scholarly journals A New 45S rDNA Locus and Its Genomic Origin in the Amphidiploid of Scilla scilloides Druce.

CYTOLOGIA ◽  
2001 ◽  
Vol 66 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Masahiro Hizume ◽  
Fukashi Shibata
Keyword(s):  
Rdna Locus ◽  
45S Rdna ◽  
Scilla Scilloides

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.

Genetic and epigenetic changes of rDNA in a synthetic allotetraploid, Aegilops sharonensis × Ae. umbellulata

Genome ◽  
2008 ◽  
Vol 51 (4) ◽  
pp. 261-271 ◽  
Author(s):  
A. B. Shcherban ◽  
E. D. Badaeva ◽  
A. V. Amosova ◽  
I. G. Adonina ◽  
E. A. Salina
Keyword(s):  
Southern Hybridization ◽  
Parental Species ◽  
Genetic Alterations ◽  
Rdna Locus ◽  
45S Rdna ◽  
Rdna Unit ◽  
Aegilops Sharonensis ◽  
New Variant ◽  
Restriction Sites ◽  
Additive Inheritance

The synthetic allotetraploid Aegilops sharonensis × Ae. umbellulata (genomic formula SshU) was used to study inheritance and expression of 45S rDNA during early stages of allopolyploid formation. Using silver staining, we revealed suppression of the NORs (nucleolar organizing regions) from the Ssh genome in response to polyploidization. Most allopolyploid plants of the S2–S4 generations retained the chromosomal location of 45S rDNA typical for the parental species, except for two S3 plants in which a deletion of the rDNA locus on one of the homologous 6Ssh chromosomes was revealed. In addition, we found a decrease in NOR signal intensity on both 6Ssh chromosomes in a portion of the S3 and S4 allopolyploid plants. As Southern hybridization showed, the allopolyploid plants demonstrated additive inheritance of parental rDNA units together with contraction of copy number of some rDNA families inherited from Ae. sharonensis. Also, we identified a new variant of amplified rDNA unit with MspAI1 restriction sites characteristic of Ae. umbellulata. These genetic alterations in the allopolyploid were associated with comparative hypomethylation of the promoter region within the Ae. umbellulata–derived rDNA units. The fast uniparental elimination of rDNA observed in the synthetic allopolyploid agrees well with patterns observed previously in natural wheat allotetraploids.

scholarly journals Peculiar phenomena of rDNA locus on chromosomes of some Chinese plants in Scilla scilloides

2014 ◽  
Vol 9 (2) ◽  
pp. 47-50 ◽  
Author(s):  
Masahiro Hizume ◽  
Katsuhiko Kondo ◽  
Shouzhou Zhang ◽  
Deyuan Hong
Keyword(s):  
Rdna Locus ◽  
Scilla Scilloides

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 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.

FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 189-197 ◽  
Author(s):  
Piotr A Ziolkowski ◽  
Jan Sadowski
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
5S Rdna ◽  
Artificial Chromosome ◽  
Rdna Locus ◽  
Fish Analysis ◽  
45S Rdna ◽  
Fish Mapping ◽  
Rdna Sequences

To improve resolution of physical mapping on Brassica chromosomes, we have chosen the pachytene stage of meiosis where incompletely condensed bivalents are much longer than their counterparts at mitotic metaphase. Mapping with 5S and 45S rDNA sequences demonstrated the advantage of pachytene chromosomes in efficient physical mapping and confirmed the presence of a novel 5S rDNA locus in Brassica oleracea, initially identified by genetic mapping using restriction fragment length polymorphism (RFLP). Fluorescence in situ hybridization (FISH) analysis visualized the presence of the third 5S rDNA locus on the long arm of chromosome C2 and confirmed the earlier reports of two 45S rDNA loci in the B. oleracea genome. FISH mapping of low-copy sequences from the Arabidopsis thaliana bacterial artificial chromosome (BAC) clones on the B. oleracea chromosomes confirmed the expectation of efficient and precise physical mapping of meiotic bivalents based on data available from A. thaliana and indicated conserved organization of these two BAC sequences on two B. oleracea chromosomes. Based on the heterologous in situ hybridization with BACs and their mapping applied to long pachytene bivalents, a new approach in comparative analysis of Brassica and A. thaliana genomes is discussed.Key words: Brassicaceae, pachytene chromosomes, FISH, rDNA, BACs.

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 Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5107 ◽  
Author(s):  
Edyta Skrzypek ◽  
Tomasz Warzecha ◽  
Angelika Noga ◽  
Marzena Warchoł ◽  
Ilona Czyczyło-Mysza ◽  
...  
Keyword(s):  
Zea Mays ◽  
Avena Sativa ◽  
Meiotic Chromosome ◽  
Rdna Locus ◽  
45S Rdna ◽  
Maize Hybrids ◽  
Complete Set ◽  
Dh Lines

Background The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds. Discussion In wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes.

scholarly journals Distribution of a Limited Sir2 Protein Pool Regulates the Strength of Yeast rDNA Silencing and Is Modulated by Sir4p

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1205-1219 ◽  
Author(s):  
Jeffrey S Smith ◽  
Carrie Baker Brachmann ◽  
Lorraine Pillus ◽  
Jef D Boeke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Simple Model ◽  
Regulatory Mechanism ◽  
Transcriptional Silencing ◽  
Rdna Locus ◽  
Genetic Manipulations ◽  
Protein Levels ◽  
Endogenous Level ◽  
Protein Pool ◽  
Negative Effect

Abstract Transcriptional silencing in Saccharomyces cerevisiae occurs at the silent mating-type loci HML and HMR, at telomeres, and at the ribosomal DNA (rDNA) locus RDN1. Silencing in the rDNA occurs by a novel mechanism that depends on a single Silent Information Regulator (SIR) gene, SIR2. SIR4, essential for other silenced loci, paradoxically inhibits rDNA silencing. In this study, we elucidate a regulatory mechanism for rDNA silencing based on the finding that rDNA silencing strength directly correlates with cellular Sir2 protein levels. The endogenous level of Sir2p was shown to be limiting for rDNA silencing. Furthermore, small changes in Sir2p levels altered rDNA silencing strength. In rDNA silencing phenotypes, sir2 mutations were shown to be epistatic to sir4 mutations, indicating that SIR4 inhibition of rDNA silencing is mediated through SIR2. Furthermore, rDNA silencing is insensitive to SIR3 overexpression, but is severely reduced by overexpression of full-length Sir4p or a fragment of Sir4p that interacts with Sir2p. This negative effect of SIR4 overexpression was overridden by co-overexpression of SIR2, suggesting that SIR4 directly inhibits the rDNA silencing function of SIR2. Finally, genetic manipulations of SIR4 previously shown to promote extended life span also resulted in enhanced rDNA silencing. We propose a simple model in which telomeres act as regulators of rDNA silencing by competing for limiting amounts of Sir2 protein.

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