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.

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 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 Subrepeats in 5s rDNAs as a molecular marker in Acer platanoides L. populations

2019 ◽  
Vol 25 ◽  
pp. 80-85 ◽  
Author(s):  
I. I. Panchuk ◽  
R. M. Kasianchuk ◽  
R. A. Volkov
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Molecular Organization ◽  
Acer Platanoides ◽  
Rdna Transcription ◽  
Rdna Sequences ◽  
Rdna Igs

Aim. To study the genetic diversity of tree species it is necessary to use only those regions of genome, which evolve at the highest rate, such as 5S rDNA. To estimate the potential of 5S rDNA to be used as a molecular marker for genogeographic studies, the molecular organization of this genomic region was compared between samples from two geogra-phically remote Bulgarian and Ukrainian populations of Norway maple, Acer platanoides. Methods. PCR amplification, cloning and sequencing. Results. It was shown that in the genome of A. platanoides the 5S rDNA sequences are highly similar. However, in the 5S rDNA intergenic spacer (IGS) of A. platanoides from the Bulgarian population three copies of GTCCGTT subrepeats are present, whereas only one copy of this sequence occurs in plants from the Ukrainian population. Except for different number of subrepeats, the 5S rDNA sequences of the Bulgarian and Ukrainian samples of A. platanoides are identical. In two taxonomically distant species, A. platanoides and A. pseudoplatanus, the region of 5S rDNA IGS, which contains the potential external elements of the promoter of RNA polymerase III, shows no difference, and therefore evolves at a lower rate than other parts of the IGS. Conclusions. The identity of the potential external promoter elements within the genus Acer supports the idea that this part of the IGS could be involved in the initiation of 5S rDNA transcription. The presence of different numbers of sub-repeats in the 5S rDNA IGS in various populations of A. platanoides makes them suitable for identification of intraspecific forms and for evaluation of the intraspecific genetic diversity of A. platanoides. Keywords: 5S rDNA, molecular evolution, sub-repetitions, intraspecific variability, Acer.

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 Organization of 5S ribosomal DNA of Litchi chinensis Sonn.

2021 ◽  
Vol 18 (1-2) ◽  
pp. 3-8
Author(s):  
O. O. Ishchenko ◽  
V. V. Kozub ◽  
I. I. Panchuk
Keyword(s):  
Ribosomal Dna ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Molecular Organization ◽  
Cloning And Sequencing ◽  
Litchi Chinensis ◽  
The Family ◽  
Repeated Unit ◽  
Eukaryotic Organisms

Aim. 5S ribosomal DNA (5S rDNA) represents a universal model for studying the evolution of repeated sequences in eukaryotic organisms. Taking into account that this region of the genome still remains almost undescribed in species of the family Sapindaceae, we investigated the molecular organization of a repeated unit of 5S rDNA in a member of this family, Litchi chinensis. Methods. PCR amplification, cloning and sequencing of 5S rDNA. Results. It was found that the length of the repeated unit of the 5S rDNA of L. chinensis is 321 -323 bp. The level of intragenomic similarity of 5S rDNA repeats is 87.1 %. Potential external elements of the RNA polymerase III promoter, which are localized in IGS, differ from those described for members of other families of angiosperms. Conclusions. In the genome of L. chinensis, at least two classes of 5S rDNA repeats are present, which differ in the sequence of external promoter elements. Keywords: 5S rDNA, molecular evolution, Litchi chinensis, Sapindaceae.

scholarly journals Molecular organization of 5S rDNA of Brunfelsia uniflora (Pohl.) D. Don

2018 ◽  
Vol 16 (1) ◽  
pp. 61-68 ◽  
Author(s):  
A. Y. Shelyfist ◽  
Y. O. Tynkevich ◽  
R. A. Volkov
Keyword(s):  
Molecular Evolution ◽  
Transcription Initiation ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Genomic Region ◽  
High Rate ◽  
Molecular Organization ◽  
Low Rank ◽  
Solanaceae Family

Aim. The 5S rDNA represents a convenient model for studying of the molecular evolution of tandemly arranged repeated sequences. However, in many groups of angiosperms this genomic region still remains poorly studied. So far, in the family Solanaceae the 5S rDNA was described only for five genera. In order to elucidate the 5S rDNA organization in representatives of other genera of Solanaceae, we decided to explore organization of this region in Brunfelsia uniflora (tribe Petunieae). Methods. PCR amplification, cloning and sequencing of 5S rDNA. Results. Three clones of 5S rDNA of Brunfelsia uniflora were sequenced. It was found that only one class of repeats ranging in length from 343 to 347 bp is present in the genome of B. uniflora. The level of intragenomic similarity for the 5S rDNA intergeneric spacer regions (IGS) ranges from 86.7 to 96.4 %. The IGSs of B. uniflora and of other members of Solanaceae family differ significantly: the sequence homology was detected only for sequence motives required for RNA polymerase III transcription initiation and termination. Conclusions. The molecular evolution of the 5S rDNA IGS occurs at a high rate in the Solanaceae family. Accordingly, the comparison of the IGS should be used to clarify the phylogenetic relationship between taxa of low rank, in particular between species and genera of the tribe Petunieae. Keywords: 5S rDNA, intergeneric spacer, molecular evolution, Brunfelsia, Solanaceae.

scholarly journals Organization of 5S rDNA repeated unit of Quercus imbricaria Michx.

2020 ◽  
Vol 17 (2) ◽  
pp. 179-186 ◽  
Author(s):  
A. S. Stratiichuk ◽  
T. O. Derevenko ◽  
Y. O. Tynkevych
Keyword(s):  
Molecular Evolution ◽  
Secondary Structure ◽  
Pcr Amplification ◽  
5S Rdna ◽  
5S Rrna ◽  
Molecular Organization ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Sequence Elements ◽  
Related Plant

Aim. The 5S rDNA repeats represent a universal model for the investigation of molecular evolution of repeated sequences. Also, comparison of 5S rDNA was successfully applied for the elucidation of phylogenetic relationships between the closely related plant species. However, there is practically no data regarding the molecular organization of 5S rDNA repeats in members of the section Lobatae, one of the largest groups of the genus Quercus. Accordingly, our aim was to investigate the 5S rDNA organization for Q. imbricaria, a species that belongs to this section. Methods. DNA extraction, PCR amplification, cloning and sequencing. Results. A complete 5S rDNA repeat of Q. imbricaria was cloned and sequenced. It has been found that in the oak genome, the 5S rDNA coding region contains five nucleotide substitutions as compared to that in Arabidopsis. Nevertheless, the predicted secondary structure of the transcript retains all typical features of 5S rRNA. Presumptive sequence elements of the external promoter were identified in the IGS. Conclusions. The nucleotide substitutions that occur in the 5S rRNA during evolution appear to be compensatory, resulting in conservation of its secondary structure. Due to considerable differences among the species of different sections, the 5S rDNA IGS can be applied for the taxonomic studies in the genus Quercus. Keywords: 5S rDNA, molecular evolution, Quercus, Lobatae.

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.

5S rDNA genome regions of Lens species

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 937-942 ◽  
Author(s):  
M Fernández ◽  
M L Ruiz ◽  
C Linares ◽  
A Fominaya ◽  
M Pérez de la Vega
Keyword(s):  
Lens Culinaris ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Nucleolar Organizer ◽  
Repeated Sequence ◽  
Nontranscribed Spacer ◽  
Selective Hybridization

The length variability of the nontranscribed spacer (NTS) of the 5S rDNA repeats was analyzed in species of the genus Lens by means of PCR amplification. The NTS ranged from ~227 to ~952 bp. The polymorphism detected was higher than previous NTS polymorphisms described in this genus. Three NTS length variants from Lens culinaris subsp. culinaris and 2 from Lens culinaris subsp. orientalis were sequenced. The culinaris NTS fragment lengths were 239, 371, and 838 bp, whereas the orientalis ones were 472 bp and 506 bp, respectively. As a result of sequence similarities, 2 families of sequences were distinguished, 1 including the sequences of 838 and 506 bp, and others with the sequences of 239, 371, and 472 bp. The 1st family was characterized by the presence of a repeated sequence designated A, whereas the 2nd family showed a single A sequence and other repeated sequences designated B, C, and D. The presence of an (AT)n microsatellite was also observed in the 2nd family of sequences. The fragments, which included the 239-bp and 838-bp NTS sequences, as well as the intergenic spacer (IGS) of the 18S–5.8S–26S ribosomal DNA also from L. culinaris subsp. culinaris, were used to localize the nucleolar organizer region (NOR) and the 5S rDNA loci in the chromosomes of several species of the genus Lens by means of fluorescence in situ hybridization (FISH). The selective hybridization of the 2 NTS probes allowed us to distinguish between different 5S rDNA chromosomal loci.Key words: Lens, lentil, ribosomal loci, 5S, FISH, NTS polymorphism, NOR.

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