Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants

The 5S rRNA gene of the soybean Glycine max (L.) Merr. has been cloned on a 556-bp fragment of DNA and sequenced. This fragment contains two copies of the soybean 5S rDNA sequence, one intact and one truncated, separated by noncoding DNA. We have used this clone to investigate the organization of the 5S genes within the soybean genome and the extent of their methylation. Our results demonstrate that soybean 5S genes are clustered, organized into tandem repeats of 330 bp, and extensively methylated. Hybridization of the 5S sequence to Southern transfers of soybean DNA digested with BamHI reveals a striking ladderlike pattern. Hybridization of the soybean 5S sequence to a wide variety of plant DNAs results in similar patterns, suggesting that the 5S rDNA sequence, gene organization, and methylation pattern are conserved in many higher plants.Key words: 5S rDNA, sequence, methylation, soybean, repeat conservation.

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

Genome ◽

10.1139/g00-095 ◽

2001 ◽

Vol 44 (1) ◽

pp. 143-146 ◽

Cited By ~ 2

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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Nucleotide sequence and chromosomal mapping of the 5S rDNA repeat of the crustacean Proasellus coxalis

Genome ◽

10.1139/g97-110 ◽

1998 ◽

Vol 41 (1) ◽

pp. 129-133 ◽

Cited By ~ 8

Author(s):

F Pelliccia ◽

R Barzotti ◽

E V Volpi ◽

E Bucciarelli ◽

A Rocchi

Keyword(s):

Tandem Repeats ◽

5S Rdna ◽

5S Rrna ◽

Chromosomal Mapping ◽

Rrna Genes ◽

Crustacean Species ◽

Sequence Identity ◽

Pcr Product ◽

5S Rrna Genes ◽

5S Rdna Sequence

In this investigation we analysed the 5S rRNA genes of the isopod crustacean Proasellus coxalis. 5S rDNA hybridization of digested genomic DNA and amplification by PCR demonstrate that these genes are organized in tandem repeats of 589 bp, 120 of which represent the coding sequence and 469 the spacer sequence. Proasellus coxalis is the first crustacean species in which 5S rRNA genes have been found tandemly arranged without being linked to other repeated genes. The PCR product has been used as a probe in FISH to locate the 5S rRNA genes on two chromosome pairs of the P. coxalis karyotype. Comparison of the 5S rDNA sequence of this species with previously published sequences of six other crustacean species shows the existence of a good correlation between phylogenetic relationships and sequence identity.

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

International Journal of Molecular Sciences ◽

10.3390/ijms21082931 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2931 ◽

Cited By ~ 5

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.

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Genetic and chromosomal localization of the 5S rDNA locus in sugar beet (Beta vulgaris L.)

Genome ◽

10.1139/g97-024 ◽

1997 ◽

Vol 40 (2) ◽

pp. 171-175 ◽

Cited By ~ 11

Author(s):

J. Schondelmaier ◽

T. Schmidt ◽

C. Jung ◽

J. S. Heslop-Harrison

Keyword(s):

In Situ Hybridization ◽

Linkage Group ◽

Sugar Beet ◽

Beta Vulgaris ◽

5S Rdna ◽

Rdna Locus ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene

A digoxigenin-labelled 5S rDNA probe containing the 5S rRNA gene and the adjacent intergenic spacer was used for in situ hybridization to metaphase and interphase chromosomes of a trisomic stock from sugar beet (Beta vulgaris L.). Three chromosomes of primary trisomic line IV (T. Butterfass. Z. Bot. 52: 46–77. 1964) revealed signals close to the centromeres. Polymorphisms of 5S rDNA repeats in a segregating population were used to map genetically the 5S rRNA genes within a cluster of markers in linkage group II of sugar beet. The concentration of genetic markers around the centromere presumably reflects the suppressed recombination frequency in centromeric regions. The correlation of physical and genetic data allowed the assignment of a linkage group to sugar beet chromosome IV according to line IV of the primary trisomics.Key words: Beta vulgaris, sugar beet, 5S rRNA, in situ hybridization, RFLPs, trisomics.

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The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.)

Genome ◽

10.1139/g96-019 ◽

1996 ◽

Vol 39 (1) ◽

pp. 140-149 ◽

Cited By ~ 36

Author(s):

Bernard R. Baum ◽

Douglas A. Johnson

Keyword(s):

Phylogenetic Analysis ◽

5S Rdna ◽

Hordeum Spontaneum ◽

Wild Relatives ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Sequence Comparisons ◽

Rdna Sequences ◽

Cultivated Barley

5S rRNA genes from several accessions of Hordeum spontaneum and Hordeum bulbosum, wild relatives of cultivated barley, Hordeum vulgare, have been amplified by the polymerase chain reaction, cloned, and sequenced. Evaluation of aligned sequences along with principal coordinate analysis demonstrates that the two classes of 5S rDNA sequences found in cultivated barley, and subclasses (groups) of these sequences, can also be found in its closest wild relatives. The two classes of units, formerly categorized as containing short or long 5S rDNA repeats, are distinguishable by the presence or absence of a TAG repeating unit. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for further phylogenetic analysis in the genus Hordeum and possibly in the Triticeae. Key words : 5S rDNA, barley, sequence diversity, phylogenetic analysis.

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Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes

Genome ◽

10.1139/g05-068 ◽

2006 ◽

Vol 49 (1) ◽

pp. 79-86 ◽

Cited By ~ 41

Author(s):

Manuel Manchado ◽

Eugenia Zuasti ◽

Ismael Cross ◽

Alejandro Merlo ◽

Carlos Infante ◽

...

Keyword(s):

5S Rdna ◽

5S Rrna ◽

Rrna Genes ◽

Solea Senegalensis ◽

Rrna Gene ◽

Small Nuclear Rna ◽

5S Rrna Gene ◽

Nuclear Rna ◽

Pcr Products ◽

Rna Genes

Some units of the 5S rDNA of Solea senegalensis were amplified by PCR and sequenced. Three main PCR products (227, 441, and 2166 bp) were identified. The 227- and 441-bp fragments were characterized by highly divergent nontranscribed spacer sequences (referred to as NTS-I and NTS-II) that were 109 and 324 bp long, respectively, yet their coding sequences were nearly identical. The 2166-bp 5S rDNA unit was composed of two 5S rRNA genes separated by NTS-I and followed by a 1721-bp spacer containing the U2, U5, and U1 small nuclear RNA genes (snRNAs). They were inverted and arranged in the transcriptional direction opposite that of the 5S rRNA gene. This simultaneous linkage of 3 different snRNAs had never been observed before. The PCR products were used as probes in fluorescence in situ hybridization experiments to locate the corresponding loci on the chromosomes of S. senegalensis. A major 5S rDNA chromosomal site was located along most of the short arm of a submetacentric pair, while a minor site was detected near the centromeric region of an acrocentric pair.Key words: soleidae, pleuronectiformes, 5S rDNA, Solea, snRNAs linkage.

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Molecular organization of 5S rDNA intergenic spacer in Gentiana pneumonanthe L. and G. punctata L.

Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv ◽

10.7124/visnyk.utgis.18.1-2.1349 ◽

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.

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

Genome ◽

10.1139/g01-069 ◽

2001 ◽

Vol 44 (5) ◽

pp. 903-910 ◽

Cited By ~ 82

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.

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Molecular organization of 5S rDNA in fishes of the genus Brycon

Genome ◽

10.1139/g01-067 ◽

2001 ◽

Vol 44 (5) ◽

pp. 893-902 ◽

Cited By ~ 39

Author(s):

Adriane Pinto Wasko ◽

Cesar Martins ◽

Jonathan M Wright ◽

Pedro Manoel Galetti Jr.

Keyword(s):

Nucleotide Sequence ◽

Chromosomal Localization ◽

5S Rdna ◽

5S Rrna ◽

Molecular Organization ◽

Rrna Genes ◽

Rrna Gene ◽

Coding Region ◽

Nontranscribed Spacer ◽

Rdna Sequencing

There are few reports on the genomic organization of 5S rDNA in fish species. To characterize the 5S rDNA nucleotide sequence and chromosomal localization in the Neotropical fishes of the genus Brycon, 5S rDNA copies from seven species were generated by PCR. The nucleotide sequences of the coding region (5S rRNA gene) and the nontranscribed spacer (NTS) were determined, revealing that the 5S rRNA genes were highly conserved, while the NTSs were widely variable among the species analyzed. Moreover, two classes of NTS were detected in each species, characterized by base substitutions and insertionsdeletions. Using fluorescence in situ hybridization (FISH), two 5S rDNA chromosome loci that could be related to the two 5S rDNA NTS classes were observed in at least one of the species studied. 5S rDNA sequencing and chromosomal localization permitted the characterization of Brycon spp. and suggest a higher similarity among some of them. The data obtained indicate that the 5S rDNA can be an useful genetic marker for species identification and evolutionary studies.Key words: Brycon, FISH, nontranscribed spacer, nucleotide sequence, 5S rDNA.

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5S ribosomal and U1 small nuclear RNA genes: A new linkage type in the genome of a crustacean that has three different tandemly repeated units containing 5S ribosomal DNA sequences

Genome ◽

10.1139/g01-012 ◽

2001 ◽

Vol 44 (3) ◽

pp. 331-335 ◽

Cited By ~ 15

Author(s):

Franca Pelliccia ◽

Rita Barzotti ◽

Elisabetta Bucciarelli ◽

Angela Rocchi

Keyword(s):

Dna Sequences ◽

Pcr Amplification ◽

5S Rdna ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Small Nuclear Rna ◽

5S Rrna Gene ◽

Nuclear Rna ◽

Pcr Products

We investigated the 5S ribosomal RNA (rRNA) genes of the isopod crustacean Asellus aquaticus. Using PCR amplification, three different tandemly repeated units containing 5S rDNA were identified. Two of the three sequences were cloned and sequenced. One of them was 1842 bp and presented a 5S rRNA gene and a U1 small nuclear RNA (snRNA) gene. This type of linkage had never been observed before. The other repeat consisted of 477 bp and contained only an incomplete 5S rRNA gene lacking the first eight nucleotides and a spacer sequence. The third sequence was 6553 bp long and contained a 5S rRNA gene and the four core histone genes. The PCR products were used as probes in fluorescent in situ hybridization (FISH) experiments to locate them on chromosomes of A. aquaticus. The possible evolutionary origin of the three repeated units is discussed.Key words: Asellus, isopoda, crustacea, 5S rDNA, U1 snDNA.

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