Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes

PLoS Genet. 2016 May 6;12(5):e1006017. doi: 10.1371/journal.pgen.1006017. eCollection 2016 May.

Abstract

Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode's response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen's genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the evolutionary arms race that exists between pathogen and host, to be studied.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Ascomycota / genetics
  • Ascomycota / pathogenicity
  • Caenorhabditis elegans / microbiology*
  • Caenorhabditis elegans / parasitology
  • Comparative Genomic Hybridization
  • Hypocreales / classification
  • Hypocreales / genetics
  • Mycoses / microbiology*
  • Mycoses / parasitology
  • Phylogeny*
  • Spiroplasma / classification
  • Spiroplasma / genetics*
  • Spiroplasma / pathogenicity
  • Spores, Fungal / classification
  • Spores, Fungal / genetics
  • Spores, Fungal / pathogenicity
  • Virulence / genetics

Grant support

This work was supported by a program grant from the ANR (ANR-12-BSV3-0001-01) and institutional funding from INSERM, CNRS and AMU. The Functional Genomics Platforms of Nice Sophia Antipolis and Toulouse are supported by the Program “Investissements d’Avenir” managed by the National Research Agency (ANR-10-09-INBS) with support from the National Infrastructure France Génomique (ANR-10-INBS-09-03 and ANR-10-INBS-09-02), the Cancéropôle PACA, the Fondation pour la Recherche Médicale (DEQ20130326464 to PB) and the Labex Signalife (ANR-11-LABX-0028-01); microscopy used the France-BioImaging infrastructure supported by ANR-10-INSB-04-01; worm sorting infrastructure supported by ANR-11-LABX-0054 (Investissements d’Avenir–Labex INFORM) and ANR-11-IDEX-0001-02 (Investissements d’Avenir–A*MIDEX). SR is supported by a Marie Curie grant (MC-CIG 334036 project SEPAraTE), a starting grant of the European Research Council (ERC-StG 336808 project VariWhim) and the French Laboratory of Excellence project TULIP (ANR-10-LABX-41; ANR-11-IDEX-0002-02). LDH received a China Scholarship Council fellowship, and NT supported by an AMU doctoral fellowship and Labex INFORM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.