Russian Journal of Genetics最新文献_第5页

Genomic Microsatellite Mining and Characteristic Analysis of Gobiidae Fish 戈壁鱼基因组微卫星挖掘与特征分析

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700224

S. Ma, N. Song

{"title":"Genomic Microsatellite Mining and Characteristic Analysis of Gobiidae Fish","authors":"S. Ma, N. Song","doi":"10.1134/s1022795424700224","DOIUrl":"https://doi.org/10.1134/s1022795424700224","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3>Microsatellites or single sequence repeats (SSRs) are widespread in the genome of eukaryotes and prokaryotes, and are usually used for studying genetic diversity and constructing the genetic map. The distribution characteristics and effective markers of microsatellites in the Gobiidae family were still unclearly. In this study, genomes of 16 Gobiidae fish were downloaded from the National Center for Biotechnology Information (NCBI) and Ensembl Genomes databases which were analyzed by bioinformatics. The content of microsatellites for Gobiidae fish occurred differently and the coverage degree varied from 0.12 to 2.36%. The total number of microsatellites ranged from 288 730 to 846 829 and the total sequence length ranged from 515 577 to 1 561 092. The mononucleotide repeats were the most common types in the microsatellites for 13 Gobiidae fish, but dinucleotide repeats were most common for Acanthogobius ommaturus, Chaenogobius annularis and Eucyclogobius newberryi. Moreover, the frequency of microsatellite motifs varied in Gobiidae fish. Within the dinucleotide repeats, the AC/GT was the most abundant microsatellite of 13 Gobiidae fish, while the most dinucleotide repeat was AG/CT of Lythrypnus dalli, Lesueurigobius sanzi and Rhinogobius similis. Our study suggested that the distribution and characteristics of microsatellites are various in these Gobiidae genomes, which may be related to the genome diversity of Gobiidae. The data could not only provide new insights into the studies of genetic evolution but also provide powerful support for the development of more microsatellites of Gobiidae.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"23 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141514244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosomal Polymorphism of Malaria Mosquitoes of Karelia and Expansion of Northern Boundaries of Species Ranges 卡累利阿疟疾蚊子的染色体多态性和物种分布区北部边界的扩展

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700194

A. V. Moskaev, A. G. Bega, V. I. Panov, V. P. Perevozkin, M. I. Gordeev

{"title":"Chromosomal Polymorphism of Malaria Mosquitoes of Karelia and Expansion of Northern Boundaries of Species Ranges","authors":"A. V. Moskaev, A. G. Bega, V. I. Panov, V. P. Perevozkin, M. I. Gordeev","doi":"10.1134/s1022795424700194","DOIUrl":"https://doi.org/10.1134/s1022795424700194","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3>Chromosomal variability in peripheral populations of malaria mosquitoes of the Anopheles genus (Diptera, Culicidae) inhabiting the territory of Karelia has been studied. The modern northern limits of the ranges inhabited by sibling species of malarial mosquitoes An. beklemishevi, An. daciae, An. messeae s. s. and An. maculipennis were established. After 2010, the boundary of distribution of malaria mosquitoes shifted northward by 170 km, from the 65th parallel to the Arctic Circle. Inversion heterozygotes XL1, XL2, 2R2, 3R1, and 3R5 were found in peripheral populations of An. beklemishevi. Peripheral populations of An. messeae s. s. were homozygous for inversion of sex chromosome XL1 and differed in the frequencies of autosome inversions from the middle taiga populations. The frequency of heterozygotes for autosomal inversions 2R1, 3R1, and 3L1 increased in populations at the edge of the species range. Chromosomal variability in peripheral populations contributes to the dispersal of malaria mosquitoes in high latitudes under warming climate conditions.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"26 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141514351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of miRNA-Target Gene-Transcription Factor Regulatory Network as Functional Motifs Involved in Glomerular Diabetic Nephropathy 鉴定参与肾小球糖尿病肾病的 miRNA-靶基因-转录因子调控网络功能基因

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700261

Gh. Nuoroozi, E. Zareie, M. Yarizadeh, P. Ghadermarzi, H. Zali, Z. Molavi

{"title":"Identification of miRNA-Target Gene-Transcription Factor Regulatory Network as Functional Motifs Involved in Glomerular Diabetic Nephropathy","authors":"Gh. Nuoroozi, E. Zareie, M. Yarizadeh, P. Ghadermarzi, H. Zali, Z. Molavi","doi":"10.1134/s1022795424700261","DOIUrl":"https://doi.org/10.1134/s1022795424700261","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3>The gene regulatory approach based on retrieving information from the database provides a detailed characterization of the molecular mechanisms of disease progression at the level of miRNAs, Transcription Factors (TFs), and genes. Moreover, gene regulatory networks can find an interaction between the miRNAs, TFs, and genes involved in diabetic nephropathy (DN), but the underlying mechanisms of motif remain unclear. We first gathered genes related to glomeruli diabetic nephropathy from GEO and CTD database. Besides, miRNAs targeting genes were collected from the public databases and GEO. Furthermore, regulator TFs were accumulated from related public databases. After that, we explored the regulatory relationships between TF-miRNA, miRNA-Gene, TF-Gene, and miRNA–TF using FANMOD software. Finally, a gene regulatory network consisting of miRNAs, genes, and TFs was constructed, helping the Cytoscape. The global const parameter in FANMOD software used to discover the interaction between miRNAs, genes, TFs, and 3-node regulatory motif types were detected in the resulting network. Among them, it led to the discovery of the two-node feedback motif (2FB) in charge of the up-regulation of miRNA-target gene-TF and TF-mediated cascade motif and co-pointing motif (COP) responsible for the down-regulation of miRNA-target gene–TF. In this study, we found a correlation between miRNAs, TFs, and target genes using a gene regulatory network. We revealed the candidate 3-node motifs associated with the progression of DN. Therefore, detected molecular mechanisms, as well as the relationship between previous studies, demonstrated targets that can help in the discovery of a novel treatment for DN.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"63 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141514348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Novel Frameshift Variant of the MYBPC3 Gene Associated with Hypertrophic Cardiomyopathy Significantly Decreases the Level of This Gene Transcript in the Myocardium 与肥厚型心肌病有关的新型 MYBPC3 基因帧移位变异会显著降低该基因在心肌中的转录水平

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s102279542470025x

I. S. Kiselev, M. S. Kozin, N. M. Baulina, M. B. Sharipova, A. S. Zotov, E. A. Stepanova, E. V. Kurilina, G. Zh. Abdullaeva, D. A. Zateyshchikov, O. O. Favorova, O. S. Chumakova

{"title":"The Novel Frameshift Variant of the MYBPC3 Gene Associated with Hypertrophic Cardiomyopathy Significantly Decreases the Level of This Gene Transcript in the Myocardium","authors":"I. S. Kiselev, M. S. Kozin, N. M. Baulina, M. B. Sharipova, A. S. Zotov, E. A. Stepanova, E. V. Kurilina, G. Zh. Abdullaeva, D. A. Zateyshchikov, O. O. Favorova, O. S. Chumakova","doi":"10.1134/s102279542470025x","DOIUrl":"https://doi.org/10.1134/s102279542470025x","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000Abstract—</h3>Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease with a prevalence of 1 : 200–1 : 500 in the general population. Most HCM-linked pathogenic (or likely pathogenic) variants are located in eight genes encoding proteins of sarcomere, the main contractile unit of cardiomyocytes, primarily in MYBPC3; MYBPC3 variants are usually associated with a relatively benign clinical course of the disease. Here, we describe a novel frameshift heterozygous variant NM_000256.3:c.2781_2782insCACA of the MYBPC3 gene, which causes familial HCM. The proband had a progressive heart failure despite the surgical removal of left ventricular tract obstruction. Evaluation of levels of transcripts produced from the mutant allele and wild-type allele of the MYBPC3 gene in proband myocardial tissue and comparison of their total levels with those in the control samples from patients without HCM showed a significant allele-specific reduction of mutant transcript levels. Our results expand the spectrum of known genetic variants with a proven role in the development of HCM.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"159 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141514247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamic of the B Chromosome System in the Population of the Korean Field Mouse Apodemus peninsulae (Mammalia, Rodentia) in the Northern Region of the Pritelets Taiga of the Altai Mountains over a 36-Year Period 阿尔泰山普里特列茨泰加北部地区朝鲜田鼠（哺乳纲，啮齿目）种群 B 染色体系统在 36 年间的动态变化

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700169

I. A. Zhigarev, Yu. M. Borisov

{"title":"Dynamic of the B Chromosome System in the Population of the Korean Field Mouse Apodemus peninsulae (Mammalia, Rodentia) in the Northern Region of the Pritelets Taiga of the Altai Mountains over a 36-Year Period","authors":"I. A. Zhigarev, Yu. M. Borisov","doi":"10.1134/s1022795424700169","DOIUrl":"https://doi.org/10.1134/s1022795424700169","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000Abstract—</h3>The process of changes in the number and morphology of B chromosomes in the populations of mice (Apodemus peninsulae) in the northern region of the Pritelets taiga of the Altai Mountains over a 36-year period (1978‒2014) was traced. Three time phases were distinguished. From 1978 to 2002 (24 years)—a phase of steady growth of the number of B chromosomes, with a relatively uniform average increase of 1.4 chromosomes per decade (from 3.17 ± 0.2 to 6.5 ± 0.54); the phase of stabilization of the indicator when it consistently ranged between 6.3 and 6.9 (2002–2012), although the indicator was at least doubled compared to early 1980s (differences are significant); and the third period (2012‒2014) of the emerging trend of decrease in the number of supplementary chromosomes (differences are also significant). The change in the conditional mass index of B chromosomes (mB) also had similar dynamics, and it was at its maximum for the species during the period of stabilization. The dynamics of different morphotypes of B chromosomes showed an unequal contribution to the overall dynamics. The main contribution was made by large, medium-sized, and small metacentric B chromosomes. Micro-B chromosomes and acrocentrics were absent in the growth phase and appeared in the stabilization phase at the maximum of other indicators.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"41 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141549101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Paleo-Siberian Substrate in the Gene Pool of Koryaks according to Data on Autosomal SNP Polymorphism and Y-Chromosome Haplogroups 根据常染色体 SNP 多态性和 Y 染色体单倍群数据确定高黎贡人基因库中的古西伯利亚基质

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700236

V. N. Kharkov, N. A. Kolesnikov, A. A. Zarubin, L. V. Valikhova, I. Yu. Khitrinskaya, M. I. Voevoda, M. A. Gubina, A. L. Sukhomyasova, V. A. Stepanov

{"title":"Paleo-Siberian Substrate in the Gene Pool of Koryaks according to Data on Autosomal SNP Polymorphism and Y-Chromosome Haplogroups","authors":"V. N. Kharkov, N. A. Kolesnikov, A. A. Zarubin, L. V. Valikhova, I. Yu. Khitrinskaya, M. I. Voevoda, M. A. Gubina, A. L. Sukhomyasova, V. A. Stepanov","doi":"10.1134/s1022795424700236","DOIUrl":"https://doi.org/10.1134/s1022795424700236","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000Abstract—</h3>The gene pool of the Koryaks was studied in comparison with other Far Eastern and Siberian peoples using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y-chromosome markers. The results of analyzing the frequencies of autosomal SNPs using various methods, the similarity in the composition of Y-chromosome haplogroups and YSTR haplotypes indicate that the gene pool of the Koryaks is as close as possible to the Chukchi one and was formed as a result of the unification of several groups whose ancestors had moved from the territory of modern Yakutia and the Amur region. The two dominant Y-chromosome haplogroups of the Koryaks with different sublines of haplotype clusters demonstrate their contacts with the Chukchi, Evens, Yukaghirs, and Eskimos. Analysis of the composition of genetic components and IBD blocks on autosomes indicates the maximum genetic proximity of the Koryaks to the Chukchi. Among the Siberian populations, the Chukchi, Koryaks, and Nivkhs form a cluster separate from the main group of Siberian populations, while the Chukchi and Koryaks are more closely related. Far Eastern populations are divided in full accordance with geographic localization into the northern group (Chukchi and Koryaks) and the southern group, including the Nivkhs and Udege. A more detailed analysis of the component composition of gene pools in some populations reveals components specific to them. The isolation of such components is associated with founder effects and a shift in allele frequencies for these populations. The Koryaks and Chukchi represent one of the most striking examples of long-standing genetic kinship. Their populations demonstrate maximum values of the level of genomic inbreeding FROH > 1.5 (0.0422, 0.0409), which is natural due to their relative isolation.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"11 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141514245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic Identification of Putative Hybrids between Grey Wolf and Golden Jackal 灰狼和金豺假定杂交种的遗传鉴定

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700200

P. A. Kazimirov, Yu. S. Belokon’, M. M. Belokon’, A. S. Mishin, V. V. Stakheev, Yu. A. Yarovenko, A. Yu. Yarovenko, D. V. Politov

{"title":"Genetic Identification of Putative Hybrids between Grey Wolf and Golden Jackal","authors":"P. A. Kazimirov, Yu. S. Belokon’, M. M. Belokon’, A. S. Mishin, V. V. Stakheev, Yu. A. Yarovenko, A. Yu. Yarovenko, D. V. Politov","doi":"10.1134/s1022795424700200","DOIUrl":"https://doi.org/10.1134/s1022795424700200","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000Abstract—</h3>We describe the results of genetic analysis of 11 phenotypically deviant individuals of grey wolf Canis lupus Linnaeus, 1758 sensu lato, collected in Voronezh State Nature Biosphere Reserve (Chernozem zone of European Russia) and Dagestan (North Caucasus, Russia), putatively identified morphologically as hybrids between grey wolf and golden jackal (Canis aureus Linnaeus, 1758). Using maternally inherited mtDNA (sequences of cytochrome b gene fragment) and paternal lineage markers Y chromosome fragments ZfY, no wolf–jackal hybrids of the first generation were identified; the possibility that the studied individuals belonged to hybrids between different F1 wolf and jackal individuals of subsequent generations is also excluded. However, it is possible that morphologically atypical individuals belong to complex hybrids, for example, various backcrosses. According to the results of analysis of a set of autosomal microsatellite loci, we putatively diagnosed a single F2 hybrid. In addition, we obtained data that can be considered as traces of hybridization in several specimens. Our results suggest the presence of a gene flow between wolf and jackal in southern regions of European Russia, albeit direct indications of introgression between these species were not found. At the same time, the results of both genetic and craniological studies could be interpreted as indication to hybridization between wolves and domestic dogs on the same territories.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"5 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141514352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessing the Genetic Diversity of Five Cattle Breeds Using SNP Markers Associated with Health 利用与健康相关的 SNP 标记评估五个牛种的遗传多样性

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700182

M. V. Bytov, V. D. Zubareva, S. V. Volskaya, A. G. Isaeva, D. Yu. Nokhrin, Yu. A. Osipova, O. V. Sokolova

引用次数: 0

Analysis of the Effectiveness of CRISPR/Cas9-Editing of the GEX2 Gene by Ribonucleoprotein Complexes in Maize Protoplasts 玉米原生质体中核糖核蛋白复合物对 GEX2 基因的 CRISPR/Cas9 编辑效果分析

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-06-19 DOI: 10.1134/s1022795424700285

E. M. Moiseeva, V. V. Fadeev, Yu. V. Fadeeva, Yu. S. Gusev, M. I. Chumakov

引用次数: 0

Genome-Wide Identification and Comparative Analysis of Elongation of Very Long-Chain Fatty Acid (Elovl) Genes in Echinoderms 棘皮动物超长链脂肪酸（Elovl）伸长基因的全基因组鉴定与比较分析

IF 0.6 4区生物学

Russian Journal of Genetics Pub Date : 2024-05-03 DOI: 10.1134/s1022795424040070

M.-Y. Liu, Q.-C. Wang, J.-Q. Li, D. Zhang, J.-H. Mu, X.-H. Shen

{"title":"Genome-Wide Identification and Comparative Analysis of Elongation of Very Long-Chain Fatty Acid (Elovl) Genes in Echinoderms","authors":"M.-Y. Liu, Q.-C. Wang, J.-Q. Li, D. Zhang, J.-H. Mu, X.-H. Shen","doi":"10.1134/s1022795424040070","DOIUrl":"https://doi.org/10.1134/s1022795424040070","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3>Elongation of very long-chain fatty acid (Elovl) proteins is the critical rate-limiting enzyme that catalyzes the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs). Echinoderms are extremely important research objects in various fields, such as regeneration studies and developmental biology. However, to date, the genome-wide characterization and analysis of Elovl genes in echinoderms have not been investigated. In this study, the identification and analysis of Elovl genes in 10 representative echinoderms were performed using bioinformatics methods. A total of 117 Elovl genes have been found in the studied echinoderms. The phylogenetic tree showed that all Elovl genes from echinoderms can be subdivided into 6 classes, Elovl3-like class, Elovl4-like class, Elovl5-like class, Elovl6-like class, Elovl7-like class, and Elovl8-like class. Furthermore, the selection pressure analysis suggested that Elovl genes in echinoderms were mainly constrained by strong purifying selection events. In general, this study provides a molecular basis for echinoderm Elovl genes and may serve as a reference for in-depth phylogenomics.","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"194 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140888600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0