Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca)

Abstract The role of reciprocal recombination in the coevolution of the ribosomal RNA gene family on the X and Y chromosomes of Drosophila melanogaster was assessed by determining the frequency and nature of such exchange. In order to detect exchange events within the ribosomal RNA gene family, both flanking markers and restriction fragment length polymorphisms within the tandemly repeated gene family were used. The vast majority of crossovers between flanking markers were within the ribosomal RNA gene region, indicating that this region is a hotspot for heterochromatic recombination. The frequency of crossovers within the ribosomal RNA gene region was approximately 10(-4) in both X/X and X/Y individuals. In conjunction with published X chromosome-specific and Y chromosome-specific sequences and restriction patterns, the data indicate that reciprocal recombination alone cannot be responsible for the observed variation in natural populations.

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The Nor-D3 locus of Triticum tauschii: natural variation and genetic linkage to markers in chromosome 5

Genome ◽

10.1139/g91-060 ◽

1991 ◽

Vol 34 (3) ◽

pp. 387-395 ◽

Cited By ~ 75

Author(s):

E. S. Lagudah ◽

R. Appels ◽

D. McNeil

Keyword(s):

Ribosomal Rna ◽

Intergenic Spacer ◽

D Genome ◽

Triticum Tauschii ◽

Intergenic Spacer Region ◽

Grain Softness ◽

High Level ◽

Rna Genes ◽

Rdna Polymorphism ◽

Grain Softness Protein

Variation in the intergenic spacer region of the ribosomal RNA genes (located at the Nor locus) was assayed in a collection of 411 accessions of Triticum tauschii from Turkey, USSR, Iran, Afghanisan, Pakistan, and China. Twenty rDNA genotypes were identified and it was demonstrated that T. tauschii accessions from the USSR and Iran have the highest diversity at the Nor locus. At least four of the rDNA genotypes were demonstrated to be alleles of a single major locus, in segregating F2 progeny analyses. The TaqI restriction fragment associated with rDNA genotype 7 was shown to be the same as the Nor-D3a allele present in all bread wheats (based on chromosome location and length of the intergenic spacer region). This genotype was significantly associated with T. t. ssp. strangulata, previously argued to be the donor of the D genome to hexaploid wheat. The Nor locus showed a high level of recombination with the 5SDna-2 locus, which was also located on chromosome 5D. The Nor locus is placed distal to the 5SDna-2 locus but proximal to the grain softness protein gene (XGsp) on the short arm of chromosome 5D.Key words: D genome, Nor-D3, rDNA polymorphism, chromosomal location.

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Characterization of the Gyrodactylus salaris Malmberg, 1957 (Platyhelminthes: Monogenea) ribosomal intergenic spacer (IGS) DNA

Parasitology ◽

10.1017/s0031182099006770 ◽

2000 ◽

Vol 121 (5) ◽

pp. 555-563 ◽

Cited By ~ 12

Author(s):

C. M. COLLINS ◽

C. O. CUNNINGHAM

Keyword(s):

Ribosomal Rna ◽

Tandem Repeats ◽

Gene Array ◽

Pcr Amplification ◽

Intergenic Spacer ◽

Sequence Motifs ◽

Ribosomal Rna Gene ◽

Intergenic Spacers ◽

Transcription Start Sites ◽

Pcr Products

The intergenic spacer of the ribosomal RNA gene array from the monogenean Gyrodactylus salaris was isolated using PCR amplification. PCR products were cloned and sequenced. Three different fragments of 0·63, 1·0 and 2·62 kb, were consistently obtained. These showed homology at the 5′ and 3′ termini but differed in their overall size and intervening sequence. The 5′ end showed homology to various 28S ribosomal RNA gene sequences, suggesting that this represented the 3′ terminus of the G. salaris 28S ribosomal RNA gene. A number of features common to other eukaryotic intergenic spacers were found in the longest sequence, including A + T rich sequences, palindromic sequences and tandemly repeated elements. Two regions of 23 bp sequences arranged in non-identical tandem repeats were identified. There were 9 repeats in both regions, separated by 81 bp of non-repetitive sequence. The repeat units from the two regions shared some similarity at their 3′ ends. The G. salaris intergenic spacer sequence was examined for sequence motifs involved in the transcription of the ribosomal RNA genes in other species. Several regions with homology to transcription start sites were identified.

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The conservation landscape of the human ribosomal RNA gene repeats

10.1101/242602 ◽

2018 ◽

Author(s):

Saumya Agrawal ◽

Austen R.D. Ganley

Keyword(s):

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Metabolic Regulation ◽

De Novo ◽

Intergenic Spacer ◽

Phylogenetic Footprinting ◽

Genomic Region ◽

Primate Species ◽

Ribosomal Rna Gene ◽

Conserved Regions

ABSTRACTRibosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed usingde novowhole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS, and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.

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