Related Experiment Video
Updated: Apr 25, 2026

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
Published on: January 22, 2018
Wide occurrence of SSU rDNA intragenomic polymorphism in foraminifera and its implications for molecular species
Alexandra Anh-Thu Weber1, Jan Pawlowski2
1Department of Genetic and Evolution, University of Geneva, Sciences III, 30, Quai Ernest Ansermet, CH-1211 Genève 4, Switzerland; Aix-Marseille Université, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, Station Marine d'Endoume, Chemin de la Batterie des Lions, F-13007 Marseille, France.
Abstract:
Ribosomal DNA is commonly used as a marker for protist phylogeny and taxonomy because of its ubiquity and its expected species specificity thanks to the mechanism of concerted evolution. However, numerous studies reported the occurrence of intragenomic (intra-individual) polymorphism in various protists and particularly in Foraminifera. To infer to what extent the SSU rDNA intragenomic variability occurs in Foraminifera, we studied 16 foraminiferal species belonging to single-chambered monothalamids and multi-chambered Globothalamea, with one to six individuals per species. We performed single-cell DNA extractions and PCRs of a 600bp fragment of SSU rDNA, and sequenced 9 to 23 clones per individual for a total of 818 sequences. We found intragenomic variability in almost all species, even after excluding singleton mutations. Intra-individual sequence divergence ranged from 0 to 5.15% and was higher than 1% in 11 species. Variability was usually located at the end of stem-loop structures and included compensatory single nucleotide polymorphisms and expansion segments polymorphisms. However, the polymorphisms did not change the secondary structure of the rRNA. Our results suggest a non-concerted evolution of rRNA genes in Foraminifera. The origin of this variability and its implications for species identification in environmental DNA studies are discussed.
More Related Videos
09:04Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
Published on: July 26, 2018
04:59Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster
Published on: March 28, 2025
Related Concept Videos
Diversity of Protists III
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Exon Recombination
Exon shuffling follows “splice frame rules.” Each exon...
Single Nucleotide Polymorphisms-SNPs
Ribosomal RNA Synthesis
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Modern Molecular Taxonomy