Genomic organization of ribosomal RNA genes in Bromus (Poaceae)

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 198-205 ◽  
Author(s):  
M. Pillay
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Length Variation ◽  
Coding Region ◽  
Rdna Genes ◽  
Repeat Units ◽  
Site Mapping ◽  
Site Variation

Restriction site maps of the rDNA genes of nine Bromus species are described. The rDNA repeat units ranged from 8.2 to 11.1 kbp in length. Intraspecific length variation was observed in the BamHI digestions in three of the nine species. Restriction site variation was observed mainly in the intergenic spacer (IGS) but was also detected in the coding region. A unique KpnI site was present in the IGS of Bromus tectorum and Bromus sericeus (subgenus Stenobromus); in addition, B. sericeus contained an extra EcoRI site. An additional DraI site was observed in the IGS of Bromus trinii (subgenus Neobromus). A BstEII site in the IGS, common to seven of the species, was absent in B. tectorum and B. sericeus. In the coding region, a 2.1-kbp BstEII fragment was present in four subgenera represented by Bromus inermis and Bromus erectus (subgenus Festucaria), Bromus marginatus and Bromus carinatus (subgenus Ceratochloa), B. tectorum and B. sericeus (subgenus Stenobromus), and B. trinii (subgenus Neobromus); a similar fragment of only 1.1 kbp was present in Bromus mollis and Bromus arvensis (subgenus Bromus). An additional BamHI site was present in the coding region of B. erectus. Ribosomal DNA data suggested that B. mollis and B. arvensis (subgenus Bromus) are genetically isolated from the other subgenera, which showed a derived relationship. Restriction site mapping of the rDNA genes could provide useful molecular data for species identification and population and evolutionary studies in Bromus. Key words : Bromus, ribosomal DNA, restriction maps, evolutionary relationships.

Genetics of Cronartium ribicola. II. Variation in the ribosomal gene cluster

1996 ◽  
Vol 74 (3) ◽  
pp. 461-468 ◽  
Author(s):  
E. E. White ◽  
B. M. Foord ◽  
B. B. Kinloch Jr.
Keyword(s):  
Restriction Site ◽  
Intergenic Spacer ◽  
Fungal Species ◽  
Ribosomal Gene ◽  
Length Variation ◽  
Cronartium Ribicola ◽  
Western North America ◽  
Size Classes ◽  
Restriction Site Variation ◽  
Site Variation

The ribosomal gene repeat in Cronartium ribicola J.C. Fisch is highly variable among spore samples from British Columbia, Canada. Both restriction site variation and length variation occur. Length heterogeneity results from differences in the number of subrepeats in the intergenic spacer (IGS). The number of IGS size classes in haploid cultures is limited but is very large and highly variable in aeciospores from single cankers. The proportions of different size classes vary among cankers on different trees, and among subsamples taken around the periphery of large old cankers. The results are consistent with the fungus having a haploid infective mycelium that produces functional pycnia that result in localized dikaryotic areas following fusion between flexuous hyphae and pycnia. Restriction site variation appears lower than has been reported in range-wide samples of endemic fungal species, consistent with the hypothesis that introduction of C. ribicola to western North America was limited and does not represent the full genetic range of the species. No particular restriction site variants or IGS size classes characterize samples from particular geographic areas. No evidence for geographic races of the fungus was obtained. Keywords: rusts, rust races, ribosomal DNA, intergenic spacer, population structure, RFLP.

Phylogenetic Implications of Ribosomal DNA Restriction Site Variation in the Plant Family Onagraceae

1990 ◽  
Vol 77 (3) ◽  
pp. 523 ◽  
Author(s):  
Jorge V. Crisci ◽  
Elizabeth A. Zimmer ◽  
Peter C. Hoch ◽  
George B. Johnson ◽  
Christy Mudd ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Plant Family ◽  
Restriction Site Variation ◽  
Phylogenetic Implications ◽  
Site Variation ◽  
Dna Restriction

Minimal intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA of lake trout (Salvelinus namaycush)

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 664-671 ◽  
Author(s):  
Lang Zhuo ◽  
S. L. Sajdak ◽  
R. B. Phillips
Keyword(s):  
Polymerase Chain Reaction ◽  
Intraspecific Variation ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Lake Trout ◽  
Intergenic Spacer ◽  
Coding Region ◽  
Chain Reaction ◽  
Internal Transcribed Spacer Region ◽  
Polymerase Chain

Intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA (rDNA) in lake trout was examined by restriction mapping and sequencing of these regions amplified by the polymerase chain reaction. The length of the first internal transcribed spacer region (ITS-1) was 566 bases and the second internal transcribed spacer region (ITS-2) was 368 bases in lake trout. When the 1.4-kb region including the ITS-1, the 5.8S coding region, and the ITS-2 was amplified from 12 individuals from four populations and digested with eight different enzymes only one intraindividual polymorphism was found that occurred in each population. When the amplified ITS-1 region was sequenced from an additional 10 individuals from five populations, no interindividual variation was found in the sequence. A 6-kb portion of the rDNA repeat unit including 1.6 kb of the 18S coding region, the 5′ external spacer region (5′ ETS), and part of the adjacent intergenic spacer was cloned and a restriction map was prepared for these regions in lake trout. No intraspecific variation was found in the region adjacent to the 18S rDNA, which includes the 5′ ETS, although intraspecific and intraindividual length variation was found in the intergenic spacer region 3–6 kb from the 18S. Sequencing of a 609-b segment of the 5′ ETS adjacent to the 18S coding region revealed the presence of two 41-b repeats. The 198-b sequence between the repeats had some similarity to the 18S coding region of other fishes. Primers were designed for amplification of 559 b of the 5′ ETS using the polymerase chain reaction. No intraspecific variation in this region in lake trout was found when the DNA amplified from this region in 12 individuals from four populations was digested with eight restriction enzymes.Key words: ribosomal DNA, internal transcribed spacer regions, 5′ external spacer region, transcribed spacer, lake trout.

Balancing selection on the number of repeats in the ribosomal intergenic spacer present in naturally occurring yellow perch (Perca flavescens) populations

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Frédérique Bélanger-Lépine ◽  
Christelle Leung ◽  
Hélène Glémet ◽  
Bernard Angers
Keyword(s):  
Microsatellite Loci ◽  
Yellow Perch ◽  
Balancing Selection ◽  
Natural Populations ◽  
Perca Flavescens ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Length Variation ◽  
Repeat Units ◽  
Ribosomal Intergenic Spacer

The ribosomal intergenic spacer (IGS), responsible for the rate of transcription of rRNA genes, is associated with the growth and fecundity of individuals. A previous study of IGS length variants in a yellow perch (Perca flavescens) population revealed the presence of two predominant alleles differing by 1 kb due to variation in the number of repeat units. This study aims to assess whether length variation of IGS is the result of selection in natural populations. Length variation of IGS and 11 neutral microsatellite loci were assessed in geographically distant yellow perch populations. Most populations displayed the very same IGS alleles; they did not differ in frequencies among populations and the FST was not significantly different from zero. In contrast, diversity at microsatellite loci was high and differed among populations (FST = 0.18). Selection test based on FST identified IGS as a significant outlier from neutral expectations for population differentiation. Heterozygote excess was also detected in one specific cohort, suggesting temporal variation in the selection regime. While the exact mechanism remains to be specified, together the results of this study support the contention that balancing selection is acting to maintain two distinct IGS alleles in natural fish populations.

Variation in ribosomal DNA among isolates of the mycorrhizal fungus Cenococcum geophilum

1991 ◽  
Vol 69 (11) ◽  
pp. 2331-2343 ◽  
Author(s):  
Katherine F. Lobuglio ◽  
Scott O. Rogers ◽  
C. J. K. Wang
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Mycorrhizal Fungus ◽  
Intergenic Spacer ◽  
Fungal Species ◽  
Nuclear Ribosomal Dna ◽  
Cenococcum Geophilum ◽  
Taxonomic Rank ◽  
Reference Isolate ◽  
Length Polymorphisms

Restriction fragment length polymorphisms in ribosomal DNA were used to assess the degree of variation among 71 Cenococcum geophilum isolates of both geographically distinct and similar origins. Southern hybridizations using cloned C. geophilum ribosomal DNA indicated extensive variation among isolates, greater than has been previously reported to occur within a fungal species. Most of the polymorphisms were located within the region from the intergenic spacer through internal transcribed spacer 1. Restriction-site and length polymorphisms also occurred within the 5.8S through 26S genic region. Sixteen size categories of length mutations, six restriction-site additions, and four restriction-site deletions were observed compared with a reference isolate. HindIII-digested DNAs displayed fewer polymorphisms in the mitochondrial 24S ribosomal RNA gene (and flanking regions) than in nuclear ribosomal DNA. UPGMA cluster analysis of shared nuclear ribosomal DNA patterns indicated 32 unique phenotypes and grouped C. geophilum isolates into a broad range of clusters ranging from 100 to 44% similarity. The amount of ribosomal DNA variation demonstrated in this study indicates that C. geophilum is either an extremely heterogenous species or a fungal complex representing a broader taxonomic rank than presently considered. Key words: Cenococcum geophilum, ribosomal DNA, restriction polymorphisms.

Molecular phylogenetics of Thlaspi s.l. (Brassicaceae) based on chloroplast DNA restriction site variation and sequences of the internal transcribed spacers of nuclear ribosomal DNA

1997 ◽  
Vol 75 (3) ◽  
pp. 469-482 ◽  
Author(s):  
Klaus Mummenhoff ◽  
Andreas Franzke ◽  
Marcus Koch
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Restriction Site ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Ploidy Levels ◽  
Restriction Site Variation ◽  
Its Regions ◽  
Site Variation ◽  
Dna Restriction

Systematics of the genus Thlaspi s.l. is difficult and controversial. Previous hypotheses have been based on morphological and anatomical data. We have analyzed sequence variation of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA) among 13 Thlaspi s.l. taxa, representing all sections of the genus. Phylogenetic relationships among ITS sequences of the Thlaspi s.l. taxa studied are in general concordance with a previously published chloroplast DNA based phylogeny of this group. Most-parsimonious trees from ITS and chloroplast DNA data support three groups that are congruent with lineages (Thlaspi s.str., Noccaea–Raparia, Microthlaspi) previously described by Meyer on the basis of seed anatomy. The ITS data grouped Microthlaspi granatense outside the Microthlaspi clade and, therefore, Microthlaspi appeared paraphyletic on the ITS tree, in contrast with the chloroplast DNA phylogeny. We speculate that concerted evolutionary forces have acted among different nrDNA arrays (brought together in M. granatense by hybridization with a related taxon), resulting in the fixation of the alien species nrDNA type in M. granatense, which, however, maintains a Microthlaspi chloroplast genome type. Both molecular data sets detected intraspecific variation among Microthlaspi perfoliatum accessions of different geographic origin and different ploidy levels. Our molecular evidence would suggest the hybrid origin of polyploid M. perfoliatum from diploid M. perfoliatum and M. natolicum. Key words: chloroplast DNA, restriction site variation, sequence analysis of nuclear ribosomal DNA ITS regions, Thlaspi s.l. (Brassicaceae), molecular phylogeny, congruence.

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