title: The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown.
abstract: BACKGROUND
  Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology.
  
  
  RESULTS
  The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases.
  
  
  CONCLUSIONS
  With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass.
authors.affiliation: INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France. anthony.levasseur@univ-amu.fr.
authors.forename: Anthony
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authors.lastname: Levasseur
authors.forename: Anne
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authors.lastname: Lomascolo
authors.forename: Olivier
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authors.lastname: Chabrol
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ruiz-Dueñas
authors.forename: Eva
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authors.lastname: Boukhris-Uzan
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authors.lastname: Piumi
authors.forename: Ursula
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authors.forename: Arthur F J
authors.initials: AF
authors.lastname: Ram
authors.forename: Claude
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authors.lastname: Murat
authors.forename: Mireille
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authors.lastname: Haon
authors.forename: Isabelle
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authors.lastname: Benoit
authors.forename: Yonathan
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authors.lastname: Arfi
authors.forename: Didier
authors.initials: D
authors.lastname: Chevret
authors.forename: Elodie
authors.initials: E
authors.lastname: Drula
authors.forename: Min Jin
authors.initials: MJ
authors.lastname: Kwon
authors.forename: Philippe
authors.initials: P
authors.lastname: Gouret
authors.forename: Laurence
authors.initials: L
authors.lastname: Lesage-Meessen
authors.forename: Vincent
authors.initials: V
authors.lastname: Lombard
authors.forename: Jérôme
authors.initials: J
authors.lastname: Mariette
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Joohae
authors.initials: J
authors.lastname: Park
authors.forename: Aleksandrina
authors.initials: A
authors.lastname: Patyshakuliyeva
authors.forename: Jean Claude
authors.initials: JC
authors.lastname: Sigoillot
authors.forename: Ad
authors.initials: A
authors.lastname: Wiebenga
authors.forename: Han A B
authors.initials: HA
authors.lastname: Wösten
authors.forename: Francis
authors.initials: F
authors.lastname: Martin
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Ronald P
authors.initials: RP
authors.lastname: de Vries
authors.forename: Angel T
authors.initials: AT
authors.lastname: Martínez
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Eric
authors.initials: E
authors.lastname: Record
mesh_terms: D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D056426:Genetic Loci; D016681:Genome, Fungal; D006031:Glycosylation; D008031:Lignin / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D010544:Peroxidases / Q000235:genetics; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D055494:Pycnoporus / Q000201:enzymology / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014934:Wood / Q000382:microbiology
chemical_list: D005656:Fungal Proteins; D020543:Proteome; C036909:lignocellulose; D008031:Lignin; D010544:Peroxidases; C042858:lignin peroxidase