Length and sequence heterogeneity in 5S rDNA of Populus deltoides

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1181-1188 ◽  
Author(s):  
Madan S Negi ◽  
Jyothi Rajagopal ◽  
Neeti Chauhan ◽  
Richard Cronn ◽  
Malathi Lakshmikumaran
Keyword(s):  
Populus Deltoides ◽  
5S Rdna ◽  
Rrna Genes ◽  
Length Variation ◽  
Spacer Length ◽  
Sequence Heterogeneity ◽  
Distance Analysis ◽  
Repeat Units ◽  
Class 1 ◽  
Dna Microsatellite

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (π) estimates that are less than 0.15% of those obtained for class 2 spacers (π = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.Key words: 5S rDNA, Populus, repetitive DNA, microsatellite, sequence heterogeneity.

Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 815-821 ◽  
Author(s):  
Michael Pillay
Keyword(s):  
Ribosomal Rna ◽  
Restriction Site ◽  
Ribosomal Rna Genes ◽  
Rrna Genes ◽  
Eragrostis Tef ◽  
Length Variation ◽  
Rdna Repeat ◽  
Spacer Length ◽  
Repeat Units ◽  
Rna Genes

Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the intergenic spacer was used as an indicator of length variation of rDNA repeat units. rDNA repeat units in E. tef ranged in size from 8.4 to 11.07 kbp. Considerable size variation of rDNA repeats was present among accessions, between individual plants within some accessions, and within single plants. A total of 19 spacer length (sl) phenotypes was observed in 16 accessions in which 11–42 plants were analyzed. A single restriction site polymorphism was detected in PI442115 that was also distinguished by having a single sl variant. Variation in the rRNA genes is a useful indicator of genetic diversity in E. tef germplasm.Key words: Eragrostis tef, ribosomal DNA, restriction map, genetic variation.

Balancing selection on the number of repeats in the ribosomal intergenic spacer present in naturally occurring yellow perch (Perca flavescens) populations

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Frédérique Bélanger-Lépine ◽  
Christelle Leung ◽  
Hélène Glémet ◽  
Bernard Angers
Keyword(s):  
Microsatellite Loci ◽  
Yellow Perch ◽  
Balancing Selection ◽  
Natural Populations ◽  
Perca Flavescens ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Length Variation ◽  
Repeat Units ◽  
Ribosomal Intergenic Spacer

The ribosomal intergenic spacer (IGS), responsible for the rate of transcription of rRNA genes, is associated with the growth and fecundity of individuals. A previous study of IGS length variants in a yellow perch (Perca flavescens) population revealed the presence of two predominant alleles differing by 1 kb due to variation in the number of repeat units. This study aims to assess whether length variation of IGS is the result of selection in natural populations. Length variation of IGS and 11 neutral microsatellite loci were assessed in geographically distant yellow perch populations. Most populations displayed the very same IGS alleles; they did not differ in frequencies among populations and the FST was not significantly different from zero. In contrast, diversity at microsatellite loci was high and differed among populations (FST = 0.18). Selection test based on FST identified IGS as a significant outlier from neutral expectations for population differentiation. Heterozygote excess was also detected in one specific cohort, suggesting temporal variation in the selection regime. While the exact mechanism remains to be specified, together the results of this study support the contention that balancing selection is acting to maintain two distinct IGS alleles in natural fish populations.

Structure of the 5S rRNA genes in birch (Betula papyrifera) and alder (Alnus incana)

Genome ◽  
1992 ◽  
Vol 35 (2) ◽  
pp. 337-341 ◽  
Author(s):  
D. A. Johnson ◽  
C. C-Y. Chan ◽  
S. G. Gottlob-McHugh ◽  
K. Mackenzie ◽  
L. Marengère ◽  
...  
Keyword(s):  
Repeat Unit ◽  
Evolutionary Relationship ◽  
5S Rdna ◽  
Repeat Sequence ◽  
Rrna Genes ◽  
Alnus Incana ◽  
Betula Papyrifera ◽  
Repeat Units ◽  
5S Rrna Genes ◽  
Triple Band

Hybridization of a 5S rDNA probe to Southern transfers of birch (Betula papyrifera) or alder (Alnus incana) DNA digested with BamH1 reveals similar triple-band "ladder-like" patterns. The sizes of sequenced 5S repeat units from both plants ranges only from 471 to 490 base pairs, suggesting that the complexity detected by Southern analysis is not due to different size classes of 5S repeats as found in other species. Within the intercistronic spacer region, conservation of large blocks of sequence between birch and alder 5S is observed implying a close evolutionary relationship between these two species. In both species, a duplication of part of the coding sequence including a restriction site for BamH1 introduces a second BamH1 site into the repeat unit. Differential methylation of the two BamH1 restriction sites can account for the observed triple-band pattern.Key words: 5S rDNA repeat, sequence, methylation, birch, alder.

Organization of 5S rDNA in species of the fish Leporinus: two different genomic locations are characterized by distinct nontranscribed spacers

Genome ◽  
2001 ◽  
Vol 44 (5) ◽  
pp. 903-910 ◽  
Author(s):  
Cesar Martins ◽  
Pedro Manoel Galetti Jr.
Keyword(s):  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Fish Genome ◽  
Nontranscribed Spacer ◽  
Repeat Units ◽  
5S Rrna Gene ◽  
A Minor ◽  
Genomic Locations

To address understanding the organization of the 5S rRNA multigene family in the fish genome, the nucleotide sequence and organization array of 5S rDNA were investigated in the genus Leporinus, a representative freshwater fish group of South American fauna. PCR, subgenomic library screening, genomic blotting, fluorescence in situ hybridization, and DNA sequencing were employed in this study. Two arrays of 5S rDNA were identified for all species investigated, one consisting of monomeric repeat units of around 200 bp and another one with monomers of 900 bp. These 5S rDNA arrays were characterized by distinct NTS sequences (designated NTS-I and NTS-II for the 200- and 900-bp monomers, respectively); however, their coding sequences were nearly identical. The 5S rRNA genes were clustered in two chromosome loci, a major one corresponding to the NTS-I sites and a minor one corresponding to the NTS-II sites. The NTS-I sequence was variable among Leporinus spp., whereas the NTS-II was conserved among them and even in the related genus Schizodon. The distinct 5S rDNA arrays might characterize two 5S rRNA gene subfamilies that have been evolving independently in the genome.Key words: 5S rDNA, 5S rRNA gene, nontranscribed spacer, Leporinus, fish.

Organization of 5S ribosomal RNA genes in tea (Camellia sinensis)

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 143-146 ◽  
Author(s):  
Dharam Singh ◽  
Mahipal Singh
Keyword(s):  
Camellia Sinensis ◽  
Tandem Repeats ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Repeat Units ◽  
Camellia Species ◽  
5S Rrna Genes ◽  
Rna Genes

The 5S rRNA genes in the Camellia sinensis (L.) O. Kuntze (tea) genome are arranged as tandem repeat units of 300 and 325 bps. The 2 classes of tandem repeats were discovered by Southern hybridisation of tea genomic DNA with a 5S rRNA gene PCR product.Key words: Camellia species, 5S rDNA, multigene family, tandem repeats, spacers.

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.

Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae)

2019 ◽  
Vol 67 (7) ◽  
pp. 521
Author(s):  
Magdalena Vaio ◽  
Cristina Mazzella ◽  
Marcelo Guerra ◽  
Pablo Speranza
Keyword(s):  
Evolutionary Dynamics ◽  
In Situ Hybridisation ◽  
5S Rdna ◽  
Its Region ◽  
Variable Number ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Rdna Sites ◽  
35S Rdna ◽  
Genome Restructuring

The Dilatata group of Paspalum includes species and biotypes native to temperate South America. Among them, five sexual allotetraploids (x = 10) share the same IIJJ genome formula: P. urvillei Steud, P. dasypleurum Kunze ex Desv., P. dilatatum subsp. flavescens Roseng., B.R. Arrill. & Izag., and two biotypes P. dilatatum Vacaria and P. dilatatum Virasoro. Previous studies suggested P. intermedium Munro ex Morong & Britton and P. juergensii Hack. or related species as their putative progenitors and donors of the I and J genome, respectively, and pointed to a narrow genetic base for their maternal origin. It has not yet been established whether the various members of the Dilatata group are the result of a single or of multiple allopolyploid formations. Here, we aimed to study the evolutionary dynamics of rRNA genes after allopolyploidisation in the Dilatata group of Paspalum and shed some light into the genome restructuring of the tetraploid taxa with the same genome formula. We used double target fluorescence in situ hybridisation of 35S and 5S rDNA probes and sequenced the nrDNA internal transcribed spacer (ITS) region. A variable number of loci at the chromosome ends were observed for the 35S rDNA, from 2 to 6, suggesting gain and loss of sites. For the 5S rDNA, only one centromeric pair of signals was observed, indicating a remarkable loss after polyploidisation. All ITS sequences generated were near identical to the one found for P. intermedium. Although sequences showed a directional homogeneisation towards the putative paternal progenitor in all tetraploid species, the observed differences in the number and loss of rDNA sites suggest independent ongoing diploidisation processes in all taxa and genome restructuring following polyploidy.

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
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