Genomics of wood-degrading fungi

Ohm, Robin A.; Riley, Robert; Salamov, Asaf; Min, Byoung Won; Choi, In Geol; Grigoriev, Igor V.

doi:10.1016/j.fgb.2014.05.001

Cited by 107 publications

(76 citation statements)

References 89 publications

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“…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).…”

Section: Resultsmentioning

confidence: 99%

“…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.…”

Section: Methodsmentioning

confidence: 99%

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

2017

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We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

2017

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“…The 1,000 Fungal Genomes Project (1000.fungalgenomes.org), in collaboration with the Fungal Genomics Program of the U.S. Department of Energy Joint Genome Institute, is a community effort to obtain, annotate, and share whole genomes of taxa representing the breadth of the fungal kingdom (203,204). By June 2014, 157 whole annotated, published genomes were publicly available at the JGI MycoCosm web portal (205).…”

Section: Analysis Of Ecosystem-related Traits Within Whole Genomesmentioning

confidence: 99%

Fungal Traits That Drive Ecosystem Dynamics on Land

Treseder

Lennon

2015

Microbiol Mol Biol Rev

456

322

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SUMMARY Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance—β-glucan synthesis, trehalose production, and cold-induced RNA helicases—were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter—lignin peroxidases, cellobiohydrolases, and crystalline cellulases—were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.

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“…This later role is important for cellular function as it prevents Fenton reactions from occurring and the concomitant accumulation of reactive oxygen species. Schizophyllum commune, a member of the order Agaricales, lacks the genes encoding lignin-acting peroxidases [4], suggesting that it degrades lignin using alternative methods, possibly using the laccases identified in the genome [47]. Laccases, however, are absent from the white-rot basidiomycete Phanerochaete chrysosporium, a member of the order Polyporales [48], indicating that fungi employ a vast diversity of mechanisms to breakdown lignin and related compounds.…”

Section: Laccase and Peroxidase Activitymentioning

confidence: 99%

Lignocellulolytic Capability of Endophytic Phyllosticta sp.

CB¹

2017

J Bacteriol Mycol

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The Dothideomycetes represent the largest fungal class of Ascomycota. It is an ubiquitous class of fungi whose members span a wide spectrum of lifestyles and host interactions. The endophytic fungus Phyllosticta is one members of the Dothideomycetes, causing disease in economic crops. Phyllosticta was screened for the degradation of lignocellulosic biomass of commercial relevance, such as rice straw, rice husk, sorghum, wheat straw, miscanthus, lavender flower, and lavender straw. The highest degrading strains were identified from an initial screen and further analyzed for the secretion of lignocellulosic enzymes during growth on the different biomasses. With Phyllosticta capitalensis (MFLUCC14-0233), maximum activity of arabinase (944.18 U/ml culture), cellulase (27.10 U/ml), xylanase (10.85 U/ml), pectinase (465.47 U/ml), and laccase (35.68 U/ml) activities could be detected in the secretome during growth on lavender flowers and lavender straw. Phyllosticta capitalensis is thus an interesting new strain for the production of lignocellulosic enzymes during growth on cheap agro-industrial biomass. Keywords:Agro-industrial residues; Biological pretreatment; Dothideomycetes; Lignocellulosic biomass; Lignocellulytic enzyme; Phyllosticta IntroductionThe Dothideomycetes represent the largest fungal class within the phylum Ascomycota. It is a ubiquitous class of fungi whose members span a wide spectrum of lifestyles and host interactions [1][2][3]. Members of the Dothideomycetes can cause disease in every major crop [4]. Approximately 1,300 genera and 19,000 species have been identified either as endophytes, plant pathogens, or as saprophytes degrading plant biomass, thus threatening agriculture and food security throughout the world [5][6][7][8]. In addition to their mode of life, the Dothideomycetes are known for producing secondary metabolites grouped into four main categories based on their biosynthetic origin: polyketides, non-ribosomal peptides, terpenoids and tryptophan derivatives [9]. These secondary metabolites can be both toxic and beneficial to plants and humankind in applications such as agrochemicals, antibiotics, immunosuppressant's, antiparasitics, antioxidants and anticancer agents [10]. New Dothideomycetes are still being discovered worldwide and a large number of these strains remained unexplored regarding their potential use in biotechnology [11][12].Endophytes provide a broad variety of bioactive secondary metabolites with unique structures and so this class of fungi could be used as potential "nanofactories" producing a range of "green" alternatives to currently employed chemicals [13]. Although the ecological significance of endophytes is not completely clear, it is known that these fungi can exploit dead leaves immediately after their senescence and before they fall from the tree [14], and so could be also exploited for the production of enzymes acting on plant biomass.A well-known representative of Dothideomycetes fungi in metabolite studies is Phyllosticta (with a Guignardia anamorph)...

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Genomics of wood-degrading fungi

Cited by 107 publications

References 89 publications

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

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

Fungal Traits That Drive Ecosystem Dynamics on Land

Lignocellulolytic Capability of Endophytic Phyllosticta sp.

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