title: Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.
abstract: 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.
authors.affiliation: Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden magnus.karlsson@slu.se.
authors.forename: Magnus
authors.initials: M
authors.lastname: Karlsson
authors.affiliation: Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Mikael Brandström
authors.initials: MB
authors.lastname: Durling
authors.affiliation: Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea.
authors.forename: Jaeyoung
authors.initials: J
authors.lastname: Choi
authors.affiliation: Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Chatchai
authors.initials: C
authors.lastname: Kosawang
authors.affiliation: Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany.
authors.forename: Gerald
authors.initials: G
authors.lastname: Lackner
authors.affiliation: Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Georgios D
authors.initials: GD
authors.lastname: Tzelepis
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Nygren
authors.affiliation: Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Mukesh K
authors.initials: MK
authors.lastname: Dubey
authors.affiliation: Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Kamou
authors.affiliation: INRA and Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, Marseille, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Levasseur
authors.affiliation: Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Zapparata
authors.affiliation: Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Jinhui
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Daniel Buchvaldt
authors.initials: DB
authors.lastname: Amby
authors.affiliation: Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Birgit
authors.initials: B
authors.lastname: Jensen
authors.affiliation: Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Sarrocco
authors.affiliation: Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Panteris
authors.affiliation: Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
authors.forename: Anastasia L
authors.initials: AL
authors.lastname: Lagopodi
authors.affiliation: Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Pöggeler
authors.affiliation: Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Vannacci
authors.affiliation: Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: David B
authors.initials: DB
authors.lastname: Collinge
authors.affiliation: Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Hoffmeister
authors.affiliation: Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, Marseille, France, and Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea.
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.affiliation: Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Dan Funck
authors.initials: DF
authors.lastname: Jensen
mesh_terms: D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D049770:Genes, Mating Type, Fungal; D016681:Genome, Fungal; D006999:Hypocreales / Q000235:genetics*; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010572:Pest Control, Biological; D010802:Phylogeny; D064210:Secondary Metabolism / Q000235:genetics
chemical_list: D005656:Fungal Proteins
keywords: ABC transporter; Bionectria ochroleuca; biological control; fungicide; phylogeny; polyketide synthase