Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics

  title={Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics},
  author={Thomas J. White},
Comparative studies of the nucleotide sequences of ribosomal RNA (rRNA) genes provide a means for analyzing phylogenetic relation­ ships over a wide range of taxonomic levels (Woese and Olsen 1986; Zimmer et al 1988; Medlin et al 1988; Jorgensen and Cluster 1989). The nuclear small-subunit rDNA sequences (16S-like) evolve rela­ tively slowly and are useful for studying distantly related organisms, whereas the mitochondrial rRNA genes evolve more rapidly and can be useful at the ordinal or… Expand

Figures and Tables from this paper

Molecular Analysis of Ribosomal RNA Genes in Rhizoctonia Fungi
The DNA sequences that encode ribosomal RNAs have been useful for understanding phylogenetic and taxonomic relationships and patterns of genetic variation in fungi and except for analysis of the small mt rRNA subunit, mt rDNA genes have not been critically examined in Rhizoctonia fungi. Expand
Amplification of mitochondrial small subunit ribosomal DNA of polypores and its potential for phylogenetic analysis
Phylogenetic relationships were resolved quite efficiently by mt SSU rDNA sequences, and they proved to be more useful in phylogenetic reconstruction of Ganoderma than nuclear internal transcribed spacer (ITS) r DNA sequences. Expand
rRNA sequence comparisons for assessing phylogenetic relationships among yeasts.
  • C. Kurtzman
  • Biology, Medicine
  • International journal of systematic bacteriology
  • 1992
The use of rRNA comparisons should allow a deciphering of the relationships among extant taxa and also answer the question of whether yeasts represent ancestral forms of the higher fungi or are reduced forms of many present-day groups and thus of polyphyletic origin. Expand
Sequencing and Analysis of Fungal rRNA Operons for Development of Broad-Range Fungal PCR Assays
These PCR assays hold promise for detection and identification of fungal pathogens in human tissues and provided the most phylogenetic information for species identification based on the distance matrices. Expand
The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny
The internal transcribed spacer (ITS) region of 18S-26S nuclear ribosomal DNA (nrDNA) has proven to be a useful source of characters for phylogenetic studies in many angiosperm families. The twoExpand
Ribosomal ITS sequences and plant phylogenetic inference.
Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis, and it is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes. Expand
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis
ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. Expand
A Conserved Motif in the 5.8S Ribosomal RNA (rRNA) Gene is a Useful Diagnostic Marker for Plant Internal Transcribed Spacer (ITS) Sequences
A conserved 14 base pair motif in the 5.8S rRNA gene is described that can be used to differentiate between flowering plants, bryophytes, and several orders of algae and fungi, including common plant pathogenic and non-pathogenic fungi. Expand
Phylogeny of the Genus Agaricus Inferred from Restriction Analysis of Enzymatically Amplified Ribosomal DNA
This is the first comprehensive attempt at systematically resolving the entire genus Agaricus using modern techniques for molecular genetic analysis and indicates that previous taxonomic schemes, based on morphological characters, are in need of revision. Expand
Clone Libraries of Ribosomal RNA Gene Sequences for Characterization of Bacterial and Fungal Communities
This chapter provides the principles and methodologies of clone library construction and sequence analyses for the purpose of investigating bacterial, archaeal and fungal community composition. Expand


Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16 S rRNA or cloning of its gene, and its phylogenetic usefulness is evaluated by examination of several 17S rRNAs whose gene sequences are known. Expand
The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions.
Oligodeoxynucleotides that are complementary to conserved regions at the 5' and 3' termini of eukaryotic 16S-like rRNAs were used to prime DNA synthesis in repetitive cycles of denaturation, reannealing, and DNA synthesis. Expand
Compilation of small ribosomal subunit RNA sequences.
The set of 452 different sequences comprises all sequences that to the authors' knowledge had been published or were available from the sequence library file servers as of December 1, 1990, and that are either complete or cover a minimum of about 70% of the complete sequence. Expand
Archaebacterial phylogeny: perspectives on the urkingdoms.
By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Expand
The nucleotide sequence at the 3'-end of Neurospora crassa 18S-rRNA and studies on the interaction with 5S-rRNA.
Findings are consistent with the idea that intermolecular base-pairing between nucleotides at the 3'-ends of 18S-rRNA and 5S- rRNA may be functionally important within the ribosome. Expand
These conditions have not been optimized for enzyme and magnesium ion concentrations
  • Part Three. Genetics and Evolution Literature
  • 1989
The characterization of enzy ­ matically amplified eukaryotic 16 S - likerRNA - codingregions
  • 1988
Hybridization of nucleic acids immobilized on solid supports.