Protist, Vol. 165, 645–661, September 2014 http://www.elsevier.de/protis Published online date 24 July 2014 ORIGINAL PAPER Wide Occurrence of SSU rDNA Intragenomic Polymorphism in Foraminifera and its Implications for Molecular Species Identification Alexandra Anh-Thu Weber a,b , and Jan Pawlowski a,1 a Department of Genetic and Evolution, University of Geneva, Sciences III, 30, Quai Ernest Ansermet, CH-1211 Genève 4, Switzerland b 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 Submitted March 6, 2014; Accepted July 16, 2014 Monitoring Editor: David Moreira 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. How- ever, 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 per- formed single-cell DNA extractions and PCRs of a 600 bp 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. © 2014 Elsevier GmbH. All rights reserved. Key words: DNA barcoding; foraminifera; intragenomic variability; protists; SSU rDNA. Introduction Ribosomal RNA genes are present in every organ- ism from bacteria to eukaryote (Woese et al. 1990). The eukaryotic genes coding for small subunit (SSU 1 Corresponding author; fax +41 22 379 67 70 e-mail jan.pawlowski@unige.ch (J. Pawlowski). or 18S) and large subunit (LSU or 28S) of the ribo- some, as well as the 5.8S rRNA, the noncoding regions of the internal transcribed spacers (ITS1 and ITS2) and the intergenic spacer (IGS) are typ- ically arranged in one transcription unit, organized in large tandem arrays. Those genes are commonly used as markers for phylogenetic and taxonomic studies as they are composed of conserved and http://dx.doi.org/10.1016/j.protis.2014.07.006 1434-4610/© 2014 Elsevier GmbH. All rights reserved.