Comparative analysis of mitochondrial genomes of Rhizophagus irregularis – syn. Glomus irregulare – reveals a polymorphism induced by variability generating elements

Authors

  • Damien Formey,

    1. Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, Castanet-Tolosan Cedex, France
    2. CNRS, UMR5546, Castanet-Tolosan Cedex, France
    3. Agro-Nutrition, Carbonne, France
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    • These authors contributed equally to this work.

  • Marion Molès,

    1. Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, Castanet-Tolosan Cedex, France
    2. CNRS, UMR5546, Castanet-Tolosan Cedex, France
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    • These authors contributed equally to this work.

  • Alexandra Haouy,

    1. Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, Castanet-Tolosan Cedex, France
    2. CNRS, UMR5546, Castanet-Tolosan Cedex, France
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  • Bruno Savelli,

    1. Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, Castanet-Tolosan Cedex, France
    2. CNRS, UMR5546, Castanet-Tolosan Cedex, France
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  • Olivier Bouchez,

    1. Plateforme Génomique, Campus INRA Chemin de Borde-Rouge, Castanet-Tolosan Cedex, France
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  • Guillaume Bécard,

    1. Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, Castanet-Tolosan Cedex, France
    2. CNRS, UMR5546, Castanet-Tolosan Cedex, France
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  • Christophe Roux

    Corresponding author
    1. CNRS, UMR5546, Castanet-Tolosan Cedex, France
    • Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, Castanet-Tolosan Cedex, France
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Author for correspondence:

Christophe Roux

Tel: +33 562 19 35 04

Email: roux@lrsv.ups-tlse.fr

Summary

  • Arbuscular mycorrhizal (AM) fungi are involved in one of the most widespread plant–fungus interactions. A number of studies on the population dynamics of AM fungi have used mitochondrial (mt) DNA sequences, and yet mt AM fungus genomes are poorly known. To date, four mt genomes of three species of AM fungi are available, among which are two from Rhizophagus irregularis.
  • In order to study intra- and interstrain mt genome variability of R. irregularis, we sequenced and de novo assembled four additional mt genomes of this species. We used 454 pyrosequencing and Illumina technologies to directly sequence mt genomes from total genomic DNA.
  • The mt genomes are unique within each strain. Interstrain divergences in genome size, as a result of highly polymorphic intergenic and intronic sequences, were observed. The polymorphism is brought about by three types of variability generating element (VGE): homing endonucleases, DNA polymerase domain-containing open reading frames and small inverted repeats. Based on VGE positioning, mt sequences and nuclear markers, two subclades of R. irregularis were characterized.
  • The discovery of VGEs highlights the great intraspecific plasticity of the R. irregularis mt genome. VGEs allow the design of powerful mt markers for the typing and monitoring of R. irregularis strains in genetic and population studies.

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