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Letters to Nature

Nature 414, 450-453 (22 November 2001) | doi:10.1038/35106579; Received 23 April 2001; Accepted 31 August 2001

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Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

Michaël D. Katinka1, Simone Duprat1, Emmanuel Cornillot2, Guy Méténier2, Fabienne Thomarat3, Gérard Prensier2, Valérie Barbe1, Eric Peyretaillade2, Philippe Brottier1, Patrick Wincker1, Frédéric Delbac2, Hicham El Alaoui2, Pierre Peyret2, William Saurin1, Manolo Gouy3, Jean Weissenbach1 & Christian P. Vivarès2

  1. Genoscope, UMR CNRS 8030, CP 5706, 91057 Evry cedex, France
  2. Parasitologie Moléculaire et Cellulaire, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Université Blaise Pascal, 63177 Aubière cedex, France
  3. Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon I, 69622 Villeurbanne cedex, France

Correspondence to: Christian P. Vivarès2 Correspondence and requests for materials should be addressed to C.P.V. (e-mail: Email: christian.vivares@lbp.univ-bpclermont.fr).

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Microsporidia are obligate intracellular parasites infesting many animal groups1. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage2 that diverged before the endosymbiotic event that led to mitochondria. The discovery of a gene for a mitochondrial-type chaperone3, 4, 5 combined with molecular phylogenetic data6, 7, 8, 9 later implied that microsporidia are atypical fungi that lost mitochondria during evolution. Here we report the DNA sequences of the 11 chromosomes of the approx2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes). Genome compaction is reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The strong host dependence is illustrated by the lack of genes for some biosynthetic pathways and for the tricarboxylic acid cycle. Phylogenetic analysis lends substantial credit to the fungal affiliation of microsporidia. Because the E. cuniculi genome contains genes related to some mitochondrial functions (for example, Fe–S cluster assembly), we hypothesize that microsporidia have retained a mitochondrion-derived organelle.

  1. Genoscope, UMR CNRS 8030, CP 5706, 91057 Evry cedex, France
  2. Parasitologie Moléculaire et Cellulaire, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Université Blaise Pascal, 63177 Aubière cedex, France
  3. Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon I, 69622 Villeurbanne cedex, France

Correspondence to: Christian P. Vivarès2 Correspondence and requests for materials should be addressed to C.P.V. (e-mail: Email: christian.vivares@lbp.univ-bpclermont.fr).