title: Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
abstract: BACKGROUND
  Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.
  
  
  RESULTS
  P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.
  
  
  CONCLUSIONS
  The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.
authors.affiliation: Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Suzuki
authors.forename: Jacqueline
authors.initials: J
authors.lastname: MacDonald
authors.forename: Khajamohiddin
authors.initials: K
authors.lastname: Syed
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Chiaki
authors.initials: C
authors.lastname: Hori
authors.forename: Andrea
authors.initials: A
authors.lastname: Aerts
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Ad
authors.initials: A
authors.lastname: Wiebenga
authors.forename: Patricia A
authors.initials: PA
authors.lastname: VanKuyk
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Pedro
authors.initials: P
authors.lastname: Coutinho
authors.forename: Yunchen
authors.initials: Y
authors.lastname: Gong
authors.forename: Masahiro
authors.initials: M
authors.lastname: Samejima
authors.forename: Radhakrishnan
authors.initials: R
authors.lastname: Mahadevan
authors.forename: Mamdouh
authors.initials: M
authors.lastname: Abou-Zaid
authors.forename: Ronald P
authors.initials: RP
authors.lastname: de Vries
authors.forename: Kiyohiko
authors.initials: K
authors.lastname: Igarashi
authors.forename: Jagjit S
authors.initials: JS
authors.lastname: Yadav
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.forename: Emma R
authors.initials: ER
authors.lastname: Master
mesh_terms: D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006026:Glycoside Hydrolases / Q000235:genetics; D020075:Phanerochaete / Q000201:enzymology / Q000235:genetics*; D011124:Polyporaceae / Q000201:enzymology / Q000235:genetics*; D014934:Wood / Q000382:microbiology*
chemical_list: D005656:Fungal Proteins; D006026:Glycoside Hydrolases; C023305:hemicellulase