title: Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood.
abstract: Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.
authors.affiliation: Department of Biomaterials Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Chiaki
authors.initials: C
authors.lastname: Hori
authors.affiliation: Department of Biomaterials Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Ishida
authors.affiliation: Department of Biomaterials Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Kiyohiko
authors.initials: K
authors.lastname: Igarashi
authors.affiliation: Department of Biomaterials Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Samejima
authors.affiliation: Department of Chemical Engineering, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: Department of Chemical Engineering, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Emma
authors.initials: E
authors.lastname: Master
authors.affiliation: Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Ferreira
authors.affiliation: Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Madrid, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ruiz-Dueñas
authors.affiliation: Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Held
authors.affiliation: Millennium Nucleus for Fungal Integrative and Synthetic Biology and Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Paulo
authors.initials: P
authors.lastname: Canessa
authors.affiliation: Millennium Nucleus for Fungal Integrative and Synthetic Biology and Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Luis F
authors.initials: LF
authors.lastname: Larrondo
authors.affiliation: Health and Environment Department, Austrian Institute of Technology GmbH, Tulin, Austria.
authors.forename: Monika
authors.initials: M
authors.lastname: Schmoll
authors.affiliation: Austrian Center of Industrial Biotechnology and Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.
authors.forename: Irina S
authors.initials: IS
authors.lastname: Druzhinina
authors.affiliation: Austrian Center of Industrial Biotechnology and Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.
authors.forename: Christian P
authors.initials: CP
authors.lastname: Kubicek
authors.affiliation: USDA, Forest Products Laboratory, Madison, Wisconsin, United States of America.
authors.forename: Jill A
authors.initials: JA
authors.lastname: Gaskell
authors.affiliation: USDA, Forest Products Laboratory, Madison, Wisconsin, United States of America.
authors.forename: Phil
authors.initials: P
authors.lastname: Kersten
authors.affiliation: USDA, Forest Products Laboratory, Madison, Wisconsin, United States of America.
authors.forename: Franz
authors.initials: F
authors.lastname: St John
authors.affiliation: University of Wisconsin Biotechnology Center, Madison, Wisconsin, United States of America.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Glasner
authors.affiliation: University of Wisconsin Biotechnology Center, Madison, Wisconsin, United States of America.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Sabat
authors.affiliation: University of Wisconsin Biotechnology Center, Madison, Wisconsin, United States of America.
authors.forename: Sandra
authors.initials: S
authors.lastname: Splinter BonDurant
authors.affiliation: Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America.
authors.forename: Khajamohiddin
authors.initials: K
authors.lastname: Syed
authors.affiliation: Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America.
authors.forename: Jagjit
authors.initials: J
authors.lastname: Yadav
authors.affiliation: Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Anthony C
authors.initials: AC
authors.lastname: Mgbeahuruike
authors.affiliation: Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Andriy
authors.initials: A
authors.lastname: Kovalchuk
authors.affiliation: Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Fred O
authors.initials: FO
authors.lastname: Asiegbu
authors.affiliation: Department of Pharmaceutical Biology at the Hans-Knöll-Institute, Friedrich-Schiller-University, Jena, Germany.
authors.forename: Gerald
authors.initials: G
authors.lastname: Lackner
authors.affiliation: Department of Pharmaceutical Biology at the Hans-Knöll-Institute, Friedrich-Schiller-University, Jena, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Hoffmeister
authors.affiliation: Instituto de Recursos Naturales y Agrobiologia de Sevilla, CSIC, Seville, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Rencoret
authors.affiliation: Instituto de Recursos Naturales y Agrobiologia de Sevilla, CSIC, Seville, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Gutiérrez
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Hui
authors.initials: H
authors.lastname: Sun
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Riley
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Aix-Marseille Université, Centre National de la Recherche Scientifique, Marseille, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August University Göttingen, Göttingen, Germany.
authors.forename: Ursula
authors.initials: U
authors.lastname: Kües
authors.affiliation: Novozymes, Inc., Davis, California, United States of America.
authors.forename: Randy M
authors.initials: RM
authors.lastname: Berka
authors.affiliation: Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Madrid, Spain.
authors.forename: Angel T
authors.initials: AT
authors.lastname: Martínez
authors.affiliation: Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America.
authors.forename: Sarah F
authors.initials: SF
authors.lastname: Covert
authors.affiliation: Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Blanchette
authors.affiliation: USDA, Forest Products Laboratory, Madison, Wisconsin, United States of America.
authors.forename: Daniel
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mesh_terms: D001487:Basidiomycota / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism*; D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D002482:Cellulose / Q000378:metabolism; D005656:Fungal Proteins / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D008031:Lignin / Q000378:metabolism; D058977:Molecular Sequence Annotation; D059467:Transcriptome; D014934:Wood / Q000378:metabolism / Q000382:microbiology*
chemical_list: D005656:Fungal Proteins; C036909:lignocellulose; D002482:Cellulose; D008031:Lignin