Polymorphism in ribosomal DNA repeat units of 12 Hordeum species

Genome ◽  
1989 ◽  
Vol 32 (6) ◽  
pp. 1124-1127 ◽  
Author(s):  
Stephen J. Molnar ◽  
George Fedak
Keyword(s):  
Ribosomal Dna ◽  
Repeat Unit ◽  
Unit Length ◽  
Intergenic Spacer ◽  
Rdna Repeat ◽  
Repeat Units ◽  
Dna Repeat ◽  
Rdna Repeat Unit ◽  
Bamhi Restriction Site ◽  
Hordeum Species

Total genomic DNA was isolated from leaves of individual accessions of 12 Hordeum species. SacI, HindIII, and BamHI restriction fragments hybridizing to the wheat rDNA probe pTA71 were compared. Thirteen rDNA repeat unit length variants were recovered, which combined to produce 11 distinct phenotypes. All rDNA repeat units had two SacI sites and no HindIII sites. The rDNA repeat units of H. secalinum, H. hrasdanicum, and H. distichum all had 3 BamHI sites, but in different configurations. The rDNA repeat units of the other species had at least 4 BamHI sites. Ladders of small hybridizing fragments in 8 of 9 of the latter accessions indicated the presence of occasional BamHI sites in some subrepeats within the intergenic spacer regions of the rDNA repeat units. Different distributions of BamHI restriction site maps within the Hordeum sections strengthen the concept of using variation in rDNA restriction sites as a taxonomic character.Key words: Hordeum, ribosomal DNA, polymorphism.

Cloning of the rDNA repeat unit from a British entomopathogenic nematode (Steinernematidae) and its potential for species identification

Parasitology ◽  
1993 ◽  
Vol 107 (5) ◽  
pp. 529-536 ◽  
Author(s):  
A. P. Reid ◽  
W. M. Hominick
Keyword(s):  
Entomopathogenic Nematode ◽  
Repeat Unit ◽  
Unit Length ◽  
Soil Survey ◽  
Rdna Repeat ◽  
Dna Repeat ◽  
Length Polymorphisms ◽  
Rdna Repeat Unit ◽  
Unique Restriction ◽  
Plasmid Puc18

SUMMARYThe entire ribosomal DNA repeat unit of a steinernematid species (Nashes isolate) was cloned as three separate EcoR I fragments in the plasmid pUC18. An equimolar cocktail of these three clones was used to identify Steinernema species on Southern blots as each species displays its own unique restriction fragment length polymorphisms. The clones also identified two new species isolated in a soil survey of coastal regions of Britain. One of the clones (pSn4.0) can detect length heterogeneities in the rDNA repeat unit of various isolates of some of the species, particularly the most common in the United Kingdom, S. feltiae. These differences in the rDNA repeat unit length remained constant over several years for one isolate of S. feltiae, but were different for each of the geographical isolates studied to date.

scholarly journals Molecular and FISH analysis of 45S rDNA on BAC molecule of Saccharina Japonica

2021 ◽  
Author(s):  
Peng-Fei Liu ◽  
Yan-Hui Bi ◽  
Li Liu ◽  
Zhi-Gang Zhou
Keyword(s):  
Physical Map ◽  
Repeat Unit ◽  
Gc Content ◽  
Intergenic Spacer ◽  
Saccharina Japonica ◽  
Fish Analysis ◽  
45S Rdna ◽  
Rdna Repeat ◽  
Bac Clone ◽  
Rdna Repeat Unit

Abstract IGS is abundant in polymorphism, which is widely used in the analysis of intraspecific genetic diversity and phylogenetic relationships among geographical populations. In this study, the 45S rDNA repeat unit of Saccharina japonica was obtained for the first time by BAC clone sequencing. The total length of 45S rDNA repeat unit of S. japonica was 8995 bp, including 5420 bp of 18s-5.8s-25s rDNA and 3575 bp of IGS (Intergenic Spacer), with the GC content of 51.4%. IGS was composed of 465 bp 3’-outer transcribed spacer (ETS), 874 bp 5’-ETS, and 2236 bp non transcribed spacer (NTS), with the GC content of 50.1%.Fiber-FISH (fiber-fluorescence in situ hybridization, fiber-FISH) analysis of 45S rDNA on the BAC molecule of female gametophytes of S. japonica illustrated that each fiber had at least five continuous moniliform hybridization signal points, indicating the distribution of 45S rDNA repeat unit on the bacterial artificial chromosome. This study provided a new candidate molecular marker for detecting intraspecific polymorphisms of S. japonica, and the successful fiber-FISH analysis of 45S rDNA on BAC molecule would contribute to the construction of the physical map and Map-based cloning of this kelp.

scholarly journals Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Maxim V. Zagoskin ◽  
Valentina I. Lazareva ◽  
Andrey K. Grishanin ◽  
Dmitry V. Mukha
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
Its2 Rdna ◽  
Minimum Evolution ◽  
Nucleotide Substitutions ◽  
Repeat Units ◽  
Dna Repeat ◽  
Ribosomal Repeat ◽  
Its1 And Its2

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that theMesocyclops,Thermocyclops,andMacrocyclopsgenera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

A rapid means of identifying wild rice species DNA using dot blots and genome-specific rDNA probes

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 391-395 ◽  
Author(s):  
C L McIntyre ◽  
B C Winberg
Keyword(s):  
Repeat Unit ◽  
Rice Genome ◽  
Intergenic Spacer ◽  
Size Class ◽  
Rdna Repeat ◽  
Wild Rice Species ◽  
Rdna Repeat Unit ◽  
Oryza Latifolia ◽  
Bamhi Site ◽  
Oryza Australiensis

Intergenic spacer fragments from the rDNA repeat unit were isolated from a single accession of each of 9 species that cover the range of genomes found in the Oryza genus (A-F). Seven of the 9 species contained 1 size class of rDNA repeat unit only, while Oryza sativa and Oryza latifolia contained 3 and 2 size classes, respectively, of which fragments were cloned for the major size class only. Oryza australiensis contained an additional BamHI site in the intergenic spacer. Dot blots were prepared and hybridised with a repeat unit from each species. Under high stringency conditions, all probes were specific to species possessing the same genome or genomes.Key words: rDNA, rice, genome-specific, dot blots.

Ribosomal DNA repeat unit polymorphism in six Aegilops species

Genome ◽  
1992 ◽  
Vol 35 (3) ◽  
pp. 510-515 ◽  
Author(s):  
W. K. Kim ◽  
R. L. Innes ◽  
E. R. Kerber
Keyword(s):  
Repeat Unit ◽  
Genotypic Diversity ◽  
Type A ◽  
Aegilops Species ◽  
Type B ◽  
Rdna Repeat ◽  
Coding Region ◽  
Repeat Units ◽  
Dna Repeat ◽  
Bamhi Site

Total genomic DNA of 27 accessions representing six Aegilops species was restricted with BamHI, EcoRI, and BamHI plus EcoRI, and the restriction fragments were probed with the ribosomal clones pMF2 containing the ribosomal RNA coding regions. The rDNA repeat lengths varied between 9.0 and 10.8 kb. Intraspecific variation among the 10 accessions of Ae. squarrosa var. strangulata ranged from 9.0 to 9.6 kb, suggesting a diversity of genotypes within as well as between species. These variations were not related to their geographical distributions. Each of 24 accessions had two BamHI sites in the coding region (type A), while three accessions of Ae. squarrosa var. strangulata had four BamHI sites (type B, two sites in the intergenic region). Results for these three accessions of Ae. squarrosa var. strangulata suggest genotypic diversity in this species. In BamHI restriction of each accession, a third DNA fragment, ranging between 9.0 and 10.8 kb in type A and 6.0 kb in type B, resulted from lack of digestion at the 26S BamHI site. In double digestion, all rDNA repeat units were restricted by EcoRI, yielding 3.9-, 0.9-, and 4.8-kb fragments, the last of which arose from the lack of digestion at the 26S BamHI site, estimated to occur in 5–20% of the repeat units, depending on the accession.Key words: Triticum tauschii, RFLP, diversity.

Ribosomal DNA, peroxidase and extensin variation in genomic DNA of Medicago laciniata (L.) Miller from Australia and Africa

1994 ◽  
Vol 45 (5) ◽  
pp. 1013 ◽  
Author(s):  
RR Young ◽  
ES Lagudah
Keyword(s):  
Restriction Endonuclease ◽  
South African ◽  
Ribosomal Dna ◽  
Genomic Dna ◽  
Repeat Unit ◽  
Cdna Clones ◽  
Genotypic Differences ◽  
Rdna Repeat ◽  
Eastern Australia ◽  
Rdna Repeat Unit

Fifty-four Medicago laciniata (L.) Miller accessions from diverse locations in eastern Australia, Africa and Israel were characterized for genotypic differences by restriction endonuclease cleavage of genomic DNA and probing with radio-labelled DNA sequences to detect restriction fragment length polymorphisms (RFLP). Digestion of the genomic DNA with the restriction endonuclease, Bam HI, and probing with the complete ribosomal DNA (rDNA) repeat unit of soybean (pGmrl) and its subclones revealed that the variable region in M. laciniata spans the Bam H1 sites of the intergenic spacer region between the 18s and 26s DNA. The length variation in the rDNA repeat unit clearly distinguished South African from Australian accessions. The rDNA variants from SA1847 (Morocco) and SA7750 (Tunisia) were the same as the Australian accessions and slightly larger than the rDNA spacer variant unique to SA3428 (Israel). When Eco R1 digested M. laciniata genomic DNA was probed with peroxidase and extensin cDNA clones, all Australian accessions were again characterized by the same RFLP genotype with further differentiation between African and Israeli accessions. An accession of unknown origin, SA3412, possessed the same RFLP genotype as the Australian accessions for all endonuclease and probe combinations. For the African accessions, differences in RFLP genotype were more frequent than differences in phenotype (leaflet laciniation and colour). However, of three South African accessions with the same RFLP genotype, SA26844, SA26847, and SA26848, SA26847 had more pronounced leaflet laciniation.

Ribosomal DNA repeat unit polymorphism in 25 Hordeum species

1989 ◽  
Vol 78 (3) ◽  
pp. 387-392 ◽  
Author(s):  
S. J. Molnar ◽  
P. K. Gupta ◽  
G. Fedak ◽  
R. Wheatcroft
Keyword(s):  
Ribosomal Dna ◽  
Repeat Unit ◽  
Dna Repeat ◽  
Hordeum Species

Ribosomal DNA intergenic spacer of indoor wood-decay fungi

Holzforschung ◽  
2008 ◽  
Vol 62 (6) ◽  
Author(s):  
Olaf Schmidt ◽  
Ute Moreth
Keyword(s):  
Ribosomal Dna ◽  
Repeat Unit ◽  
Intergenic Spacer ◽  
Wood Decay ◽  
5S Rdna ◽  
Reverse Direction ◽  
Dry Rot ◽  
Decay Fungi ◽  
Wood Decay Fungi ◽  
Rdna Repeat Unit

AbstractIndoor wood-decay fungi are economically very important. Approximately half of the total damage caused by indoor fungi in Germany is caused by species of the Coniophoraceae. The sequence of the intergenic spacer (IGS) region of the ribosomal DNA was elucidated with the following fungi of this family:Serpula lacrymans(true dry rot fungus),S. himantioides(wild merulius),Meruliporia incrassata(North American dry rot fungus),Leuco-gyrophana pinastri(mine dry rot fungus),Coniophora puteana(brown cellar fungus), andC. marmorata(marmoreus cellar fungus). The IGS length ranges between 2584 and 3785 bp and consists of the short IGS 1 (253–440 bp), the 5S rDNA (118 bp) and the long IGS 2 (2193–3310 bp). IGS 1 is phylogenetically less informative for the investigated Coniophoraceae species. 5S rDNA is transcribed in the reverse direction. IGS 2 contains extended repeat blocks of copies of different length. Intraspecific length polymorphism as a result of different copy number occurs inM. incrassataandL. pinastri. In combination with previous results, the full-length sequence of the rDNA repeat unit is available for important indoor wood-decay fungi. The various rDNA regions can now be used for future identification of unknown sequences by BLAST and also for phylogenetic studies.

A physical map of the ribosomal DNA repeat unit of Aspergillus nidulans

Gene ◽  
1982 ◽  
Vol 20 (2) ◽  
pp. 135-137 ◽  
Author(s):  
Robin A. Lockington ◽  
Graham G. Taylor ◽  
Michael Winther ◽  
Claudio Scazzocchio ◽  
R.Wayne Davies
Keyword(s):  
Aspergillus Nidulans ◽  
Ribosomal Dna ◽  
Physical Map ◽  
Repeat Unit ◽  
Dna Repeat
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