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Curr Biol. 2014 Jan 6;24(1):11-18. doi: 10.1016/j.cub.2013.11.027. Epub 2013 Dec 12.

The genome of the foraminiferan Reticulomyxa filosa.

Author information

1
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.
2
Protozoology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin.
3
Institute for Anatomy and Cell Biology, Ludwig-Maximilians-Universität München, Schillerstrasse 42, 80336 München, Germany.
4
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.
5
Department of Genetics and Evolution, University of Geneva, 4 Boulevard D'Yvoy, 1205 Genève, Switzerland.
6
Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt.
7
Genome Analysis, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.

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.

PMID:
24332546
DOI:
10.1016/j.cub.2013.11.027
[Indexed for MEDLINE]
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