5S rRNA genes in tribe Phaseoleae: array size, number, and dynamics

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 445-455 ◽  
Author(s):  
Kathleen J. Danna ◽  
Rachel Workman ◽  
Virginia Coryell ◽  
Paul Keim
Keyword(s):  
Gel Electrophoresis ◽  
Copy Number ◽  
Glycine Soja ◽  
Repeat Unit ◽  
Diploid Species ◽  
5S Rdna ◽  
5S Rrna ◽  
Array Size ◽  
Rrna Genes ◽  
5S Rrna Genes

The organization of 5S rRNA genes in plants belonging to tribe Phaseoleae was investigated by clamped homogeneous electric field gel electrophoresis and Southern blot hybridization. Representatives of subtribe Glycininae included the diploid species Neonotonia wightii and Teramnus labialis, as well as three soybean accessions: an elite Glycine max (L.) Merr. cultivar (BSR101), an unadapted G. max introduction (PI 437.654), and a wild Glycine soja (PI 468.916). A cultivar of Phaseolus vulgaris (kidney bean), a member of subtribe Phaseolinae, was also examined. We determined the number of 5S rDNA arrays and estimated the size and copy number of the repeat unit for each array. The three soybean accessions all have a single 5S locus, with a repeat unit size of ~345 bp and a copy number ranging from about 600 in 'BSR101' to about 4600 in the unadapted soybean introduction. The size of the 5S gene cluster in 'BSR101' is the same in roots, shoots, and trifoliate leaves. Given that the genus Glycine probably has an allotetraploid origin, our data strongly suggest that one of the two progenitor 5S loci has been lost during diploidization of soybean. Neonotonia wightii, the diploid species most closely related to soybean, also has a single locus but has a repeat unit of 520 bp and a copy number of about 1300. The more distantly related species T. labialis and P. vulgaris exhibited a more complex arrangement of 5S rRNA genes, having at least three arrays, each comprising a few hundred copies of a distinct repeat unit. Although each array in P. vulgaris exhibits a high degree of homogeneity with regard to the sequence of the repeat unit, heterogeneity in array size (copy number) was evident when individual plants were compared. A cis-dependent molecular drive process, such as unequal crossing-over, could account for both the homogenization of repeat units within individual arrays and the observed variation in copy number among individuals. Key words : pulsed-field gel electrophoresis, rRNA genes, soybean, tandem arrays.

scholarly journals Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

2020 ◽  
Vol 21 (8) ◽  
pp. 2931 ◽  
Author(s):  
Ruslan Kalendar ◽  
Olga Raskina ◽  
Alexander Belyayev ◽  
Alan H. Schulman
Keyword(s):  
Copy Number ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Gene Copy ◽  
Rrna Gene ◽  
Long Terminal Repeats ◽  
5S Rrna Genes ◽  
Pol Iii ◽  
Tandem Arrays

Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.

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.

The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes – a test on cultivated wheat and wheat progenitors

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 590-599 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey ◽  
Alexander Belyayev ◽  
Olga Raskina ◽  
Eviatar Nevo
Keyword(s):  
Evolutionary Dynamics ◽  
Diploid Species ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Aegilops Speltoides ◽  
Mantel Tests ◽  
Unit Classes ◽  
Unit Class ◽  
5S Rrna Genes

Data is presented on the evolutionary dynamics of non-transcribed spacers (NTSs) of 5S rRNA genes in some diploid and polyploid Triticum and Aegilops species. FISH experiments with probes representing different unit classes revealed presence and (or) absence of these sequences in genomes or separate chromosomes of the species. Among the three diploid species only Aegilops speltoides has all of the different unit classes in ribosomal clusters as detected by the probes. Triticum urartu does not have the long D1 signals and Aegilops tauschii does not have the long A1 signals. Both polyploids possess all types of sequences, but because of genome rearrangements after polyploidization there is significant repatterning of single different rDNA unit classes in chromosomal positions when compared with those in diploid progenitors. Additional refined work is needed to ascertain if the sequences in the polyploids are mixed or are located in mini clusters in close proximity to each other. Mantel tests for association between the presence of the FISH signals of the A, B, and D genomes together and separately with the unit class data of the material, i.e., the probes used in FISH, indicated that all signals were associated with their respective probe material, but that there was no association of the unit classes found and the signals to each haplome. All combinations of the partial Mantel tests, e.g., between the A and B haplomes while controlling the effect of the all probes signals, with correlations ranging from 0.48 to 0.79 were all significant. Principal coordinate analysis showed that the signals of most unit class specific probes were more or less equally distant except for the long {S1 and short G1 signals, which were not different, and that the short A1 signals were closely related to the former two, whereas the signals of the long G1 were even less related.Key words: in situ hybridization, non-transcribed spacers, 5S rRNA genes, Triticeae.

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.

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

Many transcribed regions of the Onchocerca volvulus genome contain the spliced leader sequence of Caenorhabditis elegans

1990 ◽  
Vol 10 (6) ◽  
pp. 2765-2773
Author(s):  
W L Zeng ◽  
C M Alarcon ◽  
J E Donelson
Keyword(s):  
Caenorhabditis Elegans ◽  
Repeat Unit ◽  
5S Rrna ◽  
Onchocerca Volvulus ◽  
Rrna Genes ◽  
Free Living ◽  
Spliced Leader ◽  
C Elegans ◽  
Perfect Sequence ◽  
5S Rrna Genes

Genomic DNAs of the related parasitic nematodes Onchocerca volvulus and Dirofilariae immitis, and a cDNA library of O. volvulus, were examined for the presence of the 22-nucleotide spliced leader (SL) found at the 5' ends of 10 to 15% of the mRNAs in the free-living nematode Caenorhabditis elegans. As in C. elegans, genes for the SL RNA are linked to the repetitive 5S rRNA genes of O. volvulus and D. immitis, but unlike C. elegans, they are in the same orientation as the 5S rRNA genes within the repeat unit. In O. volvulus the SL sequence is also encoded at more than 30 additional genomic locations and occurs at interior sites within many transcripts. Sequence determinations of four different cDNAs of O. volvulus, each containing an internal copy of the SL within a conserved 25mer, and one corresponding genomic DNA clone indicate that this sequence is not trans spliced onto these RNAs, but is encoded within the genes. The RNAs of two of these cDNAs appear to be developmentally regulated, since they occur in adult O. volvulus but were not detected in the infective L3 stage larvae. In contrast, actin mRNAs are present at all developmental stages, and at least one actin mRNA species contains a trans-spliced 5' SL. The internal locations of the SL in various transcripts and its perfect sequence conservation among parasitic and free-living nematodes argues that it serves specific, and perhaps multiple, functions for these organisms.

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.

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.

scholarly journals Many transcribed regions of the Onchocerca volvulus genome contain the spliced leader sequence of Caenorhabditis elegans.

1990 ◽  
Vol 10 (6) ◽  
pp. 2765-2773 ◽  
Author(s):  
W L Zeng ◽  
C M Alarcon ◽  
J E Donelson
Keyword(s):  
Caenorhabditis Elegans ◽  
Repeat Unit ◽  
5S Rrna ◽  
Onchocerca Volvulus ◽  
Rrna Genes ◽  
Free Living ◽  
Spliced Leader ◽  
C Elegans ◽  
Perfect Sequence ◽  
5S Rrna Genes

Genomic DNAs of the related parasitic nematodes Onchocerca volvulus and Dirofilariae immitis, and a cDNA library of O. volvulus, were examined for the presence of the 22-nucleotide spliced leader (SL) found at the 5' ends of 10 to 15% of the mRNAs in the free-living nematode Caenorhabditis elegans. As in C. elegans, genes for the SL RNA are linked to the repetitive 5S rRNA genes of O. volvulus and D. immitis, but unlike C. elegans, they are in the same orientation as the 5S rRNA genes within the repeat unit. In O. volvulus the SL sequence is also encoded at more than 30 additional genomic locations and occurs at interior sites within many transcripts. Sequence determinations of four different cDNAs of O. volvulus, each containing an internal copy of the SL within a conserved 25mer, and one corresponding genomic DNA clone indicate that this sequence is not trans spliced onto these RNAs, but is encoded within the genes. The RNAs of two of these cDNAs appear to be developmentally regulated, since they occur in adult O. volvulus but were not detected in the infective L3 stage larvae. In contrast, actin mRNAs are present at all developmental stages, and at least one actin mRNA species contains a trans-spliced 5' SL. The internal locations of the SL in various transcripts and its perfect sequence conservation among parasitic and free-living nematodes argues that it serves specific, and perhaps multiple, functions for these organisms.

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.

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