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 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.

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 fishes of the genus Brycon

Genome ◽  
2001 ◽  
Vol 44 (5) ◽  
pp. 893-902 ◽  
Author(s):  
Adriane Pinto Wasko ◽  
Cesar Martins ◽  
Jonathan M Wright ◽  
Pedro Manoel Galetti Jr.
Keyword(s):  
Nucleotide Sequence ◽  
Chromosomal Localization ◽  
5S Rdna ◽  
5S Rrna ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Coding Region ◽  
Nontranscribed Spacer ◽  
Rdna Sequencing

There are few reports on the genomic organization of 5S rDNA in fish species. To characterize the 5S rDNA nucleotide sequence and chromosomal localization in the Neotropical fishes of the genus Brycon, 5S rDNA copies from seven species were generated by PCR. The nucleotide sequences of the coding region (5S rRNA gene) and the nontranscribed spacer (NTS) were determined, revealing that the 5S rRNA genes were highly conserved, while the NTSs were widely variable among the species analyzed. Moreover, two classes of NTS were detected in each species, characterized by base substitutions and insertions–deletions. Using fluorescence in situ hybridization (FISH), two 5S rDNA chromosome loci that could be related to the two 5S rDNA NTS classes were observed in at least one of the species studied. 5S rDNA sequencing and chromosomal localization permitted the characterization of Brycon spp. and suggest a higher similarity among some of them. The data obtained indicate that the 5S rDNA can be an useful genetic marker for species identification and evolutionary studies.Key words: Brycon, FISH, nontranscribed spacer, nucleotide sequence, 5S rDNA.

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.

Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 732-741 ◽  
Author(s):  
Wolfgang Staiber
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Sequence Data ◽  
Structural Evolution ◽  
5S Rdna ◽  
Oligonucleotide Primer ◽  
Homologous Gene ◽  
Gene Sequences ◽  
Nucleotide Substitutions ◽  
Degenerate Oligonucleotide

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%–100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.

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.

Novel variants of the 5S rRNA genes in Eruca sativa

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 121-128 ◽  
Author(s):  
Kapil Singh ◽  
Sabhyata Bhatia ◽  
Malathi Lakshmikumaran
Keyword(s):  
Repeat Unit ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Gene Variants ◽  
Eruca Sativa ◽  
Coding Region ◽  
Coding Regions ◽  
Rdna Sequences ◽  
5S Rrna Genes

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the l-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa. The noncoding spacers of the variants V1 and V2 that make up the 1-kb family lack the EcoRI site that is present in the 0.5-kb family. The sequence analysis indicates that V1 and V2 sequences are probably pseudogenes derived from functional 5S rRNA genes. The results also suggest that the two families exist as independent clusters at different locations in the E. sativa genome.Key words: 5S rRNA genes, crucifers, Eruca sativa, organization, sequence analysis.

scholarly journals Molecular organization of 5S rDNA in sharks of the genusRhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes

2009 ◽  
Vol 91 (1) ◽  
pp. 61-72 ◽  
Author(s):  
DANILLO PINHAL ◽  
CARLOS S. ARAKI ◽  
OTTO B. F. GADIG ◽  
CESAR MARTINS
Keyword(s):  
Comparative Analysis ◽  
5S Rdna ◽  
Class Ii ◽  
Molecular Organization ◽  
Class I ◽  
Rrna Gene ◽  
Shark Species ◽  
Coding Region ◽  
Fish Genome ◽  
Repeat Class

SummaryIn this study, we attempted a molecular characterization of the 5S rDNA in two closely related species of carcharhiniform sharks,Rhizoprionodon lalandiiandRhizoprionodon porosus, as well as a further comparative analysis of available data on lampreys, several fish groups and other vertebrates. Our data show thatRhizoprionodonsharks carry two 5S rDNA classes in their genomes: a short repeat class (termed class I) composed of ~185 bp repeats, and a large repeat class (termed class II) arrayed in ~465 bp units. These classes were differentiated by several base substitutions in the 5S coding region and by completely distinct non-transcribed spacers (NTS). In class II, both species showed a similar composition for both the gene coding region and the NTS region. In contrast, class I varied extensively both within and between the two shark species. A comparative analysis of 5S rRNA gene sequences of elasmobranchs and other vertebrates showed that class I is closely related to the bony fishes, whereas the class II gene formed a separate cartilaginous clade. The presence of two variant classes of 5S rDNA in sharks likely maintains the tendency for dual ribosomal classes observed in other fish species. The present data regarding the 5S rDNA organization provide insights into the dynamics and evolution of this multigene family in the fish genome, and they may also be useful in clarifying aspects of vertebrate genome evolution.

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 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.

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