Posts Tagged ‘wood decay’

The Pizza Mushroom Genome

October 9th, 2012

The publication describing the genome from the Button Mushroom (Agaricus bisporus) was published online today  in the early Edition of the journal, the Proceedings of the National Academy of Sciences (PNAS). This paper represents a culmination of five years of work by many people from multiple institutions in France, U.S.A., U.K., The Netherlands, Finland and Germany. This was truly an amazing team effort between the JGI teams and the international consortium. Let’s see if the news coverage of this genome study is as good as the one received for the Black Truffle genome. After all, the Portobello mushroom is one of the most commonly and widely consumed mushrooms in the world.

Below is the abstract of our PNAS paper:

[Abstract. Agaricus bisporus is the model fungus for the adaptation,persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.]

Read: Morin et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences, Early Edition.

Press releases:

JGI: Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores

INRA: Le génome du champignon de Paris décrypté

Crunching Fungal Genomes at High Speed

February 19th, 2011

116-1660_IMG_2In October 2010, the US Department of Energy Joint Genome Institute (JGI) launched the Fungal Genomics Program (FGP), aimed at exploration of fungal diversity for energy and environmental sciences and applications through the scale-up of sequencing and analysis.

Within the framework of this JGI initiative, the project ‘Sequencing saprotrophic Agaricomycotina‘, lead by David Hibbett, has targeted 30 wood-decay fungi representing 12 orders. In the last few weeks, JGI has released 13 of these fungal genomes from saprotrophic white- and brown rots: Auricularia auricula-judae, Ceriporiopsis subvermisposa, Coniophora puteana, Dacryopinax spathularia, Dichomitus squalens, Fomitiporia mediterranea, Fomitopsis pinicola, Gloeophyllum trabeum, Phlebia brevispora, Punctularia strigosozonata, Stereum hirsutum, Trametes versicolor, and Wolfiporia cocos. These genome sequences are available through the JGI portal and their mining will keep us busy for months to go.

With the published genome of Schizophyllum commune and the annotated (and soon to be published) genomes of Agaricus bisporus, Heterobasidion annosum, Pleurotus ostreatus, Serpula lacrymans and Tremella mesenterica, we have now a unique opportunity to understand the biological lifestyles and lignocellulolytic strategies of the wood-decayers.

Photo: Laetiporus sulphureus © F Martin