Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

“…Previous studies indicate that, in both bacterial and eukaryotic genomes, the locations of genes are not necessarily random 30 there are examples of gene clusters encoding proteins that are involved in the production of secondary metabolites, including NRPS/PKS pathways, or in the oxidation of substrates, for example the cytochrome P450 genes in Phanerochaete chrysosporium 31 . In several Clostridium species, there is an intriguing parallel to the T. reesei CAZyme clusters in that the genes of the cellulosome complex encoding GH enzymes needed for cellulose and hemicellulose degradation are also clustered 32 .…”

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

“…Brown rot fungi represent about 6–7% of the basidiomycete fungi. Phanerochaete chrysosporium genome was the first basidiomycete complete genome sequence to be published in the year 2004 by Martinez et al (2004), which has revealed various significant facts about lignocellulose degradation mechanisms (Martinez et al 2004; Ohm et al 2014). After this study, the complete genome sequences of several basidiomycetes fungi were revealed in the recent years (Kameshwar and Qin 2016b).…”

“…We have selected (a) 14 popular white rot fungal strains – Ceriporiopsis subvermispora B (Fernandez-Fueyo et al 2012), Heterobasidion annosum v2.0 (Olson et al 2012), Fomitiporia mediterranea v1.0 (Floudas et al 2012), Phanerochaete carnosa HHB-10118 (Suzuki et al 2012), Pycnoporus cinnabarinus BRFM 137 (Levasseur et al 2014), Phanerochaete chrysosporium R78 v2.2 (Martinez et al 2004; Ohm et al 2014), Dichomitus squalens LYAD-421 SS1 (Floudas et al 2012), Trametes versicolor v1.0 (Floudas et al 2012), Punctularia strigosozonata v1.0 (Floudas et al 2012), Phlebia brevispora HHB-7030 SS6 (Binder et al 2013), Botrytis cinerea v1.0 (Amselem et al 2011), Pleurotus ostreatus PC15 v2.0 (Riley et al 2014; Alfaro et al 2016; Castanera et al 2016), Stereum hirsutum FP-91666 SS1 v1.0 (Floudas et al 2012), Pleurotus eryngii ATCC90797 (Guillen et al 1992; Camarero et al 1999; Ruiz‐Dueñas et al 1999; Matheny et al 2006); (b) 15 popular brown rot fungal strains – Postia placenta MAD 698-R v1.0 (Martinez et al 2009), Fibroporia radiculosa TFFH 294 (Tang et al 2012), Wolfiporia cocos MD-104 SS10 v1.0 (Floudas et al 2012), Dacryopinax primogenitus DJM 731 SSP1 v1.0 (Floudas et al 2012), Daedalea quercina v1.0 (Nagy et al 2015), Laetiporus sulphureus var v1.0 (Nagy et al 2015), Postia placenta MAD-698-R-SB12 v1.0 (Martinez et al 2009), Neolentinus lepideus v1.0 (Nagy et al 2015), Serpula lacrymans S7.9 v2.0 (Eastwood et al 2011), Calocera cornea v1.0 (Eastwood et al 2011), Gloeophyllum trabeum v1.0 (Floudas et al 2012), Fistulina hepatica v1.0 (Floudas et al 2015), Fomitopsis pinicola FP-58527 SS1 (Floudas et al 2015), Hydnomerulius pinastri v2.0 (Kohler et al 2015) and Coniophora puteana v1.0 (Kohler et al 2015); (c) 13 popular soft rot fungal strains – Trichoderma reesei v 2.0 (Martinez et al 2008), Rhizopus oryzae 99-880 from Broad (Ma et al 2009), Aspergillus wentii v1.0 (De Vries et al 2017), Penicillium chrysogenum Wisconsin 54-1255 (Van Den Berg et al 2008), Daldinia eschscholzii EC12 v1.0, Hypoxylon sp. CI-4A v1.0 (Wu et al 2017), Aspergillus niger ATCC 1015 v4.0 (Andersen et al 2011), Hypoxylon sp.…”

Fungal Genomic Annotation

“…Phanerochaete chrysosporium † + + + (Martinez et al 2004) Phytophthora sojae + + Phytophthora ramorum † + + …”

“…This period also saw the first filamentous fungi Neurospora crassa (Galagan et al 2003), the first basidiomycete genome of Phanerochaete chrysosporium (Martinez et al 2004) and, through the Phytophthora Genome Initiative (Waugh et al 2000), the first oomycetes, Phytophthora sojae and Phytophthora ramorum, were sequenced (genome.jgi-psf.org/sojae1 and genome.jgipsf.org/ramorum1). Large genome sequencing centers have begun to focus some of their sequencing capacity on the fungal kingdom.…”