Ribosomal DNA Polymorphism Research Articles

Taxonomy and population structure of E-strain mycorrhizal fungi inferred from ribosomal and mitochondrial DNA polymorphisms

E-strain fungi form ecto- and ectendomycorrhizal associations with many trees, and are important mycorrhizal symbionts in disturbed forest habitats and conifer nurseries. Unlike the majority of mycorrhizal fungi, which are basidiomycetes, E-strain fungi are ascomycetes belonging to the genus Wilcoxina (Pezizales). We analysed variation in the nuclear and mitochondrial ribosomal RNA genes to elucidate species concepts among E-strain fungi and to examine their population structure. We found that most E-strain isolates can be assigned to two taxa, W. mikolae and W. rehmii, that have different habitat preferences. Wilcoxina mikolae is the predominant taxon in disturbed forest habitats on soils that are often low in organic matter, such as burned sites, while W. rehmii prefers peaty soils. Analysis of mitochondrial DNA also revealed that within each species, isolates could be differentiated based upon host preference. This is the first report of population subdivision based upon host in E-strain fungi.

Correlation between DNA polymorphism and enzyme polymorphism argues in favour of the delineation of two species within Providencia alcalifaciens

Ribosomal DNA (rDNA) polymorphism was compared to enzyme polymorphism and DNA/DNA hybridization data for the intraspecies differentiation of Providencia alcalifaciens. DNA from 27 strains previously classified into two zymotypes A 1 and A 2 and discriminated by two levels of DNA/DNA hybridization (ΔT m values of 0 to 1°C and 6 to 10°C, respectively) were analysed by Southern blotting for rDNA polymorphism. The ribotypes fell into two ribogroups A 1 and A 2, which correlated with the corresponding zymotypes. This correlation argues for the proposed creation of two species within P. alcalifaciens.

Correlation between ribosomal DNA polymorphism and electrophoretic enzyme polymorphism in Yersinia

Ribosomal DNA (rDNA) polymorphism was compared with electrophoretic enzyme polymorphism for the intra- and interspecies differentiation of Yersinia enterocolitica, Y. pseudotuberculosis, Y. intermedia, Y. aldovae, Y. frederiksenii and Y. kristensenii. DNA from 90 strains previously classified into six zymotypes (Y. enterocolitica and Y. frederiksenii) and into distinct enzyme electrophoretic patterns (the four other species) was digested with EcoRI or HindIII and analysed by Southern blotting. The six species were clearly differentiated from each other. In Y. enterocolitica, the subclassification of biotype 1 into zymotypes 1A and 1B was also reflected in the rDNA and the four other bio-zymotypes gave four different classes of restriction pattern. In Y. frederiksenii, both EcoRI and HindIII gave five distinct riboclasses which correlated with the zymotypes. In the four other species, the phenotype polymorphism appeared to be better correlated with the restriction fragment length polymorphism data in some enzymes than others. The data demonstrate that the inter- and intraspecies classification by rDNA polymorphism using two restriction enzymes is similar to that based on electrophoretic enzyme polymorphism. The analysis could be refined for taxonomic and epidemiological purposes by using other restriction enzymes.

Use of mitochondrial and ribosomal DNA polymorphisms to classify clinical and soil isolates of Histoplasma capsulatum

We have developed an improved scheme for the classification of environmental and clinical isolates of Histoplasma capsulatum that is based on analysis of mitochondrial DNA (mtDNA) and ribosomal DNA (rDNA). Strains were initially divided into mtDNA groups according to restriction digests of whole-cell DNA and Southern hybridization with cloned mtDNA probes. Strains within a mtDNA class could be further grouped by polymorphisms in rDNA. The majority of soil and clinical isolates from the United States had identical mtDNA patterns; however, rDNA polymorphisms were common in both types of isolates. The combination of mtDNA and rDNA typing described in this report will be useful in resolving questions concerning the epidemiology of H. capsulatum infections.

A simple, sensitive method of analyzing bacterial ribosomal DNA polymorphism

A rapid DNA extraction procedure and random primer labelling of Escherichia coli ribosomal RNA with cloned reverse transcriptase have been used to establish a simple and highly sensitive method for studying ribosomal DNA polymorphism in bacteria. Examples of inter- and intraspecies differentiation of bacteria are given and potential applications in bacterial epidemiology and taxonomy are discussed.

Biased gene conversion and asymmetrical introgression between subspecies

Data from chromosomal in situ hybridization and restriction fragment length polymorphism (RFLP) of ribosomal DNA (rDNA) obtained from the same individuals of two subspecies of the Australian grasshopper Caledia captiva, suggest the occurrence of biased exchange of DNA sequences in hybrid individuals. Thus, there are a disproportionate number of Torresian individuals that possess Moreton ribosomal RNA gene sequences. This bias correlates with the previously described pattern of asymmetrical introgression of Moreton rDNA into Torresian populations. The present findings demonstrate the potential effect of biased gene conversion on the frequencies of introduced gene variants.

Ribosomal DNA as a convenient probe to follow segregation and possible divergency from expected homozygosity after haploidization of an androgenetic process

Restriction fragment length polymorphism of the wheat nuclear ribosomal DNA has been studied in several steps of a breeding scheme, including parental genotypes, F1 hybrid, F9 generation, and anther-derived doubled haploid lines obtained from F9. Ribosomal DNA represents a suitable molecular marker in following segregation and possible divergency from expected homozygosity after haploidization of an androgenetic process. It has been shown to undergo variations among the first cycle-doubled haploid lines in the relative amount of two different sizes of ribosomal DNA repeat units. The specificity and peculiar properties of the plant system used allowed us to assign an intrachromosomal location (short arm of the chromosomes 1B, 1R or 6B) to several ribosomal DNA repeat units that differ by the length of their nontranscribed spacer region.