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.

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.

Molecular biogeography and evolution of the Microthlaspi perfoliatum s.l. polyploid complex (Brassicaceae): chloroplast DNA and nuclear ribosomal DNA restriction site variation

1998 ◽  
Vol 76 (3) ◽  
pp. 382-396 ◽  
Author(s):  
Marcus Koch ◽  
Klaus Mummenhoff ◽  
Herbert Hurka
Keyword(s):  
Molecular Phylogeny ◽  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Species Complex ◽  
Restriction Site ◽  
Natural Populations ◽  
Nuclear Ribosomal Dna ◽  
Polyploid Complex ◽  
Northern Iran ◽  
Ploidy Levels

The genusThlaspi L. s.l. comprises numerous segregate lineages, which have been recognized as single genera. One of these, Microthlaspi, represents one such segregate. It consists of morphologically similar annual species. The species have different ploidy levels (2x, 4x, 6x) and are usually summarized under the designation Thlaspi perfoliatum agg. The assumed ancestral diploid members of the species complex, Microthlaspi granatense (Boiss. & Reut.) F.K. Meyer, Microthlaspi umbellatum (Steven ex DC.) F.K. Meyer, and Microthlaspi natolicum (Boiss.) F.K. Meyer, are restricted to northwestern Africa, southeastern Spain and Turkey, northern Iran, and Lebanon. Microthlaspi perfoliatum (L.) F.K. Meyer is widely distributed all over Europe and shows three ploidy levels. Diploid M. perfoliatum is restricted to Middle Europe, whereas tetraploid and hexaploid M. perfoliatum are distributed all over Europe. Individual plants from 125 natural populations throughout the geographic range were analysed using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) restriction site analysis. Within Microthlaspi, 31 cpDNA restriction site mutations, six nrDNA restriction site variations, and two length mutations in the IGS region of the nrDNA were found, and a molecular phylogeny of the species complex has been derived. Polymorphisms in molecular data partitioned cytotypes of M. perfoliatum. The geographical distribution patterns apparently reflect ancient speciation processes and postglacial vegetation history.Key words: chloroplast DNA, nuclear ribosomal DNA, Microthlaspi perfoliatum polyploid complex, molecular phylogeny, biogeography.

scholarly journals Analysis of Fungal Flora in Indoor Dust by Ribosomal DNA Sequence Analysis, Quantitative PCR, and Culture

2007 ◽  
Vol 74 (1) ◽  
pp. 233-244 ◽  
Author(s):  
M. Pitkäranta ◽  
T. Meklin ◽  
A. Hyvärinen ◽  
L. Paulin ◽  
P. Auvinen ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Ribosomal Dna ◽  
Large Scale ◽  
Fungal Species ◽  
Indoor Dust ◽  
Nuclear Ribosomal Dna ◽  
Indoor Environments ◽  
Internal Transcribed Spacer Region ◽  
Fungal Flora ◽  
Potential Health

ABSTRACT In recent years increasing attention has been given to the potential health effects of fungal exposure in indoor environments. We used large-scale sequencing of the fungal internal transcribed spacer region (ITS) of nuclear ribosomal DNA to describe the mycoflora of two office buildings over the four seasons. DNA sequencing was complemented by cultivation, ergosterol determination, and quantitative PCR analyses. Sequences of 1,339 clones were clustered into 394 nonredundant fungal operational taxonomical units containing sequences from 18 fungal subclasses. The observed flora differed markedly from that recovered by cultivation, the major differences being the near absence of several typical indoor mold genera such as Penicillium and Aspergillus spp. and a high prevalence of basidiomycetes in clone libraries. A total of 55% of the total diversity constituted of unidentifiable ITS sequences, some of which may represent novel fungal species. Dominant species were Cladosporium cladosporioides and C. herbarum, Cryptococcus victoriae, Leptosphaerulina americana and L. chartarum, Aureobasidium pullulans, Thekopsora areolata, Phaeococcomyces nigricans, Macrophoma sp., and several Malassezia species. Seasonal differences were observed for community composition, with ascomycetous molds and basidiomycetous yeasts predominating in the winter and spring and Agaricomycetidae basidiomycetes predominating in the fall. The comparison of methods suggested that the cloning, cultivation, and quantitative PCR methods complemented each other, generating a more comprehensive picture of fungal flora than any of the methods would give alone. The current restrictions of the methods are discussed.

The Nuclear Ribosomal DNA Intergenic Spacer as a Target Sequence To Study Intraspecific Diversity of the Ectomycorrhizal Basidiomycete Hebeloma cylindrosporum Directly on Pinus Root Systems

1999 ◽  
Vol 65 (3) ◽  
pp. 903-909 ◽  
Author(s):  
Alice Guidot ◽  
Erica Lumini ◽  
Jean-Claude Debaud ◽  
Roland Marmeisse
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Root Systems ◽  
Intraspecific Diversity ◽  
Nuclear Ribosomal Dna ◽  
Restriction Enzyme Digestion ◽  
Target Sequence ◽  
Root Tips ◽  
Hebeloma Cylindrosporum

ABSTRACT Polymorphism of the nuclear ribosomal DNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete Hebeloma cylindrosporum was studied to evaluate whether this sequence could be used in field studies to estimate the diversity of strains forming mycorrhizas on individual Pinus pinaster root systems. This sequence was amplified by PCR from 125 haploid homokaryotic strains collected in 14 P. pinaster stands along the Atlantic coast of France by using conserved oligonucleotide primers. Restriction enzyme digestion of the amplified 3.4-kbp-long IGS allowed us to characterize 24 alleles whose frequencies differed. Nine of these alleles were found only once, whereas about 60% of the strains contained four of the alleles. Local populations could be almost as diverse as the entire population along a 150-km stretch of coastline that was examined; for example, 13 alleles were found in a single forest stand. The IGS from one strain was partially sequenced, and the sequence data were used to design oligonucleotides which allowed separate PCR amplification of three different segments of the IGS. Most polymorphisms observed among the full-length IGS regions resulted from polymorphisms in an internal ca. 1,500-bp-long sequence characterized by length variations that may have resulted from variable numbers of a T2AG3 motif. This internal polymorphic sequence could not be amplified from the genomes of nine other Hebeloma species. Analysis of this internal sequence amplified from the haploid progenies of 10 fruiting bodies collected in a 70-m2 area resulted in identification of six allelic forms and seven distinct diplotypes out of the 21 possible different combinations. Moreover, optimization of the PCR conditions resulted in amplification of this sequence from more than 80% of the DNA samples extracted from individual H. cylindrosporum infectedP. pinaster mycorrhizal root tips, thus demonstrating the usefulness of this sequence for studying the below-ground diversity of mycorrhizas formed by genets belonging to the same fungal species.

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.

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.

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