Pub Date : 2024-07-27DOI: 10.1134/s1022795424700339
L. N. Spiridonova, O. P. Valchuk, Ya. A. Red’kin
Abstract—
Sequencing of a partial fragment of the mitochondrial ND5–cytb genes (1553 bp) and its nuclear copies in Phylloscopus borealis sensu lato (s.l.) individuals, belonging to different taxonomic groups from different parts of the range was carried out. The identity of the majority of taxon-specific and unique mitochondrial substitutions in examinandus and xanthodryas forms to those in nuclear copies of borealis mtDNA was demonstrated. Differences between the examinandus mitochondrial haplotypes and nuclear copies of borealis mtDNA were low (P = 0.02), and the genetic divergence in borealis–examinandus, borealis–xanthodryas, and examinandus–xanthodryas mtDNA itself considerably exceeded these values (P = 0.035, 0.044, and 0.046, respectively). For the first time, nuclear copy of the mitochondrial haplotype of the easternmost xanthodryas form was found in nuclear genome of one borealis individual from the western part of the breeding range (Komi Republic), and nuclear copies of xanthodryas mtDNA from Toyama Prefecture (Japan) were found to be close to the borealis mitochondrial haplotypes from Kytlym (Sverdlovsk oblast) (P = 0.018). Thus, the source of most substitutions in the mitochondrial DNA of the studied forms are mutations that arose in nuclear copies of mitochondrial genes. The origin of examinandus and xanthodryas mitochondrial haplotypes from nuclear copies of borealis mtDNA and close similarity of their nuclear genomes give reason to consider mitogenomes of these forms as haplotype variants of a single species, Ph. borealis s. l. With high degree of probability, it can be argued that the haplotype divergence time of the analyzed forms is considerably lower than 2.5–3 million years, as previously hypothesized by a number of authors, and the “molecular clock,” which does not take into account recombination events between nuclear and mitochondrial genomes, cannot be used in this case.
{"title":"Mitochondrial Genome “Evolution” of Arctic Warbler (Phylloscopus borealis sensu lato) Occurs in Its Nuclear Genome","authors":"L. N. Spiridonova, O. P. Valchuk, Ya. A. Red’kin","doi":"10.1134/s1022795424700339","DOIUrl":"https://doi.org/10.1134/s1022795424700339","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000<b>Abstract</b>—</h3><p>Sequencing of a partial fragment of the mitochondrial <i>ND5–cytb</i> genes (1553 bp) and its nuclear copies in <i>Phylloscopus borealis</i> sensu lato (s.l.) individuals, belonging to different taxonomic groups from different parts of the range was carried out. The identity of the majority of taxon-specific and unique mitochondrial substitutions in <i>examinandus</i> and <i>xanthodryas</i> forms to those in nuclear copies of <i>borealis</i> mtDNA was demonstrated. Differences between the <i>examinandus</i> mitochondrial haplotypes and nuclear copies of <i>borealis</i> mtDNA were low (<i>P</i> = 0.02), and the genetic divergence in <i>borealis–examinandus</i>, <i>borealis–xanthodryas</i>, and <i>examinandus–xanthodryas</i> mtDNA itself considerably exceeded these values (<i>P</i> = 0.035, 0.044, and 0.046, respectively). For the first time, nuclear copy of the mitochondrial haplotype of the easternmost <i>xanthodryas</i> form was found in nuclear genome of one <i>borealis</i> individual from the western part of the breeding range (Komi Republic), and nuclear copies of <i>xanthodryas</i> mtDNA from Toyama Prefecture (Japan) were found to be close to the <i>borealis</i> mitochondrial haplotypes from Kytlym (Sverdlovsk oblast) (<i>P</i> = 0.018). Thus, the source of most substitutions in the mitochondrial DNA of the studied forms are mutations that arose in nuclear copies of mitochondrial genes. The origin of <i>examinandus</i> and <i>xanthodryas</i> mitochondrial haplotypes from nuclear copies of <i>borealis</i> mtDNA and close similarity of their nuclear genomes give reason to consider mitogenomes of these forms as haplotype variants of a single species, <i>Ph</i>. <i>borealis</i> s. l. With high degree of probability, it can be argued that the haplotype divergence time of the analyzed forms is considerably lower than 2.5–3 million years, as previously hypothesized by a number of authors, and the “molecular clock,” which does not take into account recombination events between nuclear and mitochondrial genomes, cannot be used in this case.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"13 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141773854","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 : 2024-07-27DOI: 10.1134/s1022795424700364
K. Arslan, F. Daldaban, D. Bayram, M. H. Sohel, B. Akyüz, M. U. Çinar
Abstract
This study was aimed to investigate the expression levels of transcription factor (TF) genes (MYF6, MYOD1, MYF5, MYOG) and proteins associated with muscle growth in the longissimus dorsi (LD) and gluteal (GL) muscles in sheep. For this aim, two fat-tailed sheep breeds (Akkaraman (n = 10), Awassi (n = 10)) and two thin-tailed sheep breeds (Kivircik (n = 10) and Karayaka (n = 10)) from Türkiye’s native sheep breeds were examined. The expression level was analyzed for MYF6, MYOD1, MYF5, and MYOG genes and proteins that RNAs and proteins were isolated from fresh tissues. As a result of the statistical analysis, in the LD tissue, respectively, MYOG and MYF5 genes in the Karayaka sheep breed; MYOD1 gene in Akkaraman sheep breed; MYF5 gene in Awassi sheep breed were found to be significant (P < 0.05). In GL tissue, respectively, MYOG and MYF6 genes in Akkaraman sheep breed; MYOD1 gene in Karayaka sheep breed; MYF6 gene in Akkaraman and Awassi sheep breed were significant (P < 0.05). The MYOG (fold change 6.87) and MYOD1 (fold change 15.41) genes were upregulated in the GL muscle of the fat-tailed Akkaraman sheep breed. In addition, in the thin-tailed Karayaka sheep breed, down-regulation of MYOD1 (fold change –0.22) gene in LD muscle and up-regulation of MYOD1 (fold change 6.67) gene in GL muscle was found. As a result, it can be considered that MYOG and MYOD1 genes as potential candidate genes in molecular selection studies for Akkaraman sheep breed in terms of muscle development.
{"title":"Investigation of Expression Levels of Transcription Factor Genes in Native Sheep Breeds of Türkiye","authors":"K. Arslan, F. Daldaban, D. Bayram, M. H. Sohel, B. Akyüz, M. U. Çinar","doi":"10.1134/s1022795424700364","DOIUrl":"https://doi.org/10.1134/s1022795424700364","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>This study was aimed to investigate the expression levels of transcription factor (TF) genes (<i>MYF6, MYOD1, MYF5, MYOG</i>) and proteins associated with muscle growth in the <i>longissimus dorsi</i> (LD) and <i>gluteal</i> (GL) muscles in sheep. For this aim, two fat-tailed sheep breeds (Akkaraman (<i>n</i> = 10), Awassi (<i>n</i> = 10)) and two thin-tailed sheep breeds (Kivircik (<i>n</i> = 10) and Karayaka (<i>n</i> = 10)) from Türkiye’s native sheep breeds were examined. The expression level was analyzed for MYF6, MYOD1, MYF5, and MYOG genes and proteins that RNAs and proteins were isolated from fresh tissues. As a result of the statistical analysis, in the LD tissue, respectively, <i>MYOG</i> and <i>MYF5</i> genes in the Karayaka sheep breed; <i>MYOD1</i> gene in Akkaraman sheep breed; <i>MYF5</i> gene in Awassi sheep breed were found to be significant (<i>P</i> < 0.05). In GL tissue, respectively, <i>MYOG</i> and <i>MYF6</i> genes in Akkaraman sheep breed; <i>MYOD1</i> gene in Karayaka sheep breed; <i>MYF6</i> gene in Akkaraman and Awassi sheep breed were significant (<i>P</i> < 0.05). The <i>MYOG</i> (fold change 6.87) and <i>MYOD1</i> (fold change 15.41) genes were upregulated in the GL muscle of the fat-tailed Akkaraman sheep breed. In addition, in the thin-tailed Karayaka sheep breed, down-regulation of <i>MYOD1</i> (fold change –0.22) gene in LD muscle and up-regulation of <i>MYOD1</i> (fold change 6.67) gene in GL muscle was found. As a result, it can be considered that <i>MYOG</i> and <i>MYOD1</i> genes as potential candidate genes in molecular selection studies for Akkaraman sheep breed in terms of muscle development.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"69 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141773856","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 : 2024-07-27DOI: 10.1134/s1022795424700455
A. R. Kuluev, R. T. Matniyazov, B. R. Kuluev, L. Yu. Privalov, A. V. Chemeris
Abstract—
The chloroplast genome of the synthetic octaploid Triticum timonovum Heslot et Ferrary k-43065 (France) was sequenced for the first time. Plastome sequencing was carried out on a Genolab M sequencer (GeneMind, China). The genome assembly was carried out using the NOVOwrap program. The size of the chloroplast genome of T. timonovum was 136 158 bp. The length of the inverted repeat region was 21 552 bp, that of the SSC region was 12 795 bp, and the LSC length was 80 257 bp. The chloroplast genomes of T. timonovum and different T. timopheevii accessions from the GenBank database were compared. As for the chloroplast genome, T. timonovum was closer to T. timopheevii (AB976560.1) but differed from it by the presence of one insert A at position 47891.
摘要 首次对合成八倍体Triticum timonovum Heslot et Ferrary k-43065（法国）的叶绿体基因组进行了测序。质粒测序是在 Genolab M 测序仪（中国 GeneMind 公司）上进行的。基因组组装使用 NOVOwrap 程序进行。Timonovum 的叶绿体基因组大小为 136 158 bp。倒位重复区长度为 21 552 bp，SSC 区长度为 12 795 bp，LSC 长度为 80 257 bp。比较了 T. timonovum 和 GenBank 数据库中不同 T. timopheevii 的叶绿体基因组。在叶绿体基因组方面，T. timonovum与T. timopheevii（AB976560.1）较为接近，但在47891位存在一个插入物A。
{"title":"Sequencing and Annotation of the Chloroplast Genome of Triticum timonovum Heslot et Ferrary","authors":"A. R. Kuluev, R. T. Matniyazov, B. R. Kuluev, L. Yu. Privalov, A. V. Chemeris","doi":"10.1134/s1022795424700455","DOIUrl":"https://doi.org/10.1134/s1022795424700455","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000<b>Abstract</b>—</h3><p>The chloroplast genome of the synthetic octaploid <i>Triticum timonovum</i> Heslot et Ferrary k-43065 (France) was sequenced for the first time. Plastome sequencing was carried out on a Genolab M sequencer (GeneMind, China). The genome assembly was carried out using the NOVOwrap program. The size of the chloroplast genome of <i>T. timonovum</i> was 136 158 bp. The length of the inverted repeat region was 21 552 bp, that of the SSC region was 12 795 bp, and the LSC length was 80 257 bp. The chloroplast genomes of <i>T. timonovum</i> and different <i>T. timopheevii</i> accessions from the GenBank database were compared. As for the chloroplast genome, <i>T. timonovum</i> was closer to <i>T. timopheevii</i> (AB976560.1) but differed from it by the presence of one insert A at position 47891.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"1 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774139","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 : 2024-07-27DOI: 10.1134/s1022795424700443
E. N. Pushkova, E. M. Dvorianinova, L. V. Povkhova, T. A. Rozhmina, R. O. Novakovskiy, E. A. Sigova, A. A. Dmitriev, N. V. Melnikova
Abstract—
Flax seeds are the richest plant source of lignans, which prevent the development of many diseases. In the seeds of cultivated species Linum usitatissimum, the lignan secoisolariciresinol diglucoside (SDG) predominates. In the present study, transcriptome sequencing of flax seeds was performed at five developmental stages for eight varieties differing in lignan content and grown under three variants of conditions, and expression of the PLR1 and UGT74S1 genes, which play a key role in the SDG synthesis, was assessed. Co-expression of the PLR1 and UGT74S1 genes, as well as tenfold and hundredfold changes in the expression level of these genes during seed development were revealed, which testified to their role in the synthesis of SDG in flax seeds. Reduced temperature (16°C) and excessive watering led to a shift in the maximum expression level of both genes to a later date (14th day after flowering), compared to the conditions of insufficient watering and elevated temperature (24°C), as well as optimum conditions (20°C) (7th day after flowering). Moreover, at elevated temperatures and insufficient watering, the PLR1 and UGT74S1 expression levels were lower than under optimum conditions. No association between the lignan content in seeds of the studied flax varieties and the PLR1 and UGT74S1 expression levels was found. These findings provide insight into the contribution of genotype and environment to the expression of key genes for SDG synthesis, which, among other things, is necessary for the development of optimum approaches for obtaining the lignan-rich flax seeds.
{"title":"Expression Profiles of Genes Involved in Lignan Synthesis in Developing Flax Seeds","authors":"E. N. Pushkova, E. M. Dvorianinova, L. V. Povkhova, T. A. Rozhmina, R. O. Novakovskiy, E. A. Sigova, A. A. Dmitriev, N. V. Melnikova","doi":"10.1134/s1022795424700443","DOIUrl":"https://doi.org/10.1134/s1022795424700443","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000<b>Abstract</b>—</h3><p>Flax seeds are the richest plant source of lignans, which prevent the development of many diseases. In the seeds of cultivated species <i>Linum usitatissimum</i>, the lignan secoisolariciresinol diglucoside (SDG) predominates. In the present study, transcriptome sequencing of flax seeds was performed at five developmental stages for eight varieties differing in lignan content and grown under three variants of conditions, and expression of the <i>PLR1</i> and <i>UGT74S1</i> genes, which play a key role in the SDG synthesis, was assessed. Co-expression of the <i>PLR1</i> and <i>UGT74S1</i> genes, as well as tenfold and hundredfold changes in the expression level of these genes during seed development were revealed, which testified to their role in the synthesis of SDG in flax seeds. Reduced temperature (16°C) and excessive watering led to a shift in the maximum expression level of both genes to a later date (14th day after flowering), compared to the conditions of insufficient watering and elevated temperature (24°C), as well as optimum conditions (20°C) (7th day after flowering). Moreover, at elevated temperatures and insufficient watering, the <i>PLR1</i> and <i>UGT74S1</i> expression levels were lower than under optimum conditions. No association between the lignan content in seeds of the studied flax varieties and the <i>PLR1</i> and <i>UGT74S1</i> expression levels was found. These findings provide insight into the contribution of genotype and environment to the expression of key genes for SDG synthesis, which, among other things, is necessary for the development of optimum approaches for obtaining the lignan-rich flax seeds.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"111 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774138","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 : 2024-07-27DOI: 10.1134/s1022795424700467
Y. Pan, Y. Y. He, Y. Y. Zhang, C. F. Qu, J. L. Miao
Abstract
Macrocystis sp. isolate 501 is a brown algae in the family Laminariaceae. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of Macrocystis sp. isolate 501. The cp genome of Macrocystis sp. isolate 501 is 130 103 bp in length with a GC content of 30.86%. The assembled genome has a typical cyclic structure, containing a large single-copy (LSC) region of 76 397 bp, a small single-copy (SSC) region of 42 856 bp, and a pairof inverted repeatregions(IRs) of 10 850 bp. The cp genome contains 140 unique genes, including 105 protein-codinggenes, six rRNA genes, and 29 tRNA genes. Phylogenetic analysis showed that Macrocystis sp. isolate 501 was closely related to Phaeophyceae. The chloroplast sequence of this species was aligned on NCBI, and the highest coverage was Macrocystis pyrifera (99.18%). Macrocystis pyrifera, also known as the giant brown algae, was first described by the French naturalist Nicolas Duclos in 1750. However, the first detailed description and name of the species was given by the French naturalist Adolphe-Francois Le Jolis in 1863, an article entitled “Étude des Algues littorales de la Manche.” We named the algae we get “Macrocystis sp. isolate 501,” which is the first time that this species has been mentioned. Herein we present the first report on Macrocystis sp. isolate 501 with published genomic information.
摘要大囊藻（Macrocystis sp.在此，我们对大囊藻分离株 501 的完整叶绿体（cp）基因组进行了测序、组装和注释。大囊藻分离株 501 的 cp 基因组全长 130 103 bp，GC 含量为 30.86%。组装后的基因组具有典型的环状结构，包含一个 76 397 bp 的大单拷贝（LSC）区、一个 42 856 bp 的小单拷贝（SSC）区和一个 10 850 bp 的倒置重复区（IRs）。cp 基因组包含 140 个独特的基因，包括 105 个蛋白质编码基因、6 个 rRNA 基因和 29 个 tRNA 基因。系统进化分析表明，501 号分离物中的巨囊藻与辉绿藻科（Phaeophyceae）亲缘关系密切。该物种的叶绿体序列在 NCBI 上进行了比对，覆盖率最高的是 Macrocystis pyrifera（99.18%）。巨囊藻（Macrocystis pyrifera）又称巨褐藻，由法国博物学家尼古拉斯-杜克洛（Nicolas Duclos）于 1750 年首次描述。不过，法国博物学家阿道夫-弗朗索瓦-勒约里斯（Adolphe-Francois Le Jolis）于 1863 年发表了一篇题为 "芒什沿海藻类研究"（Étude des Algues littorales de la Manche）的文章，首次对该物种进行了详细描述并命名。我们将得到的藻类命名为 "大囊藻 501 号分离株"，这是该物种首次被提及。在此，我们首次报告了大囊藻 501 号分离株的基因组信息。
{"title":"The Complete Chloroplast Genome of Macrocystis sp. Isolate 501","authors":"Y. Pan, Y. Y. He, Y. Y. Zhang, C. F. Qu, J. L. Miao","doi":"10.1134/s1022795424700467","DOIUrl":"https://doi.org/10.1134/s1022795424700467","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p><i>Macrocystis</i> sp. isolate 501 is a brown algae in the family Laminariaceae. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of <i>Macrocystis</i> sp. isolate 501. The cp genome of <i>Macrocystis</i> sp. isolate 501 is 130 103 bp in length with a GC content of 30.86%. The assembled genome has a typical cyclic structure, containing a large single-copy (LSC) region of 76 397 bp, a small single-copy (SSC) region of 42 856 bp, and a pairof inverted repeatregions(IRs) of 10 850 bp. The cp genome contains 140 unique genes, including 105 protein-codinggenes, six rRNA genes, and 29 tRNA genes. Phylogenetic analysis showed that <i>Macrocystis</i> sp. isolate 501 was closely related to Phaeophyceae. The chloroplast sequence of this species was aligned on NCBI, and the highest coverage was <i>Macrocystis pyrifera</i> (99.18%). <i>Macrocystis pyrifera,</i> also known as the giant brown algae, was first described by the French naturalist Nicolas Duclos in 1750. However, the first detailed description and name of the species was given by the French naturalist Adolphe-Francois Le Jolis in 1863, an article entitled “Étude des Algues littorales de la Manche.” We named the algae we get “<i>Macrocystis</i> sp. isolate 501,” which is the first time that this species has been mentioned. Herein we present the first report on <i>Macrocystis</i> sp. isolate 501 with published genomic information.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"40 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774140","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 : 2024-07-27DOI: 10.1134/s1022795424700340
F. A. Tembotova, M. S. Gudova, A. Kh. Amshokova, A. Kh. Khalidov
Abstract—
Based on the analysis of a fragment of the cytochrome b (cytb) gene of mitochondrial DNA (mtDNA), the genetic diversity of the little ground squirrel Spermophilus pygmaeus Pallas, 1779 of the Central and Eastern Caucasus was studied. Phylogenetic analysis revealed the existence of two clusters A and B within the western clade of S. pygmaeus 2. Cluster A is formed by haplotypes of ground squirrels from the Eastern Caucasus and the right bank of the Volga River, while B, only haplotypes of Central Caucasian animals. The distance between clusters A and B reaches 1.3%. The relatively isolated position on the phylogenetic tree of the ground squirrel population of the Central Caucasus, the absence of identical haplotypes in Central and Eastern Caucasian animals, and the distances obtained indicate genetic heterogeneity of the ground squirrel in the North Caucasus. The results of molecular dating showed that the evolutionary age of S. pygmaeus mtDNA haplotypes from the studied areas of the Eastern Caucasus was approximately 260 000 years, and that of the Central Caucasus, 163 000 years. A decrease in haplotypic and nucleotide variability was noted in the Central Caucasian populations of the little squirrel as compared to those from the Eastern Caucasus, which in general indicates the low viability of S. pygmaeus inhabiting the mountains of the Central Caucasus.
摘要 基于对线粒体 DNA（mtDNA）细胞色素 b（cytb）基因片段的分析，研究了中东部高加索地区小地松鼠 Spermophilus pygmaeus Pallas, 1779 的遗传多样性。系统进化分析表明，在 S. pygmaeus 2 的西部支系中存在两个聚类 A 和 B。聚类 A 由来自东高加索和伏尔加河右岸的地鼠单倍型组成，而聚类 B 只有来自中高加索动物的单倍型。A 群和 B 群之间的距离为 1.3%。中高加索地区土松鼠种群在系统发生树上相对孤立的位置、中高加索和东高加索动物没有相同的单倍型以及所获得的距离都表明了北高加索地区土松鼠的遗传异质性。分子年代测定的结果表明，东高加索研究地区的侏儒鼠 mtDNA 单倍型的进化年龄约为 26 万年，中高加索地区约为 16.3 万年。与来自东高加索地区的小松鼠相比，中高加索地区的小松鼠种群的单倍型和核苷酸变异性有所下降，这总体表明居住在中高加索山区的小松鼠的生存能力较低。
{"title":"Genetic Diversity of the Little Ground Squirrel Spermophilus pygmaeus Pallas, 1779 (Sciuridae, Rodentia) in the Northern Caucasus","authors":"F. A. Tembotova, M. S. Gudova, A. Kh. Amshokova, A. Kh. Khalidov","doi":"10.1134/s1022795424700340","DOIUrl":"https://doi.org/10.1134/s1022795424700340","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\u0000<b>Abstract</b>—</h3><p>Based on the analysis of a fragment of the cytochrome b (<i>cytb</i>) gene of mitochondrial DNA (mtDNA), the genetic diversity of the little ground squirrel <i>Spermophilus pygmaeus</i> Pallas, 1779 of the Central and Eastern Caucasus was studied. Phylogenetic analysis revealed the existence of two clusters A and B within the western clade of <i>S. pygmaeus</i> 2. Cluster A is formed by haplotypes of ground squirrels from the Eastern Caucasus and the right bank of the Volga River, while B, only haplotypes of Central Caucasian animals. The distance between clusters A and B reaches 1.3%. The relatively isolated position on the phylogenetic tree of the ground squirrel population of the Central Caucasus, the absence of identical haplotypes in Central and Eastern Caucasian animals, and the distances obtained indicate genetic heterogeneity of the ground squirrel in the North Caucasus. The results of molecular dating showed that the evolutionary age of <i>S. pygmaeus</i> mtDNA haplotypes from the studied areas of the Eastern Caucasus was approximately 260 000 years, and that of the Central Caucasus, 163 000 years. A decrease in haplotypic and nucleotide variability was noted in the Central Caucasian populations of the little squirrel as compared to those from the Eastern Caucasus, which in general indicates the low viability of <i>S. pygmaeus</i> inhabiting the mountains of the Central Caucasus.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"35 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141773853","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 : 2024-07-27DOI: 10.1134/s102279542470042x
Iu. A. Koroleva, I. A. Goncharova, A. A. Zarubin, S. A. Shipulina, A. A. Sleptsov, D. S. Panfilov, B. N. Kozlov, M. S. Nazarenko
Abstract
We found hypomethylation of five CpG sites in the 5' region of TBX20 gene (7p14.2) in the tissues of atherosclerotic aortic plaque compared to dilated part of aorta in patients with ascending aortic aneurysm. Using GEO database, we found that the DNA methylation level in the chr7:35253926-35262250 region changes in opposite direction in aortic dissection and aortic atherosclerosis. The results suggest an alteration in epigenetic regulation both in aortic atherosclerosis and aortic aneurysm.
摘要 我们发现，与升主动脉瘤患者主动脉扩张部分相比，动脉粥样硬化主动脉斑块组织中TBX20基因（7p14.2）5'区的5个CpG位点甲基化水平较低。利用 GEO 数据库，我们发现在主动脉夹层和主动脉粥样硬化中，chr7:35253926-35262250 区域的 DNA 甲基化水平变化方向相反。这些结果表明，主动脉粥样硬化和主动脉瘤的表观遗传调控都发生了改变。
{"title":"Methylation Levels in the 5' Region of the TBX20 Gene in the Ascending Aorta Change in Opposite Direction in Atherosclerosis and Aneurysm","authors":"Iu. A. Koroleva, I. A. Goncharova, A. A. Zarubin, S. A. Shipulina, A. A. Sleptsov, D. S. Panfilov, B. N. Kozlov, M. S. Nazarenko","doi":"10.1134/s102279542470042x","DOIUrl":"https://doi.org/10.1134/s102279542470042x","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>We found hypomethylation of five CpG sites in the 5' region of <i>TBX20</i> gene (7p14.2) in the tissues of atherosclerotic aortic plaque compared to dilated part of aorta in patients with ascending aortic aneurysm. Using GEO database, we found that the DNA methylation level in the chr7:35253926-35262250 region changes in opposite direction in aortic dissection and aortic atherosclerosis. The results suggest an alteration in epigenetic regulation both in aortic atherosclerosis and aortic aneurysm.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"15 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141773863","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 : 2024-07-27DOI: 10.1134/s1022795424700315
J. K. Monpara, K. S. Chudasama, M. L. Vekaria, V. J. Patel, V. S. Thaker
Abstract
Tinospora cordifolia is an important medicinal plant in ayurvedic system and modern medicine in India and traditionally applied for the treatment of inflammation, allergies and various other ailments. There is no genomic information available for T. cordifolia. In the present study, first time reported complete cp genome of T. cordifolia using high throughput ion torrent genome machine with ion torrent server. The cp genome of T. cordifolia was 150 945 bp in length with GC content of 38.7%, displays a quadripartite structure with two IR regions (IRa: 22 375 bp and IRb: 22 380 bp) that are separated by the LSC region (84 899 bp) and the SSC region (21 291 bp). There are 123 gene, including 85 protein-coding genes, 29 tRNA genes, seven rRNA genes and two pseudogenes (ycf1, rps16). Phylogenetic analysis based on whole cp genome revealed that T. cordifolia is as positioned near to the Menispermum dauricum within the Menispermaceae family. Total 27 SSRs were detected inthe plastomes which include di-, tri-, tetra- penta- and hexanucleotieds repeats. Further, compared with cp genome of other species of Menispermaceae it showed ten unique SSRs. Total twenty-five hypervariable regions loci were found in genome. These data could serve as DNA barcodes for species identification.
{"title":"Plastome Analysis of Medicinal Plant Tinospora cordifolia for Species Identification and Authentication","authors":"J. K. Monpara, K. S. Chudasama, M. L. Vekaria, V. J. Patel, V. S. Thaker","doi":"10.1134/s1022795424700315","DOIUrl":"https://doi.org/10.1134/s1022795424700315","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p><i>Tinospora cordifolia</i> is an important medicinal plant in ayurvedic system and modern medicine in India and traditionally applied for the treatment of inflammation, allergies and various other ailments. There is no genomic information available for <i>T. cordifolia</i>. In the present study, first time reported complete cp genome of <i>T. cordifolia</i> using high throughput ion torrent genome machine with ion torrent server. The cp genome of <i>T. cordifolia</i> was 150 945 bp in length with GC content of 38.7%, displays a quadripartite structure with two IR regions (IRa: 22 375 bp and IRb: 22 380 bp) that are separated by the LSC region (84 899 bp) and the SSC region (21 291 bp). There are 123 gene, including 85 protein-coding genes, 29 tRNA genes, seven rRNA genes and two pseudogenes (<i>ycf1</i>, <i>rps16</i>). Phylogenetic analysis based on whole cp genome revealed that <i>T. cordifolia</i> is as positioned near to the <i>Menispermum dauricum</i> within the Menispermaceae family<i>.</i> Total 27 SSRs were detected inthe plastomes which include di-, tri-, tetra- penta- and hexanucleotieds repeats. Further, compared with cp genome of other species of Menispermaceae it showed ten unique SSRs. Total twenty-five hypervariable regions loci were found in genome. These data could serve as DNA barcodes for species identification.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"50 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774060","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 : 2024-07-27DOI: 10.1134/s1022795424700352
X. Zhang, Zh. Liu, H. Li, J. Xu, H. Dai, H. Huo, F. Yang, S. Tian, P. Wang, J. Huo
Abstract
CABYR is a protein that regulates calcium-binding tyrosine phosphorylation located in sperm flagella, which increases significantly during sperm capacitation and is primarily involved in sperm capacitation and motility. This study aimed to analyze the expression regulation pattern, sequence characteristics and potential biological function of CABYR gene in Banna mini-pig inbred line (BMI). The testes of adult BMI boars were used for RNA-seq; the complete coding sequence of CABYR was cloned; the sequence, structural characteristics, interacting proteins, KEGG and GO of CABYR were analyzed; the ceRNA regulatory network of CABYR was built using RNA-seq data. The average expression level and TPM value of CABYR gene obtained by RNA-seq was 11 187.50 and 225.29, respectively. The full-length CDS of CABYR was 1149 bp (GenBank accession number: OK042309) encoding 382 amino acids (GenBank login number: UYO37316). The amino acid sequence alignment analysis of multiple species revealed that the similarity between BMI and other species exceeded 73%, indicating a relatively conserved sequence. The CABYR protein was found to contain the DD_CABYR_SP17 conserved domain, the results of species phylogenetic tree analysis met the clustering criteria. Other analyses, including protein-protein interaction (PPI) networks, KEGG, and GO, revealed that BMI CABYR interacts with 50 proteins involved in a variety of functions, such as sexual reproduction and reproductive processes. CABYR was involved in 7 GOs, including five cellular components, one molecular functions, and one biological processes, according to functional annotation. Six miRNAs were found to regulate the CABYR gene via targeted interactions. Additionally, 8, 6, and 1 lncRNAs were found to interact with ssc-miR-4331-3p, ssc-miR-744, and ssc-miR-491, respectively, in association with CABYR. This study examines the expression of CABYR in the testis of BMI, as well as its molecular structure characteristics and expression regulatory network. These findings provide a foundation for future research on the involvement of the CABYR gene in spermatogenesis processes in BMI pigs, particularly in relation to crucial biological processes such as sperm motility and fibrous sheath development.
{"title":"Molecular Characteristics and Expression Regulation of CABYR in the Testis of Pig","authors":"X. Zhang, Zh. Liu, H. Li, J. Xu, H. Dai, H. Huo, F. Yang, S. Tian, P. Wang, J. Huo","doi":"10.1134/s1022795424700352","DOIUrl":"https://doi.org/10.1134/s1022795424700352","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>CABYR is a protein that regulates calcium-binding tyrosine phosphorylation located in sperm flagella, which increases significantly during sperm capacitation and is primarily involved in sperm capacitation and motility. This study aimed to analyze the expression regulation pattern, sequence characteristics and potential biological function of <i>CABYR</i> gene in Banna mini-pig inbred line (BMI). The testes of adult BMI boars were used for RNA-seq; the complete coding sequence of <i>CABYR</i> was cloned; the sequence, structural characteristics, interacting proteins, KEGG and GO of CABYR were analyzed; the ceRNA regulatory network of CABYR was built using RNA-seq data. The average expression level and TPM value of <i>CABYR</i> gene obtained by RNA-seq was 11 187.50 and 225.29, respectively. The full-length CDS of <i>CABYR</i> was 1149 bp (GenBank accession number: OK042309) encoding 382 amino acids (GenBank login number: UYO37316). The amino acid sequence alignment analysis of multiple species revealed that the similarity between BMI and other species exceeded 73%, indicating a relatively conserved sequence. The CABYR protein was found to contain the DD_CABYR_SP17 conserved domain, the results of species phylogenetic tree analysis met the clustering criteria. Other analyses, including protein-protein interaction (PPI) networks, KEGG, and GO, revealed that BMI CABYR interacts with 50 proteins involved in a variety of functions, such as sexual reproduction and reproductive processes. CABYR was involved in 7 GOs, including five cellular components, one molecular functions, and one biological processes, according to functional annotation. Six miRNAs were found to regulate the <i>CABYR</i> gene via targeted interactions. Additionally, 8, 6, and 1 lncRNAs were found to interact with ssc-miR-4331-3p, ssc-miR-744, and ssc-miR-491, respectively, in association with CABYR. This study examines the expression of <i>CABYR</i> in the testis of BMI, as well as its molecular structure characteristics and expression regulatory network. These findings provide a foundation for future research on the involvement of the <i>CABYR</i> gene in spermatogenesis processes in BMI pigs, particularly in relation to crucial biological processes such as sperm motility and fibrous sheath development.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"1 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141773855","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 : 2024-07-27DOI: 10.1134/s1022795424700376
D. Xu, R. Li, Y. Xu, W. Guo, S. Chen, W. Li, W. Huang, C. Lei, Z. Ma
Abstract
Yak (Bos grunniens) is a unique livestock animal originating from the Qinghai-Tibet Plateau in China. In the current study, we investigated the maternal genetic diversity, differentiation and phylogeny of wild yak population and four domestic yak breeds (Qinghai-Gaoyuan, Huanhu, Xueduo, and Yushu) in Qinghai, China by analyzing 166 mitochondrial cytochrome b (Cytb) gene sequence variations. The results showed that the five yak breeds/populations had high genetic diversity (Hd = 0.501 ± 0.088–0.770 ± 0.053) and each yak breed/population owned unique haplotypes. Estimates of FST values showed a moderate genetic differentiation between wild yak and Huanhu yak (FST = 0.0577) as well as that between Huanhu yak and Yushu yak breeds (FST = 0.0520), but a weak genetic differentiation was observed between the other yak breeds/populations (–0.0209 < FST < 0.0372). Additionally, the clustering analysis based on RST values showed that Xueduo yak and Huanhu yak were clustered into one group, and each of the other three yak breeds/populations was separated into one group, respectively. Overall, the clustering relationship between wild yak and Yushu yak was closer. Maternal phylogenetic analysis showed that wild yak and four domestic yak breeds/populations in Qinghai represented in three maternal lineages (Mt-I, Mt-II, and Mt-III), indicating three maternal origins in yak. Our study would provide valuable information for the conservation and utilization of wild yak and Qinghai domestic yak breeds.
{"title":"Maternal Genetic Diversity, Differentiation and Phylogeny of Wild Yak and Four Domestic Yak Breeds in Qinghai, China Inferred from Mitochondrial Cytb Variations","authors":"D. Xu, R. Li, Y. Xu, W. Guo, S. Chen, W. Li, W. Huang, C. Lei, Z. Ma","doi":"10.1134/s1022795424700376","DOIUrl":"https://doi.org/10.1134/s1022795424700376","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Yak (<i>Bos grunniens</i>) is a unique livestock animal originating from the Qinghai-Tibet Plateau in China. In the current study, we investigated the maternal genetic diversity, differentiation and phylogeny of wild yak population and four domestic yak breeds (Qinghai-Gaoyuan, Huanhu, Xueduo, and Yushu) in Qinghai, China by analyzing 166 mitochondrial cytochrome <i>b</i> (<i>Cytb</i>) gene sequence variations. The results showed that the five yak breeds/populations had high genetic diversity (<i>H</i><sub>d</sub> = 0.501 ± 0.088–0.770 ± 0.053) and each yak breed/population owned unique haplotypes. Estimates of <i>F</i><sub>ST</sub> values showed a moderate genetic differentiation between wild yak and Huanhu yak (<i>F</i><sub>ST</sub> = 0.0577) as well as that between Huanhu yak and Yushu yak breeds (<i>F</i><sub>ST</sub> = 0.0520), but a weak genetic differentiation was observed between the other yak breeds/populations (–0.0209 < <i>F</i><sub>ST</sub> < 0.0372). Additionally, the clustering analysis based on <i>R</i><sub>ST</sub> values showed that Xueduo yak and Huanhu yak were clustered into one group, and each of the other three yak breeds/populations was separated into one group, respectively. Overall, the clustering relationship between wild yak and Yushu yak was closer. Maternal phylogenetic analysis showed that wild yak and four domestic yak breeds/populations in Qinghai represented in three maternal lineages (Mt-I, Mt-II, and Mt-III), indicating three maternal origins in yak. Our study would provide valuable information for the conservation and utilization of wild yak and Qinghai domestic yak breeds.</p>","PeriodicalId":21441,"journal":{"name":"Russian Journal of Genetics","volume":"50 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141773858","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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