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.

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 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.

Chromosomal mapping of 18S–28S and 5S rRNA genes by two-colour fluorescent in situ hybridization in six sturgeon species

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 473-477 ◽  
Author(s):  
Francesco Fontana ◽  
Massimo Lanfredi ◽  
Leonardo Congiu ◽  
Marilena Leis ◽  
Milvia Chicca ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Close Association ◽  
5S Rdna ◽  
28S Rdna ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
Acipenser Baerii ◽  
Sturgeon Species

The number and distribution of the 18S–28S and 5S rRNA (rDNA) gene sequences were examined on mitotic chromosomes of six sturgeon species by two-colour in situ hybridization. Four of the six species, Huso huso, Acipenser stellatus, Acipenser sturio, and Acipenser ruthenus, with about 120 chromosomes, showed from six to eight 18S–28S rDNA signals, while 5S rDNA signals were on only one chromosome pair. The two species with 250–270 chromosomes, Acipenser baerii and Acipenser transmontanus, showed from 10 to 12 18S–28S sites and two chromosome pairs bearing 5S rDNA signals. In all examined species, the rather intense 5S rDNA signals apparently overlapped those of 18S–28S rDNA. These data support the diploid–tetraploid relationships between the two chromosome groups of sturgeons. The close association between the two rDNA families in species belonging to an ancestral fish order, such as Acipenseriformes, supports the hypothesis that the association represents a primitive condition.Key words: Acipenseriformes, FISH, fish cytogenetics, ribosomal genes.

scholarly journals Type I elements mediate replication fork pausing at conserved upstream sites in the Tetrahymena thermophila ribosomal DNA minichromosome.

1997 ◽  
Vol 17 (8) ◽  
pp. 4517-4525 ◽  
Author(s):  
D M MacAlpine ◽  
Z Zhang ◽  
G M Kapler
Keyword(s):  
Ribosomal Dna ◽  
Replication Fork ◽  
Tetrahymena Thermophila ◽  
Replication Initiation ◽  
Rrna Genes ◽  
Type I ◽  
Replication Forks ◽  
Coding Region ◽  
Two Dimensional Gel Electrophoresis ◽  
Directional Bias

Two-dimensional gel electrophoresis was used to study replication of the Tetrahymena thermophila ribosomal DNA (rDNA) minichromosome. During vegetative growth, the rDNA is replicated exclusively from origins in the 5' nontranscribed spacer (NTS). Whereas replication fork movement through the rest of the chromosome appears to be continuous, movement through the 5' NTS is not. Replication forks arrest transiently at three prominent replication fork pausing sites (RFPs) located in or immediately adjacent to nucleosome-free regions of the 5' NTS. Pausing at these sites is dramatically diminished during replication in Escherichia coli, suggesting that chromatin organization or Tetrahymena-specific proteins may be required. A conserved tripartite sequence was identified at each pausing site. Mutations in type I elements diminish pausing at proximal RFPs. Hence, type I elements, previously shown to control replication initiation, also regulate elongation of existing replication forks. Studies with rDNA transformants revealed a strong directional bias for fork pausing. Strong pausing only occurred in forks moving toward the rRNA-coding region. We propose that fork pausing in the 5' NTS evolved to synchronize replication and transcription of the downstream rRNA genes.

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.

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 Chromosomal characterization and physical mapping of the 5S and the 18S-5.8S-25S ribosomal DNA in Helianthus argophyllus, with new data from Helianthus annuus

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 110-115 ◽  
Author(s):  
T Cuéllar ◽  
J Orellana ◽  
E Belhassen ◽  
J L Bella
Keyword(s):  
Ribosomal Dna ◽  
Physical Mapping ◽  
Dna Sequences ◽  
5S Rdna ◽  
The Other ◽  
Mitotic Chromosomes ◽  
Introgression Breeding ◽  
C Banding ◽  
Interspecific Differences ◽  
Secondary Constrictions

The characterization of the mitotic chromosomes of Helianthus argophyllus by means of Feulgen staining, Giemsa C-banding, and the usual DNA sequence-specific fluorochromes allows a chromosomal classification of this species, and shows that two kinds of heterochromatin co-exist equilocally in its chromosomes. One type is confined to the pericentromeric areas of all the chromosomes and the other is associated with the secondary constrictions of the satellite chromosomes. This species is evolutionarily very close to H. annuus with which it is involved in introgression breeding programs. Since these two species show no intra- or interspecific differences with the above treatments, we have used C-banding followed by DAPI, chromomycin A3 or Acridine Orange, and the fluorescent in situ hybridization (FISH) with 5S and 18S-25S ribosomal DNA probes to characterize further the chromosomes of both species in an attempt to find practically applicable chromosomal markers. Our results confirm the heterogeneity of the heterochromatin in these species and show that neither its distribution nor its response to distinct fluorochrome treatments allows better discrimination of the chromosomes within or between the species. On the other hand, the 18S-5.8S-25S rDNA arrays are located in the secondary constrictions of the satellited SM7, SM10, and ST13 pairs and the 5S-rDNA genes are interstitially placed on the short arm of the SM7 and SM11 chromosomes in both species. This permits these chromosomes to be distinguished and provides markers which may be helpful for further physical mapping of DNA sequences in these species.Key words: chromosome banding, sunflower cytogenetics, heterochromatin, ribosomal DNA mapping, FISH.

Cerastoderma glaucum 5S ribosomal DNA: characterization of the repeat unit, divergence with respect to Cerastoderma edule, and PCR–RFLPs for the identification of both cockles

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 427-442 ◽  
Author(s):  
Ruth Freire ◽  
Ana Insua ◽  
Josefina Méndez
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
5S Rdna ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Coding Region ◽  
Cerastoderma Edule ◽  
Cerastoderma Glaucum ◽  
Nontranscribed Spacer

The 5S rDNA repeat unit of the cockle Cerastoderma glaucum from the Mediterranean and Baltic coasts was PCR amplified and sequenced. The length of the units was 539–568 bp, of which 120 bp were assigned to the 5S rRNA gene and 419–448 bp to the spacer region, and the G/C content was 46%–49%, 54%, and 44%–47%, respectively. Two types of units (A and B), differing in the spacer, were distinguished based on the percentage of differences and clustering in phylogenetic trees. A PCR assay with specific primers for each unit type indicated that the occurrence of both units is not restricted to the sequenced individuals. The 5S rDNA units of C. glaucum were compared with new and previously reported sequences of Cerastoderma edule. The degree of variation observed in C. edule was lower than that in C. glaucum and evidence for the existence of units A and B in C. edule was not found. The two cockles have the same coding region but displayed numerous fixed differences in the spacer region and group separately in the phylogenetic trees. Digestion of the 5S rDNA PCR product with the restriction enzymes HaeIII and EcoRV revealed two RFLPs useful for cockle identification.Key words: Cerastoderma, cockle identification, 5S ribosomal DNA, nontranscribed spacer variation, PCR-RFLP.

scholarly journals Evidence for Recurrent Paralogous Gene Conversion and Exceptional Allelic Divergence in the Attacin Genes of Drosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 659-671 ◽  
Author(s):  
Brian P Lazzaro ◽  
Andrew G Clark
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Conversion ◽  
Amino Acid Level ◽  
Antibacterial Peptides ◽  
Paralogous Gene ◽  
Coding Region ◽  
Coding Regions ◽  
Naturally Occurring ◽  
Show Evidence ◽  
Attacin A

Abstract Insects produce a limited variety of antibacterial peptides to combat a wide diversity of pathogens. These peptides are often conserved across evolutionarily distant taxa, but little is known about the level and structure of polymorphism within species. We have surveyed naturally occurring genetic variation in the promoter and coding regions of three Attacin antibacterial peptide genes from 12 lines of Drosophila melanogaster. These genes exhibit high levels of silent nucleotide variations (1–3% per nucleotide heterozygosity), but are not excessively polymorphic at the amino acid level. There is extensive variation in the Attacin promoters, some of which may affect transcriptional efficiency, and one line carries a deletion in the Attacin A coding region that renders this gene nonfunctional. Two of the genes, Attacins A and B, are arranged in tandem and show evidence of repeated interlocus gene conversion. Attacin C, more divergent and located 1.3 Mbp upstream of Attacins A and B, does not appear to have been involved in such exchanges. All three genes are characterized by divergent haplotypes, and one Attacin AB allele appears to have recently increased rapidly in frequency in the population.

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.

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