Archive for June, 2010

Closer to the Gods

June 19th, 2010

Alpine peaks

Heading to the High Valley of Maurienne in the French Alps for two weeks of hiking.

Ragged peaks, enchanting forests, rolling and lush meadows stretching out in the Vanoise National Park will help me to find fresh inspiration for the forthcoming projects. My brain is ready to take off…

Galileo’s Dream” novel from Kim Stanley Robinson is sitting in my backpack for the long starry nights. From Galileo’s heresy trial to the politics of far-futured Jupiter, from the Canals of Venice to frozen, mysterious Europa … invigorating reading.

Photo: Ancien Refuge du Chambeyron Jean Coste (2626 m) – Aiguille de Chambeyron – High Valley of Ubaye/Haute Ubaye – © F Martin

a long, hard road to the summit

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 (