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UMR 1065 Santé et Agroécologie du Vignoble

Downy mildew genomics

Génomique des populations des oomycètes du genre Plasmopara (mildiou de la vigne et mildiou du tournesol)

Downy mildew genomics: Plasmopara viticola, P. halstedii

Population genomics of plant-pathogenic oomycetes of the genus Plasmopara: grapevine and sunflower downy mildew

Overal objective

The aim of the project is to obtain the first extensive genomic data on the agents responsible for two destructive plant diseases - grapevine and sunflower downy mildew. We have used next generation sequencing technologies to release a high quality draft genome assembly and annotation for Plasmopara viticola isolate INRA-Pv221 and Plasmopara halstedii isolate INRA-710, together with polymorphim data for additional isolates. The sequencing of different isolates of these two related downy mildew species will allow and to gain new insights into the evolution of the genome of these main plant pathogenic biotrophic oomycetes.

Grapevine downy mildew

Grapevine downy mildew

Name: Plasmopara viticola (Berk. & M.A. Curtis) Berl. & De Toni, in Berlese, De Toni & Fischer, Syll. fung. (Abellini) 7: 239 (1888)

Synonym: Botrytis viticola Berk. & M.A. Curtis 1848

Position in classification: Stramenopile, Oomycetes, Peronosporales, Peronosporaceae

Genome size has been estimated at 114 Mb by Feulgen staining analysis.

  

Sunflower downy mildew

      Sunflower downy mildew

Name: Plasmopara halstedii (Farl.) Berl. & De Toni, in Berlese, De Toni & Fischer, Syll. fung. (Abellini) 7: 242 (1888)

Synonyms: Plasmopara helianthi Novotel'nova

Taxonomic position: Stramenopile, Oomycetes, Peronosporales, Peronosporaceae

Genome size : estimated to be around 100 Mb.

In this project, our specific aims are as follows:

  1. Generate a whole genome shotgun sequence assembly of P. viticola INRA-Pv221 and P. hasltedii INRA-710 as reference sequences, using Illumina HiSeq 2000 technology.
  2. Produce an automated annotation of the genome, using 454 RNA-seq data generated by this project. cDNAs of P. halstedii have been produced for four French races/pathotypes and from two different conditions: infected sunflower leaves and in vitro germinated pathogen spores. cDNAs of P. viticola have been produced for two European isolates and from two different conditions: infected grapevine leaves and in vitro germinated pathogen spores.
  3. Identify conserved and rapidly diversifying genes by generating Illumina data from additional isolates.
  4. Integrate the annotated genome sequence into the INRA PLASMOPARA genomics resource center: PLASMOPARA database.
  5. The comparative analysis of genomes will allow:
  • to evaluate the genetic diversity and to calibrate the genetic divergence between these two downy mildew species;
  • to characterize molecular markers (SNP) associated with virulence profiles ;
  • to look for genes encoding potential pathogenicity proteins;
  • to assess the level of positive selection in the global set of expressed genes, with special attention to candidates genes potentially involved in virulence.
  • to understand how obligate biotrophy has evolved by comparing the structure and the organization of these genomes with Phytophthora spp. genomes already available.  

Project organization

Project coordination: François Delmotte (P. viticola), Laurence Godiard (P. halstedii)

This research funded by the French National Agronomical Research Institute (INRA) and the French National Research Agency. Sequencing has been performed at France Génomique (Evry, France) and GenoToul (France).

Partners

  • UMR1065 SAVE, INRA Bordeaux, France (F. Delmotte, S. Richart-Cervera)
  • UMR1131 SVQV, INRA Colmar, France (P. Mestre, M.C. Piron)
  • LIPM Sunflower team, INRA Toulouse, France (L. Godiard, P. Vincourt)
  • LIPM Bioinformatics, INRA Toulouse, France (J. Gouzy, S. Carrère)

Related genomic resources on Heterokonts/Stramenopiles
 
 Oomycetes

Diatoms

  • Phaeodactylum tricornutum :  Genome
  • Thalassiosira pseudonana : Genome

 Brown algae