The molecular diversity analysis of Auricularia auricula-judae in China by nuclear ribosomal DNA intergenic spacer

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.

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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

Applied and Environmental Microbiology ◽

10.1128/aem.65.3.903-909.1999 ◽

1999 ◽

Vol 65 (3) ◽

pp. 903-909 ◽

Cited By ~ 40

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.

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Ecotypic variation of Gremmeniella abietina in northern Europe: disease patterns reflected by DNA variation

Canadian Journal of Botany ◽

10.1139/b95-166 ◽

1995 ◽

Vol 73 (10) ◽

pp. 1531-1539 ◽

Cited By ~ 42

Author(s):

M. Hellgren ◽

N. Högberg

Keyword(s):

Polymerase Chain Reaction ◽

Genetic Variation ◽

Ribosomal Dna ◽

Intergenic Spacer ◽

Principal Component ◽

Nuclear Ribosomal Dna ◽

Restriction Enzyme Digestion ◽

Chain Reaction ◽

Northern Fennoscandia ◽

Polymerase Chain

Genetic variation in Gremmeniella abietina isolated from Pinus sylvestris, Pinus contorta, and Picea abies in southern and northern Fennoscandia was studied with arbitrary primed polymerase chain reaction. Fennoscandian G. abietina isolates were clearly separated into two ecotypically distinct groups based on their amplified banding patterns. Analysis of variance based on amplified fragments, AMOVA, and principal component analysis confirmed the separation of the isolates into the two groups. One group contained isolates associated with a disease syndrome affecting young trees covered by deep snow during winter in northern Fennoscandia. The second group of isolates was found on trees between 15 and 40 years old, scattered throughout the crowns. It occurs throughout Fennoscandia but is most frequent in the southern parts. No size polymorphism was found in fragments resulting after restriction enzyme digestion of internal transcribed spacer and intergenic spacer regions of nuclear ribosomal DNA. An estimate of gene flow between populations calculated based on amplified band frequencies, FST, indicated that there was restricted genetic exchange between populations of the two groups of isolates. Key words: Gremmeniella abietina, arbitrary primed polymerase chain reaction, genetic variation, ecotypes, ribosomal DNA.

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Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex

BMC Genetics ◽

10.1186/1471-2156-12-13 ◽

2011 ◽

Vol 12 (1) ◽

pp. 13 ◽

Cited By ~ 18

Author(s):

Cheryl D Ambrose ◽

Teresa J Crease

Keyword(s):

Ribosomal Dna ◽

Daphnia Pulex ◽

Intergenic Spacer ◽

Nuclear Ribosomal Dna

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Molecular characterization of ribosomal intergenic spacer in the tadpole shrimp Triops cancriformis (Crustacea, Branchiopoda, Notostraca)

Genome ◽

10.1139/g06-047 ◽

2006 ◽

Vol 49 (8) ◽

pp. 888-893 ◽

Cited By ~ 7

Author(s):

Andrea Luchetti ◽

Franca Scanabissi ◽

Barbara Mantovani

Keyword(s):

Ribosomal Dna ◽

Concerted Evolution ◽

Intergenic Spacer ◽

Population Level ◽

Promoter Sequence ◽

Nuclear Ribosomal Dna ◽

Rrna Gene ◽

Living Fossil ◽

Triops Cancriformis ◽

External Transcribed Spacer

Nuclear ribosomal DNA constitutes a multigene family, with tandemly arranged units linked by an intergenic spacer (IGS), which contains initiation/termination transcription signals and usually tandemly arranged subrepeats. The structure and variability of the IGS region are analyzed here in hermaphroditic and parthenogenetic populations of the "living fossil" Triops cancriformis (Branchiopoda, Notostraca). The results indicate the presence of concerted evolution at the population level for this G+C-rich IGS region as a whole, with the major amount of genetic variability found outside the subrepeat region. The subrepeats region is composed of 3 complete repeats (a, c, d) intermingled with 3 repeat fragments (b, e, f) and unrelated sequences. The most striking datum is the absolute identity of subrepeats (except type d) occupying the same position in different individuals/populations. A putative promoter sequence is present upstream of the 18S rRNA gene, but not in subrepeats, which is at variance with other arthropod IGSs. The absence of a promoter sequence in the subrepeats and subrepeat sequence conservation suggests that this region acts as an enhancer simply by its repetitive nature, as observed in some vertebrates. The putative external transcribed spacer (840 bp) shows hairpin structures, as in yeasts, protozoans, Drosophila, and vertebrates.Key words: concerted evolution, Crustacea, external transcribed spacer, intergenic spacer, ribosomal DNA, subrepeats, Triops cancriformis.

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Short-spored Subulicystidium (Trechisporales, Basidiomycota): high morphological diversity and only partly clear species boundaries

MycoKeys ◽

10.3897/mycokeys.35.25678 ◽

2018 ◽

Vol 35 ◽

pp. 41-99 ◽

Cited By ~ 3

Author(s):

Alexander Ordynets ◽

David Scherf ◽

Felix Pansegrau ◽

Jonathan Denecke ◽

Ludmila Lysenko ◽

...

Keyword(s):

Ribosomal Dna ◽

Molecular Diversity ◽

Morphological Diversity ◽

Nuclear Ribosomal Dna ◽

Species Boundaries ◽

Molecular Tools ◽

Level Variation ◽

Corticioid Fungi ◽

Size And Shape ◽

Transitional Forms

Diversity of corticioid fungi (resupinate Basidiomycota), especially outside the northern temperate climatic zone, remains poorly explored. Furthermore, most of the known species are delimited by morphological concepts only and, not rarely, these concepts are too broad and need to be tested by molecular tools. For many decades, the delimitation of species in the genus Subulicystidium (Hydnodontaceae, Trechisporales) was a challenge for mycologists. The presence of numerous transitional forms as to basidiospore size and shape hindered species delimitation and almost no data on molecular diversity have been available. In this study, an extensive set of 144 Subulicystidium specimens from Paleo- and Neotropics was examined. Forty-nine sequences of ITS nuclear ribosomal DNA region and 51 sequences of 28S nuclear ribosomal DNA region from fruit bodies of Subulicystidium were obtained and analysed within the barcoding gap framework and with phylogenetic Bayesian and Maximum likelihood approaches. Eleven new species of Subulicystidium are described based on morphology and molecular analyses: Subulicystidiumboidinii, S.fusisporum, S.grandisporum, S.harpagum, S.inornatum, S.oberwinkleri, S.parvisporum, S.rarocrystallinum, S.robustius, S.ryvardenii and S.tedersooi. Morphological and DNA-evidenced borders were revised for the five previously known species: S.naviculatum, S.nikau, S.obtusisporum, S.brachysporum and S.meridense. Species-level variation in basidiospore size and shape was estimated based on systematic measurements of 2840 spores from 67 sequenced specimens. An updated identification key to all known species of Subulicystidium is provided.

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