Molecular Organization of the 25S–18S rDNA IGS of Fagus sylvatica and Quercus suber: A Comparative Analysis

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.

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A comparative analysis of foliar chemical composition and leaf construction costs of beech (Fagus sylvatica L.), sycamore maple (Acer pseudoplatanus L.) and ash (Fraxinus excelsior L.) saplings along a light gradient

Annals of Forest Science ◽

10.1051/forest/2010023 ◽

2010 ◽

Vol 67 (6) ◽

pp. 610-610 ◽

Cited By ~ 9

Author(s):

Any Mary Petritan ◽

Burghard Lüpke ◽

Ion Catalin Petritan

Keyword(s):

Comparative Analysis ◽

Chemical Composition ◽

Fagus Sylvatica ◽

Fraxinus Excelsior ◽

Acer Pseudoplatanus ◽

Construction Costs ◽

Light Gradient ◽

Fagus Sylvatica L ◽

Sycamore Maple

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

Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv ◽

10.7124/visnyk.utgis.18.1-2.1349 ◽

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.

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

Genetics Research ◽

10.1017/s0016672308009993 ◽

2009 ◽

Vol 91 (1) ◽

pp. 61-72 ◽

Cited By ~ 25

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.

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Molecular cytogenetics in different populations of Oligosarcus paranensis (Characidae): comparative analysis of the genus with 5S and 18S rDNA probes

Caryologia ◽

10.1080/00087114.2018.1440824 ◽

2018 ◽

Vol 71 (2) ◽

pp. 103-108

Author(s):

Mariana Campaner Usso ◽

Amanda Frederico Mortati ◽

Andressa Gois Morales-Blanco ◽

Lucia Giuliano-Caetano ◽

Ana Lúcia Dias

Keyword(s):

Comparative Analysis ◽

18S Rdna ◽

Molecular Cytogenetics ◽

Different Populations

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

Faktori eksperimental'noi evolucii organizmiv ◽

10.7124/feeo.v25.1143 ◽

2019 ◽

Vol 25 ◽

pp. 80-85 ◽

Cited By ~ 2

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

Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv ◽

10.7124/visnyk.utgis.14.2.691 ◽

2016 ◽

Vol 14 (2) ◽

pp. 216-220 ◽

Cited By ~ 6

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

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