Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts

Authors

  • Christine Sacerdot,

    1. Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA 2171, Université Pierre et Marie Curie-Paris 06, Paris, France
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  • Serge Casaregola,

    1. INRA CNRS AgroParisTech, UMR Microbiologie et Génétique Moléculaire, Thiverval-Grignon, France
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  • Ingrid Lafontaine,

    1. Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA 2171, Université Pierre et Marie Curie-Paris 06, Paris, France
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  • Fredj Tekaia,

    1. Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA 2171, Université Pierre et Marie Curie-Paris 06, Paris, France
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  • Bernard Dujon,

    1. Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA 2171, Université Pierre et Marie Curie-Paris 06, Paris, France
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  • Odile Ozier-Kalogeropoulos

    1. Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA 2171, Université Pierre et Marie Curie-Paris 06, Paris, France
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  • Editor: Monique Bolotin-Fukuhara

Correspondence: Christine Sacerdot, Unité de Génétique Moléculaire des Levures (URA 2171 CNRS, UFR 927 Université Pierre et Marie Curie), Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr Roux, F-75724 Paris Cedex 15, France. Tel.: +33 1 40 61 30 59; fax: +33 1 40 61 34 56; e-mail: sacerdot@pasteur.fr

Abstract

Transfer of fragments of mtDNA to the nuclear genome is a general phenomenon that gives rise to NUMTs (NUclear sequences of MiTochondrial origin). We present here the first comparative analysis of the NUMT content of entirely sequenced species belonging to a monophyletic group, the hemiascomycetous yeasts (Candida glabrata, Kluyveromyces lactis, Kluyveromyces thermotolerans, Debaryomyces hansenii and Yarrowia lipolytica, along with the updated NUMT content of Saccharomyces cerevisiae). This study revealed a huge diversity in NUMT number and organization across the six species. Debaryomyces hansenii harbors the highest number of NUMTs (145), half of which are distributed in numerous large mosaics of up to eight NUMTs arising from multiple noncontiguous mtDNA fragments inserted at the same chromosomal locus. Most NUMTs, in all species, are found within intergenic regions including seven NUMTs in pseudogenes. However, five NUMTs overlap a gene, suggesting a positive impact of NUMTs on protein evolution. Contrary to the other species, K. lactis and K. thermotolerans harbor only a few diverged NUMTs, suggesting that mitochondrial transfer to the nuclear genome has decreased or ceased in these phylogenetic branches. The dynamics of NUMT acquisition and loss are illustrated here by their species-specific distribution.

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