Organization of 5S rDNA of field maple (Acer campestre L.)

2019 ◽  
Vol 11 (1) ◽  
pp. 40-45
Author(s):  
Olha Іshchenko ◽  
Irina Panchuk ◽  
Roman Volkov
Keyword(s):  
Related Species ◽  
Sequence Similarity ◽  
Rna Polymerase Iii ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Coding Region ◽  
Closely Related Species ◽  
Acer Campestre ◽  
Convenient Model

In recent decades, molecular methods have been widely used to study plant speciation and taxonomy. The 5S rDNA, which belongs to the class of repeated sequences present in the genomes of all eukaryotes, represents a convenient model for studying the patterns of molecular evolution in plants. Each of 5S rDNA repeated units consist of a coding region and an intergenic spacer (IGS). The coding sequence is highly conserved in evolution, whereas the IGS can differ between related species and even between populations of the same species. The molecular organization of the 5S rDNA in representatives of genus Acer is still poorly explored. Accordingly, the aim of the study was to investigate the organization and variability of the 5S rDNA of the European species Acer campestre. Analysis of the obtained sequences showed, that the 5S rDNA clones of A. campestre are identical. The level of IGS sequence similarity between A. сampestre and A. platanoides amounts to 96.1%, whereas the similarity between these species and A. pseudoplatanus is lower, namely – 81,9–82,4%. Therefore, A. campestre and A. platanoides can be considered as closely related species. Only one class of 5S rDNA repeats is present in the genome of A. сampestre. The potential external elements of the RNA polymerase III promoter localized in the IGS differ from those described early for representatives of other families of angiosperms.

scholarly journals Molecular organization of 5S rDNA of perennial ryegrass Lolium perenne L.

2019 ◽  
Vol 16 (2) ◽  
pp. 166-173 ◽  
Author(s):  
O. O. Ishchenko ◽  
I. I. Panchuk
Keyword(s):  
Lolium Perenne ◽  
Sequence Similarity ◽  
Molecular Taxonomy ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Important Species ◽  
Convenient Model

Aim. Ribosomal DNA (rDNA) is an important tool for molecular taxonomy and represents a convenient model for studying the evolution of repeated sequences. However, for many groups of angiosperms, 5S rDNA remains poorly studied, in particular for such a large group as the Poaceae (Gramineae) family. Accordingly, it was decided to analyze the molecular organization of 5S rDNA in the widespread and economically important species Lolium perenne. Methods. DNA extraction, PCR amplification, cloning and sequencing. Results. Two clones of L. perenne 5S rDNA were sequenced. It was shown that only one variant of 5S rDNA repeats with a 188–189 bp-long intergenic spacer (IGS) is present in the genome of L. perenne. Putative RNA polymerase III promoter elements were detected in the IGS. The level of IGS sequence similarity between representatives of different genera of the tribe Poeae ranges from 46 to 63 %. Conclusions. Comparison of IGS can be used to clarify the phylogenetic relationship between taxa of low ranks, in particular, between species and genera of the tribe Poeae. Keywords: 5S rDNA, intergenic spacer, molecular evolution, Lolium, Poaceae.

scholarly journals Molecular structure of 5S rDNA of Mandragora autumnalis Bertol.

2020 ◽  
Vol 17 (2) ◽  
pp. 187-195
Author(s):  
A. Y. Shelyfist ◽  
D. V. Yakobyshen ◽  
R. A. Volkov
Keyword(s):  
Molecular Structure ◽  
Molecular Evolution ◽  
Sequence Similarity ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Coding Region ◽  
Eukaryotic Organisms

Aim. The region encoding 5S rRNA (5S rDNA) is present in the genome of all eukaryotic organisms. The 5S rDNA represents a universal model for studying the molecular evolution of the tandemly arranged repeated sequences. However, in the family Solanaceae, the molecular organization of 5S rDNA has been investigated only for few genera. In this regard, we decided to characterize the molecular structure of the 5S rDNA of Mandragora autumnalis, a representative of the Mandragoreae tribe, which occupies an isolated position in the nightshade family. Methods. PCR amplification, cloning and sequencing. Results. Two 5S rDNA clones of M. autumnalis were sequenced. It was found that in the genome of this species only one class of the 5S rDNA repeats possessing the 103 bp-long intergenic spacer (IGS) is present. This is the smallest size of IGS known to date for the Solanaceae family. The 5S rDNA IGS of M. autumnalis demonstrates a moderate level of sequence-similarity with the IGS of other representatives of the subfamily Solanoideae. Conclusions. The results support the current opinion about the isolated taxonomic position of the genus Mandragora within the subfamily Solanoideae. The increased level of similarity was found in the IGS regions, which contain potential external elements of the RNA polymerase III promoter and terminator. The mutations occurred in the part of the IGS up-stream of the coding region had a compensatory nature, which ensured that the external elements of the promoter were preserved during the evolution. Keywords: 5S rDNA, intergeneric spacer, molecular evolution, Mandragora autumnalis, Solanaceae.

Organization of 5S ribosomal DNA of Poa pratensis L.

2020 ◽  
Vol 12 (2) ◽  
pp. 135-140
Author(s):  
Olha Ishchenko ◽  
Roman Volkov
Keyword(s):  
Poa Pratensis ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Transcription Terminator ◽  
Coding Regions ◽  
Poaceae Family ◽  
Rdna Igs

5S rDNA, which belongs to the class of repeated sequences, represents a convenient model for studying the molecular evolution of plants. The 5S rDNA repeated unit consists of a conserved region encoding 5S rRNA and variable intergenic spacer (IGS) that contains the motifs required for initiation and termination of transcription. The IGS sequences can be used as a molecular marker for elucidation of the phylogenetic relationships of low-ranking taxa. Today, the molecular organization of 5S rDNA in species of the Poaceae family, which includes many economically important crops, is still poorly understood. Therefore, the aim of the study was to investigate the organization and polymorphism of 5S rDNA IGS in the genome of Poa pratensis L., a member of one of the largest genera of the Poaceae family. Using PCR amplification, cloning, sequencing and analysis of the SRA database, two variants of the 5S rDNA repeated units were found in the genome of P. pratensis. The two variants possess 119 bp-long coding regions, whereas the length of IGS ranges from 169 to 185 bp. At the beginning of IGS, the oligo-T sequence of the RNA polymerase III transcription terminator is present. In members of the Poaceae family, the putative external elements of the 5S rDNA promoter differ from those in previously studied groups of plants.

scholarly journals Molecular organization of 5S rDNA intergenic spacer in Gentiana pneumonanthe L. and G. punctata L.

2021 ◽  
Vol 18 (1-2) ◽  
pp. 9-15
Author(s):  
V. M. Mel’nyk ◽  
I. O. Andreev ◽  
G. Yu. Myryuta ◽  
A. Y. Shelyfist ◽  
R. A. Volkov ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
5S Rdna ◽  
5S Rrna ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Coding Region ◽  
5S Rrna Genes ◽  
Rdna Igs ◽  
Rdna Intergenic Spacer

Aim. The study was aimed at cloning and analysis of molecular organization of 5S rDNA intergenic spacer (IGS) in two Gentiana species of Ukrainian flora, G. pneumonanthe L. and G. punctata L. Methods. 5S rDNA IGS sequence was amplified using polymerase chain reaction (PCR) with a pair of primers specific for the gene coding region. The produced PCR products were fractionated by gel-electrophoresis, isolated, ligated into plasmid pUC18, cloned into E. coli, and then sequenced. Nucleotide sequences were aligned using the Muscle algorithm and analyzed in the Unipro UGENE software. Results. The intergenic spacer region of the 5S rRNA genes was cloned and sequenced for two Gentiana species of Ukrainian flora, G. pneumonanthe and G. punctata. Based on the analysis of the alignment of the IGS sequences of five Gentiana species from three sections, some features of molecular organization of IGS of 5S rRNA genes in the studied species were established. In particular, motifs typical for other angiosperm families were identified, such as conservative oligo-dT motif at the IGS 3'-end that served as a transcription termination site and AT-rich region preceding the coding region of 5S rRNA gene. However, in the region of transcription initiation, conservative GC-element in position -13 is changed to AC. Conclusions. The interspecific variation of molecular organization of 5S rDNA IGS was identified among Gentiana species that can be used to clarify the phylogenetic relationships between members of this genus.Keywords: Gentiana species, 5S rDNA intergenic spacer, molecular organization, phylogeny.

scholarly journals Molecular organization of 5S rDNA in two ukrainian populations of sycamore (Acer pseudoplatanus)

2016 ◽  
Vol 14 (2) ◽  
pp. 216-220 ◽  
Author(s):  
O. O. Rusak ◽  
V. I. Petrashchuk ◽  
I. I. Panchuk ◽  
R. A. Volkov
Keyword(s):  
Molecular Evolution ◽  
Molecular Marker ◽  
Tree Species ◽  
Sequence Similarity ◽  
Rna Polymerase Iii ◽  
5S Rdna ◽  
Molecular Organization ◽  
Acer Pseudoplatanus ◽  
Rate Of Molecular Evolution ◽  
Rdna Igs

Aim. The genetic variability of tree species has still not been studied enough at the molecular level. Considering the relatively low rate of molecular evolution in perennial tree species, it is necessary to use only those regions of genome, which demonstrate a high level of variability, such as 5S rDNA. Accordingly, to estimate the potential of 5S rDNA as a molecular marker for tree species, the organization of this genomic region was compared between samples from two geographically remote Ukrainian populations of sycamore, Acer pseudoplatanus. Methods. PCR amplification, cloning and sequencing of the 5S rDNA IGS of A.pseudoplatanus. Results. It was shown that only one variant of 5S rDNA repeat with a length of 475 bp is present in the genome of A. pseudoplatanus.  Also, it was found that the elements typical for the angiosperm RNA polymerase III promoter, which are localized in IGS, appear to be different from those previously described for species of other families. The level of IGS sequence similarity within the populations exceeds 99%, while the level of IGS sequence similarity between various populations is only 93,3-94,3%. Conclusions. High rate of molecular evolution of the 5S rDNA IGS makes them a convenient molecular marker for evaluation of intraspecific variation in populations of A. pseudoplatanus.Key words: 5S rDNA, molecular markers, intraspecific variability, Acer

scholarly journals Molecular cytogenetics of Hedysarum gmelinii Ledeb. and H. setigerum Turcz. (Fabaceae) from populations of Southern Siberia

2021 ◽  
Vol 20 (1) ◽  
pp. 517-519
Author(s):  
O. Yu. Yurkevich ◽  
T. E. Samatadze ◽  
I. Yu. Selyutina ◽  
S. A. Zoshchuk ◽  
A. V. Amosova ◽  
...  
Keyword(s):  
Chromosome Numbers ◽  
Related Species ◽  
Karyotype Analysis ◽  
Molecular Cytogenetics ◽  
5S Rdna ◽  
Chromosome Morphology ◽  
Closely Related Species ◽  
Southern Siberia ◽  
Close Relationship ◽  
First Time

For the first time, a comparative karyotype analysis of closely related species Hedysarum gmelinii andH. setigerum (Hedysarum section Multicaulia) grown in Southern Siberia, has been performed by molecular cytogeneticmarkers. Chromosome numbers in karyotypes of these species were specified – 2n = 4х = 32. In some accessions, additionalB chromosomes were revealed. FISH analyses indicated high similarities in chromosome morphology and also patternsof chromosomal distributions of 45S and 5S rDNA clusters in karyotypes of H. gmelinii and H. setigerum, which confirmsthe close relationship between their genomes.

scholarly journals Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).

scholarly journals Bacillus aciditolerans sp. nov., isolated from paddy soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1155-1161 ◽  
Author(s):  
Meng-Jiao Ding ◽  
Nian-Jie Shang ◽  
Zhi-xin Xiao ◽  
Fei Shao ◽  
Li Liu ◽  
...  
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Test Results ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
The Town

A Gram-stain-positive, motile, rod-shaped bacterial strain, YN-1T, was isolated from a rice field in the town of Jietou, Yunnan Province, PR China. Colonies were circular, 1–2 mm in diameter, creamy white, with slightly irregular margins. The isolate grew optimally at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence similarity comparisons, YN-1T clustered together with other species of the genus Bacillus and showed highest similarities with Bacillus onubensis 0911MAR22V3T (98.0 %), Bacillus humi LMG22167T (97.5 %), ' Bacillus timonensis ' 10403023 (97.4 %) and ' Bacillus sinesaloumensis' P3516 (97.1 %). However, the DNA–DNA hybridization values between YN-1T and closely related strains of species of the genus Bacillus were well below 47 %, indicating that they represent different taxa. The average nucleotide identity and the Genome-to-Genome Distance Calculator also revealed low relatedness (below 95 and 70 %, respectively) between YN-1T and type strains of closely related species of the genus Bacillus . The DNA G+C content of the strain was 40 mol%. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids and two other unidentified lipids. Physiological and biochemical test results were also different from those of the most closely related species. On the basis of the phenotypic, genetic and chemotaxonomic data, strain YN-1T is considered to represent a novel species of the genus Bacillus , for which the name Bacillus aciditolerans sp. nov. is proposed, with strain YN-1T (=CCTCC AB 2017280T=JCM 32973T) as the type strain.

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