Evolution of 5S rDNA unit arrays in the plant genus Nicotiana (Solanaceae)

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 556-562 ◽  
Author(s):  
R Matyasek ◽  
J Fulnecek ◽  
K Y Lim ◽  
A R Leitch ◽  
A Kovarik
Keyword(s):  
Unit Length ◽  
Phylogenetic Reconstruction ◽  
5S Rdna ◽  
Nicotiana Sylvestris ◽  
Nicotiana Glutinosa ◽  
Deletion Event ◽  
Rdna Unit ◽  
Rdna Loci ◽  
Nicotiana Longiflora ◽  
Family Based

Nicotiana tabacum (tobacco, Solanaceae) has two 5S ribosomal DNA (rDNA) families, one of unit length ~646 bp and the other ~430 bp, that differ in the length of the 5S rDNA non-transcribed spacer (NTS). The long 5S rDNA family, found on the T genome of tobacco and in Nicotiana tomentosiformis, contains a GC-rich subregion that is absent in the short family. We designed primers for this subregion and generated a probe that we used against a range of Nicotiana and related Solanaceous species. We demonstrated the presence of the GC-rich subregion in a range of Nicotiana species, but it was absent in Nicotiana sylvestris, Nicotiana longiflora, and two closely related genera, Petunia and Solanum. These data suggest that this subregion of the NTS is likely to have evolved with the genus Nicotiana. The absence of the subregion in N. sylvestris and N. longiflora is likely to have arisen by a deletion event in the evolution of section alatae. We demonstrate patterns of evolution in the 5S rDNA unit cluster in relation to a phylogenetic reconstruction of species relationships in section tomentosae. Nicotiana glutinosa diverged early from the section and contains a 5S rDNA family based on a 550-bp unit. After this divergence, 430- and 650-bp rDNA unit families evolved. The 650-bp family is found in all species of tomentosae (except N. glutinosa) and in tobacco. The 430-bp family within tomentosae includes the GC-rich subregion and is thus unrelated to the 430-bp family in N. sylvestris. Nicotiana setchellii is unusual in that it has three 5S rDNA loci, including one locus that is exceptionally large. This species, unique to tomentosae, has a very abundant 900-bp unit family. It is possible that this 900-bp family occurs on this one large locus. In N. tomentosa and N. kawakamii, the 650-bp family is predominant, whereas N. tomentosiformis and N. otophora have only the 650-bp family. There is no clear relationship between the number of 5S families and the number of 5S rDNA loci. Certainly the replacement of 5S rDNA units, perhaps by gene conversion, has occurred repeatedly in the evolution of genus Nicotiana.Key words: 5S rDNA, evolution, Nicotiana, Solanaceae, satellite homogenization.

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽  
1996 ◽  
Vol 39 (3) ◽  
pp. 535-542 ◽  
Author(s):  
Concha Linares ◽  
Juan González ◽  
Esther Ferrer ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Diploid Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
26S Rdna ◽  
A Genome ◽  
Rdna Loci ◽  
C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

Detection of a variable number of 18S-5.8S-26S and 5S ribosomal DNA loci by fluorescent in situ hybridization in diploid and tetraploid Arachis species

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 52-59 ◽  
Author(s):  
S N Raina ◽  
Y Mukai
Keyword(s):  
In Situ Hybridization ◽  
5S Rdna ◽  
Gene Families ◽  
Ribosomal Gene ◽  
Rrna Genes ◽  
Tetraploid Species ◽  
Arachis Species ◽  
26S Rdna ◽  
Rdna Loci

In order to obtain new information on the genome organization of Arachis ribosomal DNA, more particularly among A. hypogaea and its close relatives, the distribution of the 18S-5.8S-26S and 5S ribosomal RNA gene families on the chromosomes of 21 diploid and tetraploid Arachis species, selected from six of nine taxonomic sections, was analyzed by in situ hybridization with pTa71 (18S-5.8S-26S rDNA) and pTa794 (5S rDNA) clones. Two major 18S-5.8S-26S rDNA loci with intense signals were found in the nucleolus organizer regions (NOR) of each of the diploid and tetraploid species. In addition to extended signals at major NORs, two to six medium and (or) minute-sized signals were also observed. Variability in the number, size, and location of 18S-5.8S-26S sites could generally distinguish species within the same genome as well as between species with different genomes. The use of double fluorescence in situ hybridization enabled us to locate the positions of 5S rRNA genes in relation to the chromosomal location of 18S-5.8S-26S rRNA genes in Arachis chromosomes which were difficult to karyotype. Two or four 5S rDNA loci and 18S-5.8S-26S rDNA loci were generally located on different chromosomes. The tandemly repeated 5S rDNA sites were diagnostic for T and C genomes. In one species, each of B and Am genomes, the two ribosomal gene families were observed to occur at the same locus. Barring A. ipaensis and A. valida, all the diploid species had characteristic centromeric bands in all the 20 chromosomes. In tetraploid species A. hypogaea and A. monticola only 20 out of 40 chromosomes showed centromeric bands. Comparative studies of distribution of the two ribosomal gene families, and occurrence of centromeric bands in only 20 chromosomes of the tetraploid species suggests that A. villosa and A. ipaensis are the diploid progenitors of A. hypogaea and A. monticola. This study excludes A. batizocoi as the B genome donor species for A. hypogaea and A. monticola.Key words: Arachis species, 5S rRNA, 18S-5.8S-26S rRNA, in situ hybridization, evolution.

scholarly journals Intraspecific polymorphism of ribosomal DNA loci number and morphology in Brachypodium pinnatum and Brachypodium sylvaticum

2012 ◽  
Vol 17 (4) ◽  
Author(s):  
Ewa Breda ◽  
Elzbieta Wolny ◽  
Robert Hasterok
Keyword(s):  
5S Rdna ◽  
Staining Technique ◽  
Rdna Locus ◽  
Chromosomal Distribution ◽  
Metaphase Chromosomes ◽  
Brachypodium Sylvaticum ◽  
Rdna Sites ◽  
Rdna Loci ◽  
35S Rdna ◽  
25S Rdna

AbstractThe genus Brachypodium has become the target of extensive cytomolecular studies since one of its representatives, B. distachyon, has been accepted as a model plant for temperate cereals and forage grasses. Recent preliminary studies suggested that intraspecific rDNA polymorphism can occur in at least two members of the genus, B. sylvaticum and B. pinnatum, so the aim of this study was to further analyse this phenomenon. FISH with 25S rDNA and 5S rDNA probes was performed on somatic metaphase chromosomes, supplemented by the silver staining technique which distinguishes transcriptionally active from inactive 18S-5.8S-25S rDNA loci. The number, size and chromosomal distribution of 5S rDNA loci were very constant: two loci were invariably observed in all studied diploid accessions of both species, while four 5S rDNA loci were present in the tetraploid B. pinnatum. In contrast to 5S rDNA loci, those of the 35S rDNA were more variable. Two or three loci were observed in the diploid B. pinnatum and four in tetraploid accessions. In chromosome complements of B. sylvaticum accessions from two to six 35S rDNA sites were detected. Regardless of total rDNA locus number, only two were transcriptionally active in diploid accessions of both species, while two or four were active in the tetraploid B. pinnatum. Additionally, the fluorescent CMA/DAPI banding method was used to identify the relation between rDNA sites and CMA+ bands. It was revealed that the number and chromosomal distribution of CMA+ bands are in congruence only with 35S rDNA loci which gave strong FISH signals.

Plant 5S rDNA has multiple alternative nucleosome positions

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 840-850 ◽  
Author(s):  
Jaroslav Fulnecek ◽  
Roman Matyasek ◽  
Ales Kovarik
Keyword(s):  
Tandem Repeats ◽  
5S Rdna ◽  
Nicotiana Sylvestris ◽  
Micrococcal Nuclease ◽  
Dna Curvature ◽  
Cleavage Sites ◽  
Computer Prediction ◽  
Theoretical Computer ◽  
Nontranscribed Spacer ◽  
Multiple Alternative

In plants, 5S ribosomal DNA (5S rDNA) is typically found in hundreds of copies of tandemly arranged units. Nucleotide database searches revealed that the majority of 5S genes (>90%) have repeat lengths that are not simple multiples of a plant nucleosomal unit, ranging in plants from 175–185 bp. To get insight into the chromatin structure, we have determined positions of nucleosomes in the Nicotiana sylvestris and Nicotiana tomentosiformis 5S rDNA units with repeat lengths of about 430 and 645 bp, respectively. Mapping experiments carried out on isolated nucleo somal DNA revealed many (>50) micrococcal nuclease cleavage sites in each class of repeats. Permutation analysis and theoretical computer prediction showed multiple DNA bend sites, mostly located in the nontranscribed spacer region. The distance between bend sites, however, did not correspond to the average spacing of nucleosomes in 5S chromatin (~180 bp). These data indicate that 5S rDNA does not have fixed nucleosomal positioning sites and that units can be wrapped in a number of alternative nucleosome frames. Consequently, accessibility of transcription factors to cognate motifs might vary across the tandem array, potentially influencing gene expression.Key words: Nicotiana, 5S rDNA, heterochromatin, tandem repeats, nucleosomes, DNA curvature.

scholarly journals Evidence of the occurrence of structural chromosome changes at the initial diploid diversification of the autopolyploid Turnera sidoides L. (Passifloraceae) complex

Genome ◽  
2016 ◽  
Vol 59 (2) ◽  
pp. 127-136
Author(s):  
Juan M. Roggero Luque ◽  
E.M. Sara Moreno ◽  
I. Evelin Kovalsky ◽  
J. Guillermo Seijo ◽  
Viviana G. Solís Neffa
Keyword(s):  
5S Rdna ◽  
Chromosome Analysis ◽  
Dapi Staining ◽  
Chromosome Markers ◽  
Rdna Loci ◽  
Structural Chromosome ◽  
Turnera Sidoides ◽  
Perennial Herbs ◽  
Diploid Level ◽  
Secondary Constrictions

Turnera sidoides is an autopolyploid complex of obligate outcrossing perennial herbs. It includes five subspecies and five morphotypes in which diploid to octoploid cytotypes were found. Based on phenetic analyses of the complex and karyotype data of polyploid cytotypes, it has been hypothesized that morphological and chromosome differentiation of T. sidoides occurred at the diploid level. To test this hypothesis, we present the first detailed chromosome analysis of diploid populations of three subspecies and four morphotypes. CMA+/DAPI− bands were restricted to secondary constrictions (except in the andino morphotype) and varied in number and position among taxa. By contrast, DAPI staining was uniform in all the materials investigated. The number and position of 45S rDNA loci were coincident with the CMA+/DAPI− bands associated with secondary constrictions. Only one pair of 5S rDNA loci was detected in all the taxa (except in subsp. holosericea), but its position was variable. The identified chromosome markers varied among the three subspecies analyzed, but they were more conserved among the morphotypes of subsp. pinnatifida. Cluster analysis of these chromosome markers supports the current taxonomic arrangement of diploids and demonstrates that structural chromosome changes would have led or accompanied the initial differentiation of T. sidoides at the diploid level.

The 5S rRNA gene in wall barley (Hordeum murinum L. sensu lato): Sequence variation among repeat units and relationship to the Y haplome in the genus Hordeum (Poaceae: Triticeae)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 854-866 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Current Model ◽  
5S Rdna ◽  
Rrna Gene ◽  
Sequence Information ◽  
Rdna Unit ◽  
Repeat Units ◽  
Unit Classes ◽  
Unit Class ◽  
Hordeum Murinum ◽  
Cladistic Analyses

The molecular diversity of the 5S rDNA units in 13 accessions of wall barley, which include Hordeum murinum, H. leporinum, and H. glaucum, is reported. Our analyses, based on 54 sequenced clones, indicate the presence of two sequence classes not previously seen in other barley species; namely, the long Y1 unit class and the short Y1 unit class. In addition, the accumulation of new sequence information has allowed us to refine previous groups. Using these new results, along with previously published work, we present a summary of all the unit classes described to date and potential correspondences between 5S rDNA unit classes and haplomes identified previously. In H. murinum, we found the long H1 and long X2 unit classes, and in one of six accessions referable to H. glaucum we found the unique short Y1 unit class. Our cladistic analyses, using orthologous sequences, provide support for the current model for the relationships among several species within the Triticeae.Key words: 5S rDNA, Y haplome, genomes, wall barley, Triticeae.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

scholarly journals The genome structure of Arachis hypogaea (Linnaeus, 1753) and an induced Arachis allotetraploid revealed by molecular cytogenetics

2018 ◽  
Vol 12 (1) ◽  
pp. 111-140 ◽  
Author(s):  
Eliza F. de M. B. do Nascimento ◽  
Bruna V. dos Santos ◽  
Lara O. C. Marques ◽  
Patricia M. Guimarães ◽  
Ana C. M. Brasileiro ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Structure ◽  
Diploid Species ◽  
Molecular Cytogenetics ◽  
5S Rdna ◽  
Rdna Locus ◽  
Genetic Changes ◽  
Rdna Loci ◽  
Cultivated Plant ◽  
Fish Signal

Peanut,Arachishypogaea(Linnaeus, 1753) is an allotetraploid cultivated plant with two subgenomes derived from the hybridization between two diploid wild species,A.duranensis(Krapovickas & W. C. Gregory, 1994) andA.ipaensis(Krapovickas & W. C. Gregory, 1994), followed by spontaneous chromosomal duplication. To understand genome changes following polyploidy, the chromosomes ofA.hypogaea, IpaDur1, an induced allotetraploid (A.ipaensis×A.duranensis)4xand the diploid progenitor species were cytogenetically compared. The karyotypes of the allotetraploids share the number and general morphology of chromosomes; DAPI+bands pattern and number of 5S rDNA loci. However, one 5S rDNA locus presents a heteromorphic FISH signal in both allotetraploids, relative to corresponding progenitor. Whilst forA.hypogaeathe number of 45S rDNA loci was equivalent to the sum of those present in the diploid species, in IpaDur1, two loci have not been detected. Overall distribution of repetitive DNA sequences was similar in both allotetraploids, althoughA.hypogaeahad additional CMA3+bands and few slight differences in the LTR-retrotransposons distribution compared to IpaDur1. GISH showed that the chromosomes of both allotetraploids had preferential hybridization to their corresponding diploid genomes. Nevertheless, at least one pair of IpaDur1 chromosomes had a clear mosaic hybridization pattern indicating recombination between the subgenomes, clear evidence that the genome of IpaDur1 shows some instability comparing to the genome ofA.hypogaeathat shows no mosaic of subgenomes, although both allotetraploids derive from the same progenitor species. For some reasons, the chromosome structure ofA.hypogaeais inherently more stable, or, it has been at least, partially stabilized through genetic changes and selection.

Analysis of 5S rDNA Loci among Arabidopsis Ecotypes and Subspecies

2002 ◽  
Vol 1 (3) ◽  
pp. 115-122 ◽  
Author(s):  
S. Tutois ◽  
C. Cloix ◽  
O. Mathieu ◽  
C. Cuvillier ◽  
S. Tourmente
Keyword(s):  
5S Rdna ◽  
Rdna Loci

Molecular and cytological characterization of genomic variability in hexaploid wheat 'Lindström'

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 895-904
Author(s):  
Pedro Costa-Nunes ◽  
Teresa Ribeiro ◽  
Margarida Delgado ◽  
Leonor Morais-Cecílio ◽  
Neil Jones ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Large Scale ◽  
Expression Patterns ◽  
5S Rdna ◽  
Rdna Locus ◽  
B Chromosomes ◽  
Addition Line ◽  
Rdna Loci

'Lindström' wheat (AABBDD + rye B chromosomes) was used to study the effects of alien chromatin introgressed into a wheat genetic background, subjecting the wheat genome to a new and transient allopolyploidisation episode. Using this experimental material, we have previously demonstrated that no large-scale chromosomal translocations occurred as a result of the genomic constitution of the addition line. However, we have shown that the presence of a number of rye B chromosomes is associated with changes in the interphase organization and expression patterns of wheat rDNA loci. We have now extended our studies to focus on a further characterization of 'Lindström' 5S rDNA loci and also on high molecular weight glutenin subunit (HMW-GS) patterns. In the process, we have uncovered an unusually large variant of the 5S rDNA locus on wheat chromosome 1B (not to be confused with rye B chromosomes) and 2 novel HMW glutenin y-type alleles. These changes are not directly related to variation in rye B chromosome number in the present material, but the fact that a new, and still segregating, 1Dy HMW-GS gene was identified indicates a recent timescale for its origin. Strikingly, the 'Lindström' 5S rDNA 1B locus integrates a unit sharing 94% homology with a rye 5S rDNA sequence, suggesting the possibility that the wheat locus was colonized by highly homologous rye sequences during the breeding of 'Lindström', when the rye and wheat genomes were together, albeit briefly, in the same nucleus.Key words: Triticum aestivum 'Lindström', allopolyploidisation, 5S rDNA, NTS, high molecular weight glutenin (HMW-GS).

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