Pub Date : 2024-06-19DOI: 10.1134/s1022795424700224
S. Ma, N. Song
Abstract
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.
{"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><p>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 <i>Acanthogobius ommaturus</i>, <i>Chaenogobius annularis</i> and <i>Eucyclogobius newberryi</i>. 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 <i>Lythrypnus dalli</i>, <i>Lesueurigobius sanzi</i> and <i>Rhinogobius similis</i>. 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.</p>","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}
Pub Date : 2024-06-19DOI: 10.1134/s1022795424700194
A. V. Moskaev, A. G. Bega, V. I. Panov, V. P. Perevozkin, M. I. Gordeev
Abstract
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.
摘要 对栖息在卡累利阿境内的按蚊属（双翅目，库蚊科）疟疾蚊子外围种群的染色体变异性进行了研究。研究确定了疟蚊同胞种 An. beklemishevi、An. daciae、An. messeae s. s. 和 An. maculipennis 居住范围的现代北部界限。2010 年后，疟蚊的分布边界向北移动了 170 公里，从北纬 65 度线移至北极圈。在贝克勒米舍维蚊（An. beklemishevi）的外围种群中发现了反转杂合子 XL1、XL2、2R2、3R1 和 3R5。介壳虫外围种群的性染色体 XL1 为同源染色体倒位，其自体染色体倒位的频率与泰加中部种群不同。在物种分布区边缘的种群中，常染色体倒位 2R1、3R1 和 3L1 的杂合子频率有所增加。在气候变暖的条件下，边缘种群的染色体变异有助于疟蚊在高纬度地区的扩散。
{"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><p>Chromosomal variability in peripheral populations of malaria mosquitoes of the <i>Anopheles</i> 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 <i>An. beklemishevi</i>, <i>An. daciae</i>, <i>An. messeae</i> s. s. and <i>An. maculipennis</i> 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 XL<sub>1</sub>, XL<sub>2</sub>, 2R<sub>2</sub>, 3R<sub>1</sub>, and 3R<sub>5</sub> were found in peripheral populations of <i>An. beklemishevi</i>. Peripheral populations of <i>An. messeae</i> s. s. were homozygous for inversion of sex chromosome XL<sub>1</sub> and differed in the frequencies of autosome inversions from the middle taiga populations. The frequency of heterozygotes for autosomal inversions 2R<sub>1</sub>, 3R<sub>1</sub>, and 3L<sub>1</sub> 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.</p>","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}
Pub Date : 2024-06-19DOI: 10.1134/s1022795424700261
Gh. Nuoroozi, E. Zareie, M. Yarizadeh, P. Ghadermarzi, H. Zali, Z. Molavi
Abstract
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.
{"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><p>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.</p>","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}
Pub Date : 2024-06-19DOI: 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
Abstract—
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.
{"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\">\u0000<b>Abstract</b>—</h3><p>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 <i>MYBPC3</i>; <i>MYBPC3</i> 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 <i>MYBPC3</i> 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 <i>MYBPC3</i> 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.</p>","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}
Pub Date : 2024-06-19DOI: 10.1134/s1022795424700169
I. A. Zhigarev, Yu. M. Borisov
Abstract—
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.
摘要 追踪了阿尔泰山普里特列茨泰加北部地区小鼠（Apodemus peninsulae）种群的B染色体数量和形态在36年间（1978-2014年）的变化过程。研究分为三个时间阶段。从 1978 年到 2002 年（24 年）--B 染色体数量稳定增长阶段，每十年平均增加 1.4 条染色体（从 3.17 ± 0.2 到 6.5 ± 0.54），相对均匀；指标稳定阶段，指标持续在 6.3 到 6.9 之间（2002-2012 年）。3和6.9之间（2002-2012年），尽管该指标与20世纪80年代初相比至少翻了一番（差异显著）；第三个阶段（2012-2014年），补充染色体数量呈下降趋势（差异也显著）。B 染色体的条件质量指数（mB）的变化也有类似的动态变化，在稳定期达到该物种的最大值。不同形态的 B 染色体的动态变化对总体动态变化的影响不均等。主要是大型、中型和小型偏心 B 染色体。微型 B 染色体和尖头 B 染色体在生长阶段不存在，而在稳定阶段出现，并达到其他指标的最大值。
{"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\">\u0000<b>Abstract</b>—</h3><p>The process of changes in the number and morphology of B chromosomes in the populations of mice (<i>Apodemus peninsulae</i>) 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 (<i>mB</i>) 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.</p>","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}
Pub Date : 2024-06-19DOI: 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
Abstract—
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.
摘要 利用全基因组的常染色体单核苷酸多态性标记和 Y 染色体标记，将科里亚克人的基因库与其他远东和西伯利亚民族进行了比较研究。使用各种方法分析常染色体 SNPs 频率、Y 染色体单倍群和 YSTR 单倍型组成的相似性的结果表明，科里亚克人的基因库尽可能接近楚科奇人的基因库，是由祖先从现代雅库特和阿穆尔地区迁来的几个群体统一形成的。科里亚克人的两个主要 Y 染色体单倍群具有不同的单倍群亚系，这表明他们与楚科奇人、伊文思人、尤卡吉尔人和爱斯基摩人有接触。对常染色体上的遗传成分和 IBD 块组成的分析表明，科里亚克人与楚科奇人在遗传上最为接近。在西伯利亚人群中，楚科奇人、科里亚克人和尼夫赫人形成了一个独立于西伯利亚人群主群的群落，而楚科奇人和科里亚克人的关系更为密切。远东人群完全按照地理定位分为北方人群（楚科奇人和科里亚克人）和南方人群（包括尼夫赫人和乌代格人）。对某些种群的基因库成分进行更详细的分析后，发现了这些种群特有的成分。这些成分的分离与这些种群的始祖效应和等位基因频率的变化有关。科里亚克人和楚科奇人是长期遗传亲缘关系最显著的例子之一。它们的种群显示了基因组近亲繁殖水平的最大值 FROH > 1.5 (0.0422, 0.0409)，这是由于它们的相对隔离而自然形成的。
{"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\">\u0000<b>Abstract</b>—</h3><p>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.</p>","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}
Pub Date : 2024-06-19DOI: 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
Abstract—
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.
摘要--我们描述了在沃罗涅日国家自然生物圈保护区（俄罗斯欧洲切尔诺泽姆地区）和达吉斯坦（俄罗斯北高加索地区）采集的 11 头表型异常的灰狼（Canis lupeus Linnaeus, 1758 sensu lato）个体的遗传分析结果，这些个体从形态上被认为是灰狼和金豺（Canis aureus Linnaeus, 1758）的杂交种。利用母系遗传的 mtDNA（细胞色素 b 基因片段序列）和父系标记 Y 染色体片段 ZfY，没有鉴定出第一代狼-豺杂交种；也排除了研究个体属于不同 F1 狼和豺个体之间的后代杂交种的可能性。然而，形态上不典型的个体有可能属于复杂的杂交种，例如各种回交。根据一组常染色体微卫星位点的分析结果，我们推断出了一个单一的 F2 杂交种。此外，我们还获得了一些数据，这些数据可被视为几个标本中的杂交痕迹。我们的研究结果表明，在俄罗斯欧洲南部地区，狼和豺之间存在基因流，尽管没有发现这两个物种之间的直接引种迹象。同时，遗传学和颅骨学研究的结果也可以解释为狼和家犬在同一地区杂交的迹象。
{"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\">\u0000<b>Abstract</b>—</h3><p>We describe the results of genetic analysis of 11 phenotypically deviant individuals of grey wolf <i>Canis lupus</i> 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 (<i>Canis aureus</i> Linnaeus, 1758). Using maternally inherited mtDNA (sequences of cytochrome <i>b</i> gene fragment) and paternal lineage markers Y chromosome fragments <i>ZfY,</i> 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.</p>","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}
Pub Date : 2024-06-19DOI: 10.1134/s1022795424700182
M. V. Bytov, V. D. Zubareva, S. V. Volskaya, A. G. Isaeva, D. Yu. Nokhrin, Yu. A. Osipova, O. V. Sokolova
Abstract
Currently genetic evaluation of animals is an important part of the development of the agricultural complex. The improvement of molecular technologies every year makes it possible to carry out genetic research aimed at finding the most valuable animals in a cheaper and faster way. Indigenous breeds of cattle are an attractive object for such research because they have greater adaptive potential and resistance to diseases. However, modern comparative data on the genetic diversity of most local breeds based on SNP markers associated with health are lacking. Genetic association tests using these genetic markers for the Tagil, Sychev, Suksun and Istoben breeds are still to be carried out. The purpose of this work was to compare the genetic diversity of five cattle breeds using SNP markers associated with the development of ketosis, mastitis and productive longevity.
摘要目前，动物遗传评估是农业综合体发展的重要组成部分。随着分子技术的逐年提高，人们有可能以更便宜、更快捷的方式开展遗传研究，以找到最有价值的动物。本地牛种是此类研究的一个有吸引力的对象，因为它们具有更大的适应潜力和抗病能力。然而，目前还缺乏基于与健康相关的 SNP 标记的大多数地方品种遗传多样性的现代比较数据。使用这些遗传标记对塔吉尔、西切夫、苏克松和伊斯托本品种进行的遗传关联测试仍有待进行。这项工作的目的是利用与酮病发展、乳腺炎和生产寿命相关的 SNP 标记，比较五个牛种的遗传多样性。
{"title":"Assessing the Genetic Diversity of Five Cattle Breeds Using SNP Markers Associated with Health","authors":"M. V. Bytov, V. D. Zubareva, S. V. Volskaya, A. G. Isaeva, D. Yu. Nokhrin, Yu. A. Osipova, O. V. Sokolova","doi":"10.1134/s1022795424700182","DOIUrl":"https://doi.org/10.1134/s1022795424700182","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Currently genetic evaluation of animals is an important part of the development of the agricultural complex. The improvement of molecular technologies every year makes it possible to carry out genetic research aimed at finding the most valuable animals in a cheaper and faster way. Indigenous breeds of cattle are an attractive object for such research because they have greater adaptive potential and resistance to diseases. However, modern comparative data on the genetic diversity of most local breeds based on SNP markers associated with health are lacking. Genetic association tests using these genetic markers for the Tagil, Sychev, Suksun and Istoben breeds are still to be carried out. The purpose of this work was to compare the genetic diversity of five cattle breeds using SNP markers associated with the development of ketosis, mastitis and productive longevity.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"4 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141549102","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}
Pub Date : 2024-06-19DOI: 10.1134/s1022795424700285
E. M. Moiseeva, V. V. Fadeev, Yu. V. Fadeeva, Yu. S. Gusev, M. I. Chumakov
Abstract—
The GEX2 protein is expressed in the maize gamete membranes and is necessary during fertilization at the stage of contact (adhesion) of gamete membranes. Knockout of GEX2 gene can presumably lead to impaired fertilization and, as a result, to the formation of matroclinic haploid maize embryos. The purpose of this study is to analyze the efficiency of CRISPR/Cas9 editing of the GEX2 gene after PEG-mediated transfection of maize protoplasts by ribonucleoprotein (RNP) complexes with different gRNAs. For the first time, constructs for CRISPR/Cas9 editing of the maize GEX2 gene have been created, the effectiveness of which has been proven on protoplasts and reaches 10.7%, depending on the selected gRNA and the ratio and number of components in the RNP complexes.
{"title":"Analysis of the Effectiveness of CRISPR/Cas9-Editing of the GEX2 Gene by Ribonucleoprotein Complexes in Maize Protoplasts","authors":"E. M. Moiseeva, V. V. Fadeev, Yu. V. Fadeeva, Yu. S. Gusev, M. I. Chumakov","doi":"10.1134/s1022795424700285","DOIUrl":"https://doi.org/10.1134/s1022795424700285","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000<b>Abstract</b>—</h3><p>The GEX2 protein is expressed in the maize gamete membranes and is necessary during fertilization at the stage of contact (adhesion) of gamete membranes. Knockout of <i>GEX2</i> gene can presumably lead to impaired fertilization and, as a result, to the formation of matroclinic haploid maize embryos. The purpose of this study is to analyze the efficiency of CRISPR/Cas9 editing of the <i>GEX2</i> gene after PEG-mediated transfection of maize protoplasts by ribonucleoprotein (RNP) complexes with different gRNAs. For the first time, constructs for CRISPR/Cas9 editing of the maize <i>GEX2</i> gene have been created, the effectiveness of which has been proven on protoplasts and reaches 10.7%, depending on the selected gRNA and the ratio and number of components in the RNP complexes.</p>","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":"141514350","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}
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.
{"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><p>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.</p>","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}
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