Vavilovskii Zhurnal Genetiki i Selektsii最新文献

{"title":"The liver-brain axis under the influence of chronic Opisthorchis felineus infection combined with prolonged alcoholization in mice.","authors":"D F Avgustinovich, I V Chadaeva, A V Kizimenko, A V Kovner, D V Bazovkina, D V Ponomarev, V I Evseenko, V A Naprimerov, M N Lvova","doi":"10.18699/vjgb-25-11","DOIUrl":"https://doi.org/10.18699/vjgb-25-11","url":null,"abstract":"<p><p>Our purpose was to model a combination of a prolonged consumption of ethanol with Opisthorchis felineus infection in mice. Four groups of C57BL/6 mice were compiled: OF, mice infected with O. felineus for 6 months; Eth, mice consuming 20 % ethanol; Eth+OF, mice subjected to both adverse factors; and CON, control mice not exposed to these factors. In the experimental mice, especially in Eth+OF, each treatment caused well-pronounced periductal and cholangiofibrosis, proliferation of bile ducts, and enlargement of areas of inflammatory infiltration in the liver parenchyma. Simultaneously with liver disintegration, the infectious factor caused - in the frontal cerebral cortex - the growth of pericellular edema (OF mice), which was attenuated by the administration of ethanol (Eth+OF mice). Changes in the levels of some proteins (Iba1, IL-1β, IL-6, and TNF) and in mRNA expression of genes Aif1, Il1b, Il6, and Tnf were found in the hippocampus and especially in the frontal cortex, implying region-specific neuroinflammation. Behavioral testing of mice showed that ethanol consumption influenced the behavior of Eth and Eth+OF mice in the forced swimming test and their startle reflex. In the open field test, more pronounced changes were observed in OF mice. In mice of all three experimental groups, especially in OF mice, a disturbance in the sense of smell was detected (fresh peppermint leaves). The results may reflect an abnormality of regulatory mechanisms of the central nervous system as a consequence of systemic inflammation under the combined action of prolonged alcohol consumption and helminth infection.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"92-107"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721435","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":"Studying concatenation of the Cas9-cleaved transgenes using barcodes.","authors":"A V Smirnov, A N Korablev, I A Serova, A M Yunusova, A A Muravyova, E S Valeev, N R Battulin","doi":"10.18699/vjgb-25-04","DOIUrl":"https://doi.org/10.18699/vjgb-25-04","url":null,"abstract":"<p><p>In pronuclear microinjection, the Cas9 endonuclease is employed to introduce in vivo DNA double-strand breaks at the genomic target locus or within the donor vector, thereby enhancing transgene integration. The manner by which Cas9 interacts with DNA repair factors during transgene end processing and integration is a topic of considerable interest and debate. In a previous study, we developed a barcode-based genetic system for the analysis of transgene recombination following pronuclear microinjection in mice. In this approach, the plasmid library is linearized with a restriction enzyme or a Cas9 RNP complex at the site between a pair of barcodes. A pool of barcoded molecules is injected into the pronucleus, resulting in the generation of multicopy concatemers. In the present report, we compared the effects of in vivo Cas9 cleavage (RNP+ experiment) and in vitro production of Cas9- linearized transgenes (RNP- experiment) on concatenation. In the RNP+ experiment, two transgenic single-copy embryos were identified. In the RNP- experiment, six positive embryos were identified, four of which exhibited lowcopy concatemers. Next-generation sequencing (NGS) analysis of the barcodes revealed that 53 % of the barcoded ends had switched their initial library pairs, indicating the involvement of the homologous recombination pathway. Out of the 20 transgene-transgene junctions examined, 11 exhibited no mutations and were presumably generated through re-ligation of Cas9-induced blunt ends. The majority of mutated junctions harbored asymmetrical deletions of 2-4 nucleotides, which were attributed to Cas9 end trimming. These findings suggest that Cas9-bound DNA may present obstacles to concatenation. Conversely, clean DNA ends were observed to be joined in a manner similar to restriction-digested ends, albeit with distinctive asymmetry. Future experiments utilizing in vivo CRISPR/ Cas cleavage will facilitate a deeper understanding of how CRISPR-endonucleases influence DNA repair processes.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"26-34"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721899","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":"MiceDEGdb: a knowledge base on differentially expressed mouse genes as a model object in biomedical research.","authors":"O A Podkolodnaya, I V Chadaeva, S V Filonov, N L Podkolodnyy, D A Rasskazov, N N Tverdokhleb, K A Zolotareva, A G Bogomolov, E Yu Kondratyuk, D Yu Oshchepkov, M P Ponomarenko","doi":"10.18699/vjgb-25-18","DOIUrl":"https://doi.org/10.18699/vjgb-25-18","url":null,"abstract":"<p><p>The fundamental understanding of many biological processes that unfold in a human body has become possible due to experimental studies on animal models. The backbone of modern biomedical research is the use of mouse models for studying important pathophysiological mechanisms, assessing new therapeutic approaches and making decisions on acceptance or rejection of new candidate medicines in preclinical trials. The use of mice is advantageous because they have small size, are easy to keep and to genetically modify. Mice make up more than 90 % of the rodents used for pharmaceutical research. We present the pilot version of MiceDEGdb, a knowledge base on the genes that are differentially expressed in the mouse used as a model object in biomedical research. MiceDEGdb is a collection of published data on gene expression in mouse strains used for studying age-related diseases, such as hypertension, periodontal disease, bone fragility, renal fibrosis, smooth muscle remodeling, heart failure and circadian rhythm disorder. The pilot release of MiceDEGdb contains 21,754 DEGs representing 9,769 unique Mus musculus genes the transcription levels whereof were found as being changed in 25 RNA-seq experiments involving eight tissues - gum, bone, kidney, right ventricle, aortic arch, hippocampus, skeletal muscle and uterus - in six genetic mouse strains (C57BL/6J, Ren1cCre|ZsGreen, B6.129S7(Cg)-Polgtm1Prol/J, BPN/3J, BPH/2J and Kunming) used as models of eight human diseases - all these data were based on information in 10 original articles. MiceDEGdb is novel in that it features a curated annotation of changes in the expression levels of mouse DEGs using independent biomedical publications about same-direction changes in the expression levels of human homologs in patients with one disease or the other. In its pilot release, MiceDEGdb documented 85,092 such annotations for 318 human genes in 895 diseases, as suggest to 912 scientific articles referenced by their PubMed ID. The information contained in MiceDEGdb may be of interest to geneticists, molecular biologists, bioinformatics scientists, clinicians, pharmacologists and genetic advisors in personalized medicine. MiceDEGdb is freely available at https://www.sysbio.ru/MiceDEGdb.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"153-161"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721898","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":"Chickpea diversity driven by transposon insertion polymorpism.","authors":"V A Stanin, М A Duk, А A Kanapin, А A Samsonova, S Yu Surkova, М G Samsonova","doi":"10.18699/vjgb-25-08","DOIUrl":"https://doi.org/10.18699/vjgb-25-08","url":null,"abstract":"<p><p>Chickpea is the second most important legume crop, which is used as a food by people in different parts of the world due to its high nutritive value. Omics technologies have revolutionized the characterization of chickpea genetic diversity by considering single-nucleotide polymorphisms, while structural variants and transposons have been overlooked. The specific contribution of transposons to the phenotypic diversification of crop species is still poorly documented, therefore its characterization is important. We focused on landraces collected before the \"green revolution\", as they are a valuable source of species diversity and can be used to broaden the genetic base of modern cultivars. Analyzing 190 chickpea genomes, we found 42,324 new transposon insertion sites from 83 families and showed that such sites are highly polymorphic. Most insertions were caused by mobilization of retrotransposons (67 % of insertions); among DNA transposons, the highest number of insertions was found for the superfamilies MuDR, PIF, hAT, CMC, and TcMar. We also demonstrated an uneven distribution of insertion sites along chromosomes. Analysis of the localization of transposon insertion sites relative to genes and their structural elements has shown that the largest number of insertions in all transposon superfamilies falls on introns and the smallest, on exons. We also showed that transposon insertion sites, which until recently have been overlooked by population genomics, are an important factor that diversifies phenotypes and can be used in GWAS as markers replacing SNPs. Comparative analysis of landraces collected in different geographic regions showed that the Ethiopian accessions have many unique transposon insertion sites. Our results highlight the unique role of transposon mobilization in chickpea diversification and have important implications for breeding improved chickpea varieties adapted to global climate change.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"61-71"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721878","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":"Diurnal fluctuations in the content of soluble sugars and the expression of the TAI and LIN6 invertase genes and the STP1 sugar transporter gene in the leaves of the tomato (Solanum lycopersicum L.).","authors":"M A Filyushin, A V Shchennikova, E Z Kochieva","doi":"10.18699/vjgb-25-07","DOIUrl":"https://doi.org/10.18699/vjgb-25-07","url":null,"abstract":"<p><p>The content of hexoses (fructose, glucose) essential for the fruit of the tomato (Solanum lycopersicum L.) is regulated by the joint activity of sucrose hydrolysis enzymes (including invertases), invertase inhibitors, and sugar transporters. In addition to fruit taste, soluble sugars are closely related to the stress resistance of the tomato plant. In this work, we determined the diurnal dynamics of the content of soluble sugars (sucrose, fructose and glucose) and the expression of genes for sucrose hydrolysis enzymes (vacuolar invertase TAI, cell wall invertase LIN6) and the hexose transporter (STP1) in the leaves of the tomato variety Korneevsky. It was shown that both the amount of sugars and the level of transcripts of the TAI, LIN6 and STP1 genes depend on the circadian rhythm and correspond to the biological processes occurring in the plant at different periods of the day. The content of sucrose and hexoses changes in a similar way during the day. At the beginning of the light phase, the concentration of sugars is minimal, at the end it has the highest daily values; at the beginning of the dark phase, it shows a residual increase and then decreases towards the end of the phase. In silico analysis of organ-specific expression of TAI, LIN6 and STP1 in S. lycopersicum cv. Micro-Tom showed the presence of mRNA of all three genes in all tissues. The TAI gene was expressed most strongly in ripe fruits, while the level of LIN6 and STP1 transcripts was extremely low. The level of TAI mRNA in the leaves was ~2 times higher than that of LIN6 and ~27 times higher than that of STP1. Analysis using qRT-PCR of the diurnal dynamics of TAI, LIN6 and STP1 expression in the cv. Korneevsky leaves showed that all three genes were expressed at all points analyzed. Fluctuations in their expression levels occur in a similar manner: mRNA levels reach peak values in the middle of the light and dark phases. The results obtained are important for understanding the functions of invertases and sugar transporters in the tomato plant, and can be used in predicting the stress resistance of plants in tomato breeding.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"55-60"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721881","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":"Generation and characterisation of seven induced pluripotent stem cell lines from two patients with Parkinson's disease carrying the pathological variant c.1087G>T of the LGR4 gene.","authors":"V S Podvysotskaya, E V Grigor'eva, A A Malakhova, J M Minina, Y V Vyatkin, E A Khabarova, J A Rzaev, S P Medvedev, L V Kovalenko, S M Zakian","doi":"10.18699/vjgb-25-03","DOIUrl":"https://doi.org/10.18699/vjgb-25-03","url":null,"abstract":"<p><p>Parkinson's disease is a neurodegenerative disorder affecting dopaminergic neurons of the substantia nigra pars compacta. The known pathological genetic variants may explain the cause of only 5 % of cases of the disease. In our study, we found two patients with a clinical diagnosis of Parkinson's disease with the genetic variant c.1087G>T (p.Gly363Cys) of the LGR4 gene. The LGR4 gene encodes the membrane receptor LGR4 (leucine rich repeat containing G protein-coupled receptor 4) associated with the G protein. We hypothesize that the LGR4 gene may be either a direct cause or a risk factor for this disease, since it is one of the main participants of the WNT/β-catenin signalling pathway. This signalling pathway is necessary for the proliferation of neurons during their differentiation, which may lead to Parkinson's disease. To study the relationship between this genetic variant and Parkinson's disease, an ideal tool is a cellular model based on induced pluripotent stem cells (iPSCs) and their differentiated derivatives, dopaminergic neurons. We reprogrammed the peripheral blood mononuclear cells of the two patients with the c.1087G>T variant of the LGR4 gene with non-integrating episomal vectors expressing OCT4, SOX2, KLF4, LIN28, L-MYC and mp53DD proteins. The obtained seven lines of induced pluripotent stem cells were characterised in detail. The iPSCs lines obtained meet all the requirements of pluripotent cells, namely, they stably proliferate, form colonies with a morphology characteristic of human pluripotent cells, have a normal diploid karyotype, express endogenous alkaline phosphatase and pluripotency markers (OCT4, NANOG, SSEA-4 and SOX2) and are capable to differentiate into derivatives of the three germ layers. The iPSC lines obtained in this work can be used as a tool to generate a relevant model to study the effect of the pathological variant c.1087G>T of the LGR4 gene on dopaminergic neuron differentiation.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"15-25"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721894","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":"Genetic characteristics of local horse breeds by microsatellite DNA loci.","authors":"N V Blohina, L A Khrabrova","doi":"10.18699/vjgb-25-13","DOIUrl":"https://doi.org/10.18699/vjgb-25-13","url":null,"abstract":"<p><p>Russia has a significant pedigree diversity of horse breeds with unique gene pools that are well adapted to a wide variety of harsh natural and climatic conditions, are characterized by universal performance and high productive qualities, and are of significant interest to the world horse breeding. Genetic studies of population diversity in horse breeding are very relevant, since many domestic horse breeds are under threat of extinction. Biomaterials (hair, blood, semen) from horses of 15 local breeds bred in the Russian Federation and neighboring countries (CIS) were selected for the research. The sample included 2,193 horses, including: Altaiskaya (n = 48), Bashkirskaya (n = 130), Buryatskaya (n = 30), Vyatskaya (n = 220), Zabaikalskaya (n = 34), Kyrgyzskaya (n = 100), Mezenskaya (n = 148), Mugalzharskaya (n = 109), Novoaltaiskaya (n = 514), Pechorskaya (n = 31), Shetland pony (n = 47), Priobskaya (n = 85), Tuvinskaya (n = 600), Khakasskaya (n = 47) and Yakutskaya (n = 50) breeds. The following indicators were used in the genetic and population analysis: the total number of allele variants (Na) in 17 microsatellite loci, the level of polymorphism (Ae), the average number of alleles per locus (Nv), observed (Ho) and expected (He) heterozygosity, coefficients of genetic similarity and genetic distances, as well as the coefficient of intrapopulation inbreeding (Fis). Modern local horse breeds, even relatively small in number, have a high level of biodiversity and a peculiar genetic structure, often with the presence of private alleles, which persists despite periodic crossing with stud breeds of different specializations. It was found that horses of local breeds possess a number of unique alleles, including ASB2T, HMS7S, HMS6J, HMS6H, HMS2T, HMS1O, HTG7L, HTG6L, HTG6H, VHL20S, ASB17Z, ASB17X, ASB17U, LEX3S, LEX3R and CA425E, which were not detected in representatives of stud breeds in the studied European populations. The majority of the studied breeds were characterized by a negative Fis value and the absence of inbreeding. The coefficients of genetic similarity of local breeds varied in a relatively wide range (0.828-0.973) and testified to the uniqueness of the gene pools of most local horse breeds of the Russian Federation, as well as confirmed the common origin of the Kyrgyzskaya horse with the horse populations of Southern Siberia.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"113-121"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721895","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":"Interrelations between the main seed quality characteristics of narrowleaf lupine from the VIR collection.","authors":"T V Shelenga, A V Salikova, V S Popov, G P Egorova, L L Malyshev, M A Vishnyakova","doi":"10.18699/vjgb-25-05","DOIUrl":"https://doi.org/10.18699/vjgb-25-05","url":null,"abstract":"<p><p>The widespread use of narrowleaf lupine (NLL, Lupinus angustifolius L.) as a feed and food crop requires source material for breeding cultivars with high-quality seeds. The priority criterion for attributing NLL cultivars to the feed or food category is the content of alkaloids. At the same time, equally important seed quality indicators are the protein and oil content, as well as moisture content, which determines the possibility of long-term storage of seeds. For the first time in Russian lupine science, an attempt was made to study the relationships between all the listed characteristics of narrowleaf lupine seeds under the conditions of Northwest Russia (Pushkin town). Sixty-two accessions from the VIR collection were studied in 2019, 2020 and 2022. The range of variability of the studied characteristics was 27.8-37.6 % for protein, 3.9-7.3 % for oil, 1.6-2017.4 mg/100 g of dry matter (D.M.) for alkaloids, and 6.4-7.3 % for moisture. A significant negative correlation between the oil and protein content (-0.33) was observed only in 2019. No significant correlations between the protein and alkaloid content were found in the studied sample. Significant negative relationships were identified between the content of oil and alkaloids only in 2019 and 2020 (-0.38 and -0.27, respectively). In 2022, no correlations were identified. Obviously, the identification of regularities in these correlations requires many years of research taking into account weather conditions. The influence of weather on the concentration of alkaloids in seeds has been proven. The average amount of alkaloids for the sample in 2019 was 504.2 ± 77.7 mg/100 g D.M., 263.7 ± 38.6 mg/100 g D.M. in 2020, and 319.8 ± 51.4 mg/100 g D.M. in 2022. It confirmed the data previously obtained by the authors that the content of alkaloids in seeds increases significantly along with the precipitation deficiency. The temperature regime during this research did not affect this indicator. An increased air temperature contributed to the accumulation of oil, and an increase in precipitation contributed to the accumulation of protein. The most stable indicator independent of environmental conditions was the seed moisture. Accessions with the optimal combination of the main biochemical parameters that determine seed quality have been identified for breeding narrowleaf lupine cultivars in the region in question for feed and food purposes, as well as for green manure.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"35-43"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721897","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":"Orthoweb: a software package for evolutionary analysis of gene networks.","authors":"R A Ivanov, A M Mukhin, F V Kazantsev, Z S Mustafin, D A Afonnikov, Y G Matushkin, S A Lashin","doi":"10.18699/vjgb-24-95","DOIUrl":"https://doi.org/10.18699/vjgb-24-95","url":null,"abstract":"<p><p>This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (Ka/Ks) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene's emergence (and thus indirectly the approximate time of its origin, known as \"evolutionary age\") to be assessed based on the analysis of orthologous genes across closely and distantly related taxa. Additionally, Orthoweb supports the calculation of the transcriptome age index (TAI) and the transcriptome divergence index (TDI). These indices are important for understanding the dynamics of gene expression and its impact on the development and adaptation of organisms. Orthoweb also includes optional analytical features, such as the ability to explore Gene Ontology (GO) terms associated with genes, facilitating functional enrichment analyses that link evolutionary origins of genes to biological processes. Furthermore, it offers tools for SNP enrichment analysis, enabling the users to assess the evolutionary significance of genetic variants within specific genomic regions. A key feature of Orthoweb is its ability to integrate these indices with gene network analysis. The software offers advanced visualization tools, such as gene network mapping and graphical representations of phylostratigraphic index distributions of network elements, ensuring intuitive interpretation of complex evolutionary relationships. To further streamline research workflows, Orthoweb includes a database of pre-calculated indices for numerous taxa, accessible via an application programming interface (API). This feature allows the users to retrieve pre-computed phylostratigraphic and divergence data efficiently, significantly reducing computational time and effort.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"874-881"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411013","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":"Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods.","authors":"E A Antropova, A R Volyanskaya, A V Adamovskaya, P S Demenkov, I V Yatsyk, T V Ivanisenko, Y L Orlov, Ch Haoyu, M Chen, V A Ivanisenko","doi":"10.18699/vjgb-24-103","DOIUrl":"https://doi.org/10.18699/vjgb-24-103","url":null,"abstract":"<p><p>Although nitrogen fertilizers increase rice yield, their excess can impair plant resistance to diseases, particularly sheath blight caused by Rhizoctonia solani. This pathogen can destroy up to 50 % of the crop, but the mechanisms underlying reduced resistance under excess nitrogen remain poorly understood. This study aims to identify potential marker genes to enhance rice resistance to R. solani under excess nitrogen conditions. A comprehensive bioinformatics approach was applied, including differential gene expression analysis, gene network reconstruction, biological process overrepresentation analysis, phylostratigraphic analysis, and non-coding RNA co-expression analysis. The Smart crop cognitive system, ANDSystem, the ncPlantDB database, and other bioinformatics resources were used. Analysis of the molecular genetic interaction network revealed three potential mechanisms explaining reduced resistance of rice to R. solani under excess nitrogen: the OsGSK2-mediated pathway, the OsMYB44-OsWRKY6-OsPR1 pathway, and the SOG1-Rad51-PR1/PR2 pathway. Potential markers for breeding were identified: 7 genes controlling rice responses to various stresses and 11 genes modulating the immune system. Special attention was given to key participants in regulatory pathways under excess nitrogen conditions. Non-coding RNA analysis revealed 30 miRNAs targeting genes of the reconstructed gene network. For two miRNAs (Osa-miR396 and Osa-miR7695), about 7,400 unique long non-coding RNAs (lncRNAs) with various co-expression indices were found. The top 50 lncRNAs with the highest co-expression index for each miRNA were highlighted, opening new perspectives for studying regulatory mechanisms of rice resistance to pathogens. The results provide a theoretical basis for experimental work on creating new rice varieties with increased pathogen resistance under excessive nitrogen nutrition. This study opens prospects for developing innovative strategies in rice breeding aimed at optimizing the balance between yield and disease resistance in modern agrotechnical conditions.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"960-973"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143410466","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}