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Genome Biol Evol. 2015 Jan 8;7(2):465-80. doi: 10.1093/gbe/evu292.

Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.

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Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea.
Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark.
Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany.
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
INRA and Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, Marseille, France.
Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany.
Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, Marseille, France, and Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.


Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here, we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mb, and contains 14,268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. Clonostachys rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases, and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), whereas an increase in subgroup C (multidrug resistance-associated proteins) is evident in Trichoderma virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes was induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chlororaphis. The data suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea.


ABC transporter; Bionectria ochroleuca; biological control; fungicide; phylogeny; polyketide synthase

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