scholarly journals Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Judith Fehrer ◽  
Renáta Slavíková ◽  
Ladislava Paštová ◽  
Jiřina Josefiová ◽  
Patrik Mráz ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Phylogenetic Analyses ◽  
General Pattern ◽  
5S Rdna ◽  
Rdna Locus ◽  
Intergeneric Hybridization ◽  
45S Rdna ◽  
Rdna Loci

Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.

scholarly journals Ribosomal DNA, tri- and bi-partite pericentromeres in the permanent translocation heterozygote Rhoeo spathacea

2010 ◽  
Vol 15 (4) ◽  
Author(s):  
Hieronim Golczyk ◽  
Robert Hasterok ◽  
Marek Szklarczyk
Keyword(s):  
Ribosomal Dna ◽  
5S Rdna ◽  
Rdna Locus ◽  
45S Rdna ◽  
Chromomycin A3 ◽  
Specific Fluorescence ◽  
Translocation Heterozygote ◽  
Differential Amplification ◽  
Chromosome Arm

AbstractHigh- and low-stringency FISH and base-specific fluorescence were performed on the permanent translocation heterozygote Rhoeo spathacea (2n = 12). Our results indicate that 45S rDNA arrays, rDNA-related sequences and other GC-rich DNA fraction(s) are located within the pericentromeric regions of all twelve chromosomes, usually colocalizing with the chromomycin A3-positive bands. Homogenization of the pericentromeric regions appears to result from the concerted spread of GC-rich sequences, with differential amplification likely. We found new 5S rDNA patterns, which suggest a variability in the breakpoints and in the consequent chromosome reorganizations. It was found that the large 5S rDNA locus residing on each of the 8E and 9E arms consisted of two smaller loci. On each of the two chromosome arms 3b and 4b, in addition to the major subtelomeric 5S rDNA locus, a new minor locus was found interstitially about 40% along the arm length. The arrangement of cytotogenetic landmarks and chromosome arm measurements are discussed with regard to genome repatterning in Rhoeo.

Uniparental loss of ribosomal DNA in the allotetraploid grass Zingeria trichopoda (2n = 8)

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 156-163 ◽  
Author(s):  
Violetta Kotseruba ◽  
Dorota Gernand ◽  
Armin Meister ◽  
Andreas Houben
Keyword(s):  
Ribosomal Dna ◽  
5S Rdna ◽  
45S Rdna ◽  
Rdna Sequences ◽  
Genome Wide ◽  
Rdna Sites ◽  
Rdna Loci ◽  
Subsequent Elimination ◽  
Genome Level

Analysis of the grass Zingeria trichopoda (2n = 8, 2C = 5.3 pg) revealed a dynamic evolution with the following characteristics. (i) Genomic in situ hybridization (GISH) demonstrates that Z. trichopoda evolved from an interspecific hybrid involving a species like contemporary Zingeria biebersteiniana (2n = 4) and a second species with a similar low number of chromosomes. The nucleus of Z. trichopoda is spatially organized at the genome level and the two parental genomes occupy distinct and separate domains of lateral arrangements. (ii) The copy number of the Z. biebersteiniana specific pericentromeric tandem repeat family Zbcen1 is drastically reduced in Z. trichopoda. (iii) GISH in combination with labeled rDNA sequences simultaneously discriminated the two parental genomes and the corresponding 5S and 45S rDNA sites. Hence, following allopolyploidization of Z. trichopoda the Z. biebersteiniana like parental chromosomes probably underwent drastic loss of 45S rDNA. This could have arisen either through the loss ofZ. biebersteiniana derived 45S rDNA or through Z. trichopoda genome-wide homogenization of Z. biebersteiniana type 45S rDNA and subsequent elimination of 45S rDNA loci from Z. biebersteiniana derived chromosomes. Finally, 5S rDNA loci are present in both subgenomes of Z. trichopoda and the chromosomal position of these loci is similar for both Z. biebersteiniana and the Z. biebersteiniana like parental genome of Z. trichopoda.Key words: genome evolution, polyploidy, ribosomal DNA, Poaceae.

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.

Chromosomal localization and characterization of rDNA loci in the Brassica A and C genomes

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 582-587 ◽  
Author(s):  
R. J. Snowdon ◽  
W. Köhler ◽  
A. Köhler
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Ribosomal Dna ◽  
Diploid Species ◽  
Rdna Locus ◽  
Chromosome Morphology ◽  
Rdna Site ◽  
A Genome ◽  
Rdna Loci

Using fluorescence in situ hybridization, we located ribosomal DNA loci on prometaphase chromosomes of the diploid species Brassica rapa and Brassica oleracea and their amphidiploid Brassica napus. Based on comparisons of chromosome morphology and hybridization patterns, we characterized the individual B. napus rDNA loci according to their presumed origins in the Brassica A and C genomes. As reported in other studies, the sum of rDNA loci observed on B. rapa (AA genome) and B. oleracea (CC genome) chromosomes was one greater than the total number of loci seen in their amphidiploid B. napus (AACC). Evidence is presented that this reduction in B. napus rDNA locus number results from the loss of the smallest A genome rDNA site in the amphidiploid.Key words: Brassica, fluorescence in situ hybridization, ribosomal DNA, rDNA.

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.

Heterochromatin patterns and ribosomal DNA loci distribution in diploid and polyploid Crotalaria species (Leguminosae, Papilionoideae), and inferences on karyotype evolution

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 718-726 ◽  
Author(s):  
Mateus Mondin ◽  
Margarida L.R. Aguiar-Perecin
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Karyotype Evolution ◽  
5S Rdna ◽  
Rdna Locus ◽  
Variable Number ◽  
Chromosome 1 ◽  
Distamycin A ◽  
Rdna Sites

Most Crotalaria species display a symmetric karyotype with 2n = 16, but 2n = 14 is found in Chrysocalycinae subsection Incanae and 2n = 32 in American species of the section Calycinae. Seven species of the sections Chrysocalycinae, Calycinae, and Crotalaria were analyzed for the identification of heterochromatin types with GC- and AT-specific fluorochromes and chromosomal location of ribosomal DNA loci using fluorescent in situ hybridization (FISH). A major 45S rDNA locus was observed on chromosome 1 in all the species, and a variable number of minor ones were revealed. Only one 5S rDNA locus was observed in the species investigated. Chromomycin A3 (CMA) revealed CMA+ bands colocalized with most rDNA loci, small bands unrelated to ribosomal DNA on two chromosome pairs in Crotalaria incana, and CMA+ centromeric bands that were quenched by distamycin A were detected in species of Calycinae and Crotalaria sections. DAPI+ bands were detected in C. incana. The results support the species relationships based on flower specialization and were useful for providing insight into mechanisms of karyotype evolution. The heterochromatin types revealed by fluorochromes suggest the occurrence of rearrangements in repetitive DNA families in these heterochromatic blocks during species diversification. This DNA sequence turnover and the variability in number/position of rDNA sites could be interpreted as resulting from unequal crossing over and (or) transposition events. The occurrence of only one 5S rDNA locus and the smaller chromosome size in the polyploids suggest that DNA sequence losses took place following polyploidization events.

scholarly journals Chromosome polymorphism in species of the genus Hedysarum L. (Fabaceae) originated from Southern Sibеria

2020 ◽  
Vol 19 (1) ◽  
pp. 14-16
Author(s):  
O. Yu. Yurkevich ◽  
T. E. Samatadze ◽  
I. Yu. Selyutina ◽  
S. I. Romashkina ◽  
S. A. Zoshchuk ◽  
...  
Keyword(s):  
Close Relationships ◽  
5S Rdna ◽  
Chromosomal Polymorphism ◽  
Rdna Locus ◽  
Chromosome Polymorphism ◽  
45S Rdna ◽  
High Similarity ◽  
Southern Siberia ◽  
Molecular Cytogenetic ◽  
First Time

For the first time, chromosomal polymorphism in karyotypes of three species from the section Hedysarum (= syn. Gamotion) of the genus Hedysarum L. (Fabaceae) grown in Southern Siberia has been studied with the useof molecular cytogenetic markers. This comparative molecular cytogenetic analysis revealed high similarity in morphology of chromosomes in H. alpinum L., H. austrosibiricum B. Fedtsch. and H. theinum Krasnob. as well as in patterns ofdistribution of 45S and 5S rDNA loci in their karyotypes confirming their close relationships. Considerable intra-specificpolymorphism on 45S rDNA chromosome localization was detected in H. theinum. In karyotype of H. alpinum, unlikethe other two species, two chromosome pairs bearing 5S rDNA locus were observed which could be used as additionalspecies-specific markers.

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.

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).

scholarly journals Analyses of the Updated “Animal rDNA Loci Database” with an Emphasis on Its New Features

2021 ◽  
Vol 22 (21) ◽  
pp. 11403
Author(s):  
Jana Sochorová ◽  
Francisco Gálvez ◽  
Roman Matyášek ◽  
Sònia Garcia ◽  
Aleš Kovařík
Keyword(s):  
Sex Chromosomes ◽  
5S Rdna ◽  
High Variability ◽  
Rrna Genes ◽  
45S Rdna ◽  
Data Analyses ◽  
Rdna Sites ◽  
Rdna Loci ◽  
Staining Methods ◽  
Active Nors

We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists. 

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