Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays

Authors

  • ANTOINE LE QUÉRÉ,

    1. Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden,
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    • Present address: Université de Genève, Département de Biologie Végétale, LBMPS — Science III, 30 Quai Ernest-Ansermet, CH-1211 Geneve 4, Switzerland.

    • These authors contributed equally to this work.

  • KASPER ASTRUP ERIKSEN,

    1. Complex System Division, Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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    • These authors contributed equally to this work.

  • BALAJI RAJASHEKAR,

    1. Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden,
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  • ANDRES SCHÜTZENDÜBEL,

    1. Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden,
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    • §

      Present address: Institute of Forest Botany, Department of Forest Botany and Tree Physiology, Georg-August-Universität, Büsgenweg 2, DE-37077 Göttingen, Germany.

  • BJÖRN CANBÄCK,

    1. Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden,
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  • TOMAS JOHANSSON,

    1. Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden,
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  • ANDERS TUNLID

    Corresponding author
    1. Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden,
      Anders Tunlid, Fax: +46-46-222 4158; E-mail: anders.tunlid@mbioekol.lu.se.
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Anders Tunlid, Fax: +46-46-222 4158; E-mail: anders.tunlid@mbioekol.lu.se.

Abstract

We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest evolutionary relative to P. involutus that has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging within Paxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over-representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis.

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