Sidorov, S D Nikonov, O Y Leplina, A A Ostanin, E R Chernykh, N A Kolchanov, A S Proskurina, S S Bogachev","doi":"10.18699/vjgb-26-18","DOIUrl":"https://doi.org/10.18699/vjgb-26-18","url":null,"abstract":"<p><p>To assess the possibility of integrating extracellular double-stranded DNA fragments into the recipient genome of hematopoietic stem cells, a complex substrate was constructed consisting of the entire M13F-AluI-M13R fragment and its two restrictive derivatives, appearing after hydrolysis with restriction endonucleases EcoRI and HindIII: M13F-AluI-EcoRI and M13R-AluI-HindIII. The substrate contained a pBlueScript+ plasmid polylinker sequence, absent in the human genome, which framed the human AluI fragment cloned at the EcoRV site. Human bone marrow cells were treated with the DNA of the constructed complex substrate; taking into account the repair time of pangenomic single-strand breaks, preparations of metaphase plates were obtained. FISH revealed specific fluorescent signals. Simultaneously, DNA isolated from colonies obtained from bone marrow cells treated with a complex substrate was sequenced. Two rounds of sequencing were carried out: whole-genome and selective after targeted hybridization on metal beads. The results obtained indicate that homologous exchange between extrachromosomal and chromosomal DNA is possible. Integration into the genome via the single-strand annealing mechanism, involving microhomologies, is also possible. Intermediates were discovered that suggest the existence of an unusual integration into the genome at the nick of one end of the fragment and the other end of the fragment hanging freely into the interchromosomal space. A direct assessment of the possibility of integrating TAMRA-labeled fragments of fragmented human DNA and E. coli DNA into the genome of recipient cells was carried out using a human bone marrow cell model. The results obtained indicate that specific signals of homologous DNA are distributed throughout the chromosome body (human bone marrow cell model). Signals from nonhomologous E. coli DNA are predominantly concentrated in the centromeric regions of chromosomes. The ratio of the number of obtained reads with integration elements and FISH signals suggested the existence of a strong interaction between extracellular fragments and chromosomal DNA. Experiments have been conducted showing that linear plasmid DNA, after internalization into hematopoietic stem cells, forms a monomer ring. Internalized into the intracellular space, extracellular plasmid DNA is isolated together with chromosomal DNA after stringent purification and fractionation procedures. This fact suggests the existence of a strong ring associate of plasmid DNA and chromosome DNA formed without the participation of a protein framework in the form of a looped chromosomal strand.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"30 2","pages":"163-180"},"PeriodicalIF":1.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}