scholarly journals Chromosomal mapping of H3 histone and 5S rRNA genes in eight species of Astyanax (Pisces, Characiformes) with different diploid numbers: syntenic conservation of repetitive genes

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 167-172 ◽  
Author(s):  
Diovani Piscor ◽  
Patricia Pasquali Parise-Maltempi
Keyword(s):  
Genomic Organization ◽  
5S Rdna ◽  
Gene Families ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
Rdna Sequences ◽  
Cytogenetic Studies ◽  
5S Rrna Genes ◽  
Syntenic Conservation

The genus Astyanax is widely distributed from the southern United States to northern Patagonia, Argentina. While cytogenetic studies have been performed for this genus, little is known about the histone gene families. The aim of this study was to examine the chromosomal relationships among the different species of Astyanax. The chromosomal locations of the 5S rRNA and H3 histone genes were determined in A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, A. mexicanus (all 2n = 50), A. fasciatus (2n = 46), and A. schubarti (2n = 36). All eight species exhibited H3 histone clusters on two chromosome pairs. In six species (A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, and A. fasciatus), syntenic clusters of H3 histone and 5S rDNA were observed on metacentric (m) or submetacentric (sm) chromosomes. In seven species, clusters of 5S rDNA sequences were located on one or two chromosome pairs. In A. mexicanus, 5S rDNA clusters were located on four chromosome pairs. This study demonstrates that H3 histone clusters are conserved on two chromosome pairs in the genus Astyanax, and specific chromosomal features may contribute to the genomic organization of the H3 histone and 5S rRNA genes.

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.

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

Genome ◽  
1998 ◽  
Vol 41 (1) ◽  
pp. 129-133 ◽  
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.

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

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.

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 ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 140-149 ◽  
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.

Chromosomal mapping of mouse 5S rRNA genes by direct R-banding fluorescence in situ hybridization

1994 ◽  
Vol 66 (4) ◽  
pp. 246-249 ◽  
Author(s):  
Y. Matsuda ◽  
K. Moriwaki ◽  
V.M. Chapman ◽  
Y. Hoi-Sen ◽  
J. Akbarzadeh ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
5S Rrna Genes

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.

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.

Chromosomal mapping of 18S–28S and 5S rRNA genes by two-colour fluorescent in situ hybridization in six sturgeon species

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 473-477 ◽  
Author(s):  
Francesco Fontana ◽  
Massimo Lanfredi ◽  
Leonardo Congiu ◽  
Marilena Leis ◽  
Milvia Chicca ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Close Association ◽  
5S Rdna ◽  
28S Rdna ◽  
5S Rrna ◽  
Chromosomal Mapping ◽  
Rrna Genes ◽  
Acipenser Baerii ◽  
Sturgeon Species

The number and distribution of the 18S–28S and 5S rRNA (rDNA) gene sequences were examined on mitotic chromosomes of six sturgeon species by two-colour in situ hybridization. Four of the six species, Huso huso, Acipenser stellatus, Acipenser sturio, and Acipenser ruthenus, with about 120 chromosomes, showed from six to eight 18S–28S rDNA signals, while 5S rDNA signals were on only one chromosome pair. The two species with 250–270 chromosomes, Acipenser baerii and Acipenser transmontanus, showed from 10 to 12 18S–28S sites and two chromosome pairs bearing 5S rDNA signals. In all examined species, the rather intense 5S rDNA signals apparently overlapped those of 18S–28S rDNA. These data support the diploid–tetraploid relationships between the two chromosome groups of sturgeons. The close association between the two rDNA families in species belonging to an ancestral fish order, such as Acipenseriformes, supports the hypothesis that the association represents a primitive condition.Key words: Acipenseriformes, FISH, fish cytogenetics, ribosomal genes.

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