Posts Tagged ‘Mushroom’

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


August 9th, 2012

This Summer, I’m devoting my free time to write a book on Fungi/Mushrooms (Champignons in french) for the Editions Quae: “200 Clès pour comprendre les champignons” (Mushrooms Facts: 200 Questions & Answers). Mushrooms possess considerable mystique and they have been the subject of numerous papers, accounts and books, and I’m browsing the web to search for documents on these fascinating organisms … and they are great gems, including superbe paintings as follows:

Image from Meyers Blitz-Lexikon ‘Die Schnellauskunft für jedermann in Wort und Bild‘ © Wikimedia Commons

Fungal Fruiting Bodies and Fanatics

August 8th, 2012

In her review of  two recent books, Mushroom (by Nicholas Money) and Mycophilia (by Eugenia Bone) devoted to the standing of mushrooms in nature and in human culture, Linnaea Ostroff wrote a short, but vibrant, description of fungal fruiting bodies and sex in these exciting organisms:

[“Mushrooms are the sex organs of fungi. They are ballistics experts that emerge when the fungus is ready to reproduce, launch spores by the billion, and vanish. Or rather, they puff up and deflate. The sudden appearance of mushroom on a lawn or under a log, like many illusions, is achieved with extensive advance setup and hydraulics. After a spore germinates, it sends filaments out underground in all directions in search of food and other fungi. When two fungal colonies—or three or more, as fungi are substantially less constrained than animals—of the same species meet, their cells merge and their DNA combines in the mushroom version of mating. New spores are produced, and the cells of the future mushroom are organized around them. This process occurs at the tips of the filaments, accounting for mushrooms’ quirk of appearing in rings. When the conditions are right, water rushes in and pressurizes the assembly, swelling the cells and inflating the mushroom. In many species, that takes only a few hours, the spores are soon released, and the mushroom shrivels by sundown. Others survive a week or more, and some tougher forms may last for months.” ]. Read more

‘Mushroom’ by Nicholas P. Money, Oxford University Press, New York, 2011. 221 pp.

Mycophilia. Revelations from the Weird World of Mushrooms by Eugenia Bone, Rodale, New York, 2011. 368 pp..




Zwerg & Fliegenpilz

November 19th, 2011

Zwerg und Fliegenpilz

The Fly Agaric, Amanita muscaria, is amongst the most easily recognised “toadstool”. This mushroom is frequently depicted in fairy stories and on greeting cards. It is often associated with gnomes or ‘lutins’. – Zenodot Verlagsgesellschaft mbH


Shigeru Ban’s musHRoom

November 13th, 2011


Yesterday, I visited the recent modern arts museum ‘Centre Pompidou-Metz‘ in Metz. The building is remarkable for its wooden roof structure, one of the largest and most complex built to date, which was inspired by a Chinese hat found in Paris by the japanese architect Shigeru Ban … a Chinese hat or a gigantic mushroom?

From Wikipedia: ‘The Centre Pompidou Metz is a museum of modern and contemporary arts designed by architects Shigeru Ban and Jean de Gastines and located in Metz, capital of Lorraine, France. It is built in the Amphitheatre District, near the Metz railway station and the German Imperial District. The Centre Pompidou-Metz is a branch of Pompidou arts centre of Paris, and features temporary exhibitions from the large collection of the French National Museum of Modern Art, the largest European collection of 20th and 21st century arts. The museum is the largest temporary exhibition space outside Paris in France . The building was inaugurated on May  2010.’

Photo: Centre Pompidou-Metz (© F Martin)


The Inky Cap Mushroom Genome

June 16th, 2010

coprinopsisOver the last five years, several genomes of basidiomycetes have been published, including Cryptococcus neoformans, Ustilago maydis, Phanerochaete chrysosporium, Malassezia globosa, and Postia placenta. These fungi produce inconspicuous fruiting bodies. In contrast, the number of published genomes from basidiomycetous mushrooms was scarce and limited to the ectomycorrhizal Laccaria bicolor. The genome of the mushroom model species Coprinopsis cinerea (= Coprinus cinereus) has been sequenced in 2003 and was publicly available on the Broad Institute web site since then. The paper describing this genome is now available online at PNAS.

Coprinopsis cinerea is a saprobic mushroom belonging to the family Psathyrellaceae and it has been used for decades for studying the developmental process leading to the formation of the multicellular reproductive structure, so-called mushroom. In the old times, the ink-like liquid produced by dissolving gills after maturation of the spores has been used for writing. Now this fungus is an excellent lab model for study of sexual reproduction and development in basidiomycetes because of its short-life cycle, capability to grow and fruit on artificial media under laboratory conditions. The genome analysis led by Jason Stajich and Pat Pukkila is providing novel insights into the evolution of mushroom-forming fungi. The 37-megabase genome was sequenced by WGS and assembled into 13 chromosomes from telomere to telomere. Although C. cinerea coding space is much lower than L. bicolor, 13,342 versus 19,040 protein-coding genes, it also contains several expanding gene families. The largest family, with 133 members, FunK1, has unusual modifications in conserved kinase motifs and appears to be specific to Agaricomycotina and Pezizomycotina, but not in other fungi, suggesting a potential link between this kinase family and the multicellularity of these fungi.

~40% of the assembled C. cinerea genome displays a synteny with the version 1.0 of the L. bicolor assembly; 3.5 to 4.5 chromosomal rearrangements per million years have accumulated along each lineage since separation of their common ancestor ~100-200 Mya. This rate is at the high end of the range described previously for eukaryotes. It remains to be determined whether the transposon overdose observed in L. bicolor played a role in these frequent chromosomal rearrangements. The syntenic regions are detected mainly in genomic regions with low meiotic recombination rates on the five largest chromosomes. They lack transposable elements and are enriched in genes annotated to basic structures and processes such as nitrogen metabolism, the cytoskeleton, and metabolic regulation, as well as in particular G protein-coupled receptors. In contrast, paralogous gene families are overrepresented near chromosome ends, in regions of average or high meiotic recombination, and low synteny with L. bicolor.

The release of additional cool ‘shrooms genomes, such as those of Schizophyllum, Agaricus and Pleurotus, will undoubtly provide additional insights into the evolution of this fascinating, ecologically important, group of fungi.

Stajich et al. (2010) nsights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). doi: 10.1073/pnas.1003391107

Photo ©  J.K. Lindsey (

Slug Bites

May 30th, 2010

slug biteTranscript profiling of mushrooms, such as Coprinopsis cinereaLaccaria bicolor and Tuber melanosporum, have showed a striking accumulation of transcripts coding for various types of sugar-binding lectins in fruiting bodies. It has been suggested (e.g., by Markus Künzler at ETH-Zürich) that this accumulation of lectins, such as galectins, plays a role defense against fungivores. Clearly, mushrooms growing on the horse manure composting in the back of my garden are not accumulating enough lectins to deter slugs. Dozen of fruiting bodies have mushroomed today after the overnight rains … and now this is a slug feast.

For more info: Glycans and Lectins in the Defense of Fungi against Predators and Parasites (Institute of Microbiology, ETH).

Photo: © F Martin

Rose de Pré

November 8th, 2009

www.mssf.orgThe JGI have announced the pre-release of the Agaricus bisporus var. bisporus (H97) v1.0 assembly. The genome size is 30.2 Mbp with an average coverage of 8.5x. based on ab initio prediction, protein alignment and ESTs, ~10,000 genes have been predicted by automated annotation. The annotation may be browsed, searched, downloaded and expanded with your curations at the Agaricus bisporus var. bisporus (H97) portal: Because this is a pre-release only approved users will be able to get access to this portal.

Cartoon: ©