Home • Phanerochaete chrysosporium RP-78 v4.0
Phanerochaete chrysosporium colonizing wood chips. Image courtesy of Tom Volk.
Phanerochaete chrysosporium colonizing wood chips. Image courtesy of Tom Volk.

White rot fungi produce unique extracellular oxidative enzymes that degrade lignin and related compounds found in explosive contaminated materials, pesticides, and toxic wastes. To elucidate the genetic basis of this technologically important behavior, we have sequenced the approximately thirty million base-pair genome of the white rot fungus Phanerochaete chrysosporium to generate a near chromosome-level assembly using a whole genome shotgun method. P. chrysosporium was the first basidiomycete genome to be sequenced, and this improved assembly provides significantly more contiguity than previously available.

Lignin plays a key role in the carbon cycle as the most abundant aromatic compound in nature, providing the protective matrix surrounding the cellulose microfibrils of plant cell walls. This amorphous and insoluble polymer lacks stereoregularity and, in contrast to cellulose and hemicellulose, it is not susceptible to hydrolytic attack. Although lignin is a formidable substrate, its degradation by certain fungi was recognized and described over 125 years ago. Collectively referred to as white rot fungi (since lignin removal often leaves a bleached appearance), these are the only microbes capable of efficient depolymerization and mineralization of lignin. All are basidiomycetes, a fungal group that includes edible mushrooms, mycorrhiza, and plant pathogens such as smuts and rust.

P. chrysosporium has been the most intensively studied white rot fungus. White rot fungi secrete an array of peroxidases and oxidases that act non-specifically via the generation of lignin free radicals, which then undergo spontaneous cleavage reactions. The non-specific nature and exceptional oxidation potential of the enzymes has attracted considerable interest for application in bioprocesses such as organopollutant degradation and fiber bleaching.

P. chrysosporium has several features that might make it very useful in biotechnology applications. First, it efficiently depolymerizes all the major components of wood. Additionally, it has a very high optimum temperature (about 40 °C), which means it can grow on wood chips in compost piles, which attain a very high temperature.

This is an improved draft assembly of P. chrysosporium, sequenced using PacBio. The genome assembly used in the previous annotation, Phchr3_2, has been re-annotated using a combination of PacBio transcriptomic data (IsoSeq) as well as new Illumina RNAseq data.