title: The genome of the foraminiferan Reticulomyxa filosa.
abstract: BACKGROUND
  Rhizaria are a major branch of eukaryote evolution with an extensive microfossil record, but only scarce molecular data are available. The rhizarian species Reticulomyxa filosa, belonging to the Foraminifera, is free-living in freshwater environments. In culture, it thrives only as a plasmodium with thousands of haploid nuclei in one cell. The R. filosa genome is the first foraminiferal genome to be deciphered.
  
  
  RESULTS
  The genome is extremely repetitive, and the large amounts of identical sequences hint at frequent amplifications and homologous recombination events. Presumably, these mechanisms are employed to provide more gene copies for higher transcriptional activity and to build up a reservoir of gene diversification in certain gene families, such as the kinesin family. The gene repertoire indicates that it is able to switch to a single-celled, flagellated sexual state never observed in culture. Comparison to another rhizarian, the chlorarachniophyte alga Bigelowiella natans, reveals that proteins involved in signaling were likely drivers in establishing the Rhizaria lineage. Compared to some other protists, horizontal gene transfer is limited, but we found evidence of bacterial-to-eukaryote and eukaryote-to-eukaryote transfer events.
  
  
  CONCLUSIONS
  The R. filosa genome exhibits a unique architecture with extensive repeat homogenization and gene amplification, which highlights its potential for diverse life-cycle stages. The ability of R. filosa to rapidly transport matter from the pseudopodia to the cell body may be supported by the high diversification of actin and kinesin gene family members.
authors: Institute for Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany; Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB Müggelseedamm 301, 12587 Berlin, Germany. Electronic address: gernot.gloeckner@uni-koeln.de.
authors: Gernot
authors: G
authors: Glöckner
authors: Protozoology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin.
authors: Norbert
authors: N
authors: Hülsmann
authors: Institute for Anatomy and Cell Biology, Ludwig-Maximilians-Universität München, Schillerstrasse 42, 80336 München, Germany.
authors: Michael
authors: M
authors: Schleicher
authors: Institute for Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany.
authors: Angelika A
authors: AA
authors: Noegel
authors: Institute for Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany.
authors: Ludwig
authors: L
authors: Eichinger
authors: Institute for Anatomy and Cell Biology, Ludwig-Maximilians-Universität München, Schillerstrasse 42, 80336 München, Germany.
authors: Christoph
authors: C
authors: Gallinger
authors: Department of Genetics and Evolution, University of Geneva, 4 Boulevard D'Yvoy, 1205 Genève, Switzerland.
authors: Jan
authors: J
authors: Pawlowski
authors: Department of Genetics and Evolution, University of Geneva, 4 Boulevard D'Yvoy, 1205 Genève, Switzerland.
authors: Roberto
authors: R
authors: Sierra
authors: Institute for Anatomy and Cell Biology, Ludwig-Maximilians-Universität München, Schillerstrasse 42, 80336 München, Germany.
authors: Ursula
authors: U
authors: Euteneuer
authors: Department of Genetics and Evolution, University of Geneva, 4 Boulevard D'Yvoy, 1205 Genève, Switzerland.
authors: Loic
authors: L
authors: Pillet
authors: Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt.
authors: Ahmed
authors: A
authors: Moustafa
authors: Genome Analysis, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.
authors: Matthias
authors: M
authors: Platzer
authors: Genome Analysis, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.
authors: Marco
authors: M
authors: Groth
authors: Genome Analysis, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.
authors: Karol
authors: K
authors: Szafranski
authors: Institute for Anatomy and Cell Biology, Ludwig-Maximilians-Universität München, Schillerstrasse 42, 80336 München, Germany.
authors: Manfred
authors: M
authors: Schliwa
mesh_terms: D003599:Cytoskeleton / Q000235:genetics; D022761:Gene Transfer, Horizontal; D018503:Genome, Protozoan; D008540:Meiosis; D008969:Molecular Sequence Data; D056901:Rhizaria / Q000166:cytology / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors