Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera

Genome ◽  
2012 ◽  
Vol 55 (1) ◽  
pp. 33-44 ◽  
Author(s):  
Daniel Campo ◽  
Eva García-Vázquez
Keyword(s):  
Gene Family ◽  
5S Rdna ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Structural Elements ◽  
Coding Region ◽  
Evolutionary Patterns ◽  
Nontranscribed Spacer ◽  
5S Rrna Genes ◽  
Rdna Organization

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a “two-speed” evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

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.

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.

5S rDNA and U2 snRNA are linked in the genome of Crassostrea angulata and Crassostrea gigas oysters: does the (CT)n·(GA)n microsatellite stabilize this novel linkage of large tandem arrays?

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1116-1119 ◽  
Author(s):  
I Cross ◽  
L Rebordinos
Keyword(s):  
Crassostrea Gigas ◽  
Concerted Evolution ◽  
5S Rdna ◽  
Rrna Genes ◽  
Small Nuclear Rna ◽  
Inverted Position ◽  
U2 Snrna ◽  
Nontranscribed Spacer ◽  
Crassostrea Angulata ◽  
5S Rrna Genes

The 5S rRNA genes from 2 species of the Ostreidae family, Crassostrea angulata and Crassostrea gigas, were molecularly characterized. The genes were amplified, cloned, and sequenced. The results revealed a 5S rDNA tandem array with a nucleotide sequence in an inverted position within the nontranscribed spacer region that corresponded to the U2 small nuclear RNA (snRNA) gene. The sequence analysis indicated that both genes could be functionally active. The presence of the microsatellite (CT)n·(GA)n at the 3′ end of both genes and the possible involvement of concerted evolution are discussed.Key words: Crassostrea angulata, Crassostrea gigas, 5S rDNA, U2 snRNA, microsatellite, concerted evolution.

scholarly journals Ribosomal DNA localization on Lathyrus species chromosomes by FISH

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Hoda B. M. Ali ◽  
Samira A. Osman
Keyword(s):  
Genome Mapping ◽  
Chromosome Complement ◽  
5S Rdna ◽  
Rdna Locus ◽  
5S Rrna ◽  
Rrna Genes ◽  
45S Rdna ◽  
Metaphase Chromosomes ◽  
Lathyrus Odoratus ◽  
5S Rrna Genes

Abstract Background Fluorescence In Situ Hybridization (FISH) played an essential role to locate the ribosomal RNA genes on the chromosomes that offered a new tool to study the chromosome structure and evolution in plant. The 45S and 5S rRNA genes are independent and localized at one or more loci per the chromosome complement, their positions along chromosomes offer useful markers for chromosome discriminations. In the current study FISH has been performed to locate 45S and 5S rRNA genes on the chromosomes of nine Lathyrus species belong to five different sections, all have chromosome number 2n=14, Lathyrus gorgoni Parl, Lathyrus hirsutus L., Lathyrus amphicarpos L., Lathyrus odoratus L., Lathyrus sphaericus Retz, Lathyrus incospicuus L, Lathyrus paranensis Burkart, Lathyrus nissolia L., and Lathyrus articulates L. Results The revealed loci of 45S and 5S rDNA by FISH on metaphase chromosomes of the examined species were as follow: all of the studied species have one 45S rDNA locus and one 5S rDNA locus except L. odoratus L., L. amphicarpos L. and L. sphaericus Retz L. have two loci of 5S rDNA. Three out of the nine examined species have the loci of 45S and 5S rRNA genes on the opposite arms of the same chromosome (L. nissolia L., L. amphicarpos L., and L. incospicuus L.), while L. hirsutus L. has both loci on the same chromosome arm. The other five species showed the loci of the two types of rDNA on different chromosomes. Conclusion The detected 5S and 45S rDNA loci in Lathyrus could be used as chromosomal markers to discriminate the chromosome pairs of the examined species. FISH could discriminate only one chromosome pair out of the seven pairs in three species, in L. hirsutus L., L. nissolia L. and L. incospicuus L., and two chromosome pairs in five species, in L. paranensis Burkart, L. odoratus L., L. amphicarpos L., L. gorgoni Parl. and L. articulatus L., while it could discriminate three chromosome pairs in L. sphaericus Retz. these results could contribute into the physical genome mapping of Lathyrus species and the evolution of rDNA patterns by FISH in the coming studies in future.

scholarly journals Interindividual size heteromorphism of NOR and chromosomal location of 5S rRNA genes in Iheringichthys labrosus

2007 ◽  
Vol 50 (1) ◽  
pp. 141-146 ◽  
Author(s):  
Rafael Augusto de Carvalho ◽  
Ana Lúcia Dias
Keyword(s):  
Chromosomal Location ◽  
5S Rdna ◽  
Rrna Genes ◽  
Telomeric Region ◽  
Fluorescent Staining ◽  
Homologous Chromosomes ◽  
Rdna Probe ◽  
5S Rrna Genes ◽  
Iheringichthys Labrosus

Twenty-five specimens of Iheringichthys labrosus from the Capivara Reservoir were analysed cytogenetically. AgNORs were detected in a pair of ST chromosomes, in the telomeric region of the long arm. Some individuals showed size heteromorphism of this region between homologous chromosomes. Treatment with CMA3 displayed GC-rich regions corresponding to the AgNOR pair, plus other fluorescent staining. In situ hybridization by fluorescence (FISH) with the 18S rDNA probe showed only one pair of stained chromosomes, confirming the heteromorphism observed with AgNO3 and CMA3 in some individuals. The 5S rDNA probe revealed telomeric staining on the long arm of a pair of chromosomes of the ST-A group, probably different from the NOR pair.

Localization of the 5S rRNA genes and evidence for diversity in the 5S rDNA region of maize

Gene ◽  
1981 ◽  
Vol 15 (1) ◽  
pp. 7-20 ◽  
Author(s):  
P.N. Mascia ◽  
I. Rubenstein ◽  
R.L. Phillips ◽  
A.S. Wang ◽  
Lu Zhen Xiang
Keyword(s):  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
5S Rrna Genes

scholarly journals Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

2020 ◽  
Vol 21 (8) ◽  
pp. 2931 ◽  
Author(s):  
Ruslan Kalendar ◽  
Olga Raskina ◽  
Alexander Belyayev ◽  
Alan H. Schulman
Keyword(s):  
Copy Number ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Gene Copy ◽  
Rrna Gene ◽  
Long Terminal Repeats ◽  
5S Rrna Genes ◽  
Pol Iii ◽  
Tandem Arrays

Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.

Cytogenetic characterization by in situ hybridization techniques and molecular analysis of 5S rRNA genes of the European hazelnut (Corylus avellana)

Genome ◽  
2013 ◽  
Vol 56 (3) ◽  
pp. 155-159 ◽  
Author(s):  
E. Falistocco ◽  
G. Marconi
Keyword(s):  
Chromosome Structure ◽  
5S Rdna ◽  
Corylus Avellana ◽  
The Self ◽  
Rrna Genes ◽  
Additional Information ◽  
Cytogenetic Characterization ◽  
5S Rrna Genes ◽  
Corylus Avellana L

The European hazelnut (Corylus avellana L.) is widespread in Europe, where it has been cultivated for centuries. Despite progress in genetics, most of the cytogenetic aspects of this species have been overlooked. The aim of this study was to fill in this gap and obtain basic information on the chromosome structure of this species. Karyomorphological analysis confirmed the chromosome number 2n = 22 and showed that, despite their apparent uniformity, the chromosomes could be separated into three groups of different size: large (L), medium (M), and small (S). As a first step towards the physical mapping of the hazelnut chromosomes, we applied FISH to localize the position of rRNA genes (rDNA). The sites of 45S and 5S rDNA enabled us to identify two chromosome pairs belonging, respectively, to the L and S groups. The self-GISH procedure revealed that repetitive DNA is concentrated in the pericentromeric regions of the chromosomes, as with other species with rather small genomes. The analysis of 5S rDNA repeats offered additional information on the hazelnut genome by obtaining the whole sequence of the transcribed region so far unpublished. The overall results constitute a substantial advance in hazelnut cytogenetics. Further investigation of other species of Corylus could be an effective approach to understanding the phylogenesis of the genus and resolving taxonomic problems.

Genomic organization and evolution of the 5S ribosomal DNA in the ancient fish sturgeon

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 18-28 ◽  
Author(s):  
Francisca Robles ◽  
Roberto de la Herrán ◽  
Arne Ludwig ◽  
Carmelo Ruiz Rejón ◽  
Manuel Ruiz Rejón ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Ribosomal Dna ◽  
5S Rdna ◽  
Rrna Genes ◽  
Coding Region ◽  
Coding Regions ◽  
Interspecific Differences ◽  
Sturgeon Species ◽  
Selective Forces ◽  
5S Gene

Ribosomal DNA in sturgeon is informative when analyzed at the molecular level because it bears unique characteristics that are, to a certain extent, ancestral within vertebrates. In this paper, we examine the structure and the molecular evolution of the 5S ribosomal DNA (rDNA) region in 13 sturgeon species, comparing both the 5S ribosomal RNA (rRNA) genes and the non-transcribed spacer (NTS) sequences between the coding regions. We have found that different NTS and 5S gene variants are intermixed in the 5S rDNA arrays of the different sturgeon species and that all variants are ancestral, having been maintained over many millions of years. Using predictive models, we have found similar levels of sequence diversity in the coding regions, as well as in the non-coding region, but fixed interspecific differences are underrepresented for 5S genes. However, contrary to the expectations, we have not found fixed differences between NTS sequences when comparing many pairs of species. Specifically, when they belong to the same phylogeographic clade of the four into which the sturgeon is divided, but fixation of mutations and divergence is found between species belonging to different phylogeographic clades. Our results suggest that the evolution of the two parts of the 5S rDNA region cannot be explained exclusively as the outcome of a balance between mutational, homogenizing (i.e., gene conversion as a predominant force in sturgeon), and selective forces. Rather, they suggest that other factors (i.e., hybridization) might be superimposed over those forces and thus could to some extent be masking their effects.Key words: sturgeon, 5S rDNA, NTS sequence, 5S gene, concerted evolution, sequence homogenization, gene conversion, hybridization.

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