Open Access Highly Accessed Research article

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Hitoshi Suzuki1, Jacqueline MacDonald1, Khajamohiddin Syed2, Asaf Salamov3, Chiaki Hori5, Andrea Aerts3, Bernard Henrissat4, Ad Wiebenga8, Patricia A vanKuyk8, Kerrie Barry3, Erika Lindquist3, Kurt LaButti3, Alla Lapidus3, Susan Lucas3, Pedro Coutinho4, Yunchen Gong7, Masahiro Samejima5, Radhakrishnan Mahadevan1, Mamdouh Abou-Zaid6, Ronald P de Vries8, Kiyohiko Igarashi5, Jagjit S Yadav2, Igor V Grigoriev3 and Emma R Master1*

Author Affiliations

1 Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada

2 Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0056, USA

3 US Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California, 94598, USA

4 Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS, UMR 6098, 163 Avenue de Luminy, 13288, Marseille, France

5 Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, l-l-l, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan

6 Great Lakes Forestry Centre, 1219 Queen Street East, Sault Ste. Marie, Ontario, Canada, P6A 2E5

7 Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B3

8 CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands

For all author emails, please log on.

BMC Genomics 2012, 13:444  doi:10.1186/1471-2164-13-444

Published: 2 September 2012

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.

Keywords:
Phanerochaete carnosa; Comparative genomics; Phanerochaete chrysosporium; Softwood degradation