title: Wide occurrence of SSU rDNA intragenomic polymorphism in foraminifera and its implications for molecular species identification.
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.
authors.affiliation: Department 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.
authors.forename: Alexandra Anh-Thu
authors.initials: AA
authors.lastname: Weber
authors.affiliation: Department of Genetic and Evolution, University of Geneva, Sciences III, 30, Quai Ernest Ansermet, CH-1211 Genève 4, Switzerland. Electronic address: jan.pawlowski@unige.ch.
authors.forename: Jan
authors.initials: J
authors.lastname: Pawlowski
mesh_terms: D016000:Cluster Analysis; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics*; D056908:Foraminifera / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S
keywords: DNA barcoding; SSU rDNA.; foraminifera; intragenomic variability; protists