Get access

454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant–rust interaction

Authors

  • DIANA FERNANDEZ,

    1. IRD, Institut de Recherche pour le Développement, UMR 186 IRD-Cirad-UM2 Résistance des Plantes aux Bioagresseurs, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
    Search for more papers by this author
  • EMILIE TISSERANT,

    1. INRA, Institut National de la Recherche Agronomique, UMR 1136 INRA/Nancy Université Interactions Arbres/Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France
    Search for more papers by this author
  • PEDRO TALHINHAS,

    1. CIFC/IICT, Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal
    Search for more papers by this author
  • HELENA AZINHEIRA,

    1. CIFC/IICT, Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal
    Search for more papers by this author
  • ANA VIEIRA,

    1. CIFC/IICT, Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal
    Search for more papers by this author
  • ANNE-SOPHIE PETITOT,

    1. IRD, Institut de Recherche pour le Développement, UMR 186 IRD-Cirad-UM2 Résistance des Plantes aux Bioagresseurs, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
    Search for more papers by this author
  • ANDREIA LOUREIRO,

    1. CIFC/IICT, Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal
    Search for more papers by this author
  • JULIE POULAIN,

    1. Genoscope, Centre National de Séquençage, CEA, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
    Search for more papers by this author
  • CORINNE DA SILVA,

    1. Genoscope, Centre National de Séquençage, CEA, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
    Search for more papers by this author
  • MARIA DO CÉU SILVA,

    1. CIFC/IICT, Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal
    Search for more papers by this author
  • SÉBASTIEN DUPLESSIS

    Corresponding author
    1. INRA, Institut National de la Recherche Agronomique, UMR 1136 INRA/Nancy Université Interactions Arbres/Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France
    Search for more papers by this author

Email: duplessi@nancy.inra.fr

SUMMARY

Coffee (Coffea arabica L.), one of the key export and cash crops in tropical and subtropical countries, suffers severe losses from the rust fungus Hemileia vastatrix. The transcriptome of H. vastatrix was analysed during a compatible interaction with coffee to obtain an exhaustive repertoire of the genes expressed during infection and to identify potential effector genes. Large-scale sequencing (454-GS-FLEX Titanium) of mixed coffee and rust cDNAs obtained from 21-day rust-infected leaves generated 352 146 sequences which assembled into 22 774 contigs. In the absence of any reference genomic sequences for Coffea or Hemileia, specific trinucleotide frequencies within expressed sequence tags (ESTs) and blast homology against a set of dicots and basidiomycete genomes were used to distinguish pathogen from plant sequences. About 30% (6763) of the contigs were assigned to H. vastatrix and 61% (13 951) to C. arabica. The majority (60%) of the rust sequences did not show homology to any genomic database, indicating that they were potential novel fungal genes. In silico analyses of the 6763 H. vastatrix contigs predicted 382 secreted proteins and identified homologues of the flax rust haustorially expressed secreted proteins (HESPs) and bean rust transferred protein 1 (RTP1). These rust candidate effectors showed conserved amino-acid domains and conserved patterns of cysteine positions suggestive of conserved functions during infection of host plants. Quantitative reverse transcription-polymerase chain reaction profiling of selected rust genes revealed dynamic expression patterns during the time course of infection of coffee leaves. This study provides the first valuable genomic resource for the agriculturally important plant pathogen H. vastatrix and the first comprehensive C. arabica EST dataset.

Ancillary