Tag Archives: mushroom

Will mushrooms save the world?

Paul Stamets thinks so and he’s done work to make this happen.  The founder of FungiPerfecti and author many books on mushroom cultivation spoke at a TED talk recently that is worth taking a look. 

We also wrote about how Paul has contributed (and donated in some cases) Pleurotus spawn as part of Dioxin cleanup in Ft Bragg, CA and cleaning up the SF Bay with hair and mushrooms

See Paul Stamets’ TED talk.

Comparing development

PZ Meyers has a post summarizing of an older paper from Elliot Meyerowitz (2002) that comapares plant and animal development. In particular there is are some major themes summarized about how plants and animals form patterns and cell to cell signaling as part of development. What’s missing is what we’ve learned about within group comparisons where there are multiple lineages of single-celled and multicelled forms like choanozoa/metazoa (See M. brevicolis genome paper) and green algae (VolvoxChlamydomonas comparisons are forthcoming, but see Chlamydomonas genome paper).

I hope some of our work will provide more data to include in the comparison of fungal, animal, and plant development in the not too distant future.

Phytopathogenic Fungi: what have we learned from genome sequences?

ResearchBlogging.orgA review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte ancestors.

They infer from phylogenies we’ve published (Fitzpatrick et al, James et al) that plant pathogenic capabilities have arisen at least 5 times in the fungi and at least 7 times in the eukaryotes. In addition they use data on gene duplication and loss in the ascomycete fungi (Wapinski et al) to infer there large numbers of losses and gains of genes have occurred in fungal lineages.

Continue reading Phytopathogenic Fungi: what have we learned from genome sequences?

Sex in fungi: MAT locus cloned from a Zygomycete

On the cover of this week’s Nature is a picture of Phycomyces blakesleeanus Nature Coverhighlighting the discovery of the MAT locus in this Zygomycete fungus from Alex Idnurm and Joe Heitman and colleagues. While it was previously known that Zygomycetes (the Orange lineage represented by R. oryzae in the tree below) mate, the specific locus has until now, never been discovered. The authors in this study identified the MAT locus through a sequence search looking for HMG-box genes knowing that these are found the Mating Type locus in Basidiomycetes and Ascomycetes. They confirmed the identity through a through set of experiments that included PCR, sequencing and crosses of (+) and (-) strains of P. blakesleeanus, and Southern blots.

Continue reading Sex in fungi: MAT locus cloned from a Zygomycete

Willi Hennig Superstar

Willi HennigThe Willi Hennig Society, homebase for all good cladists, has subsidized the license fee for TNT so that it is now a freely available program (although it is not open-source). TNT implements phylogenetic analysis under parsimony with a fast tree searching algorithm. I believe TNT was one of the software tools that CIPRES was targeting for optimization as well so this may reflect some of that work.

From EvolDir.

Evolutionary morphology of mushroom-forming fungi

Blogging about Peer-Reviewed ResearchDave Hibbett wrote a great article for Mycological Research that describes the current state of systematics and evolutionary studies of morphology in mushroom-forming Agaricomycete fungi. His article, dedicated to the late, great mycologist Orson K Miller, Jr and entitled “After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century” describes the how classification and systematics has changed in the last two hundred years and macromorphology to the more than “108,000 nucleotide sequences of ‘homobasidiomycetes’, filed under 7300 unique names.”

The article contains some beautiful pictures many of which are taken from some of the eminent mycological photographers and mycologists Michael Wood and Taylor Lockwood.

Continue reading Evolutionary morphology of mushroom-forming fungi

Saccharomyces strain sequencing

Blogging on Peer-Reviewed ResearchWhile many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled “Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789”.

Continue reading Saccharomyces strain sequencing

This fungus will trap you (if you are a Nematode)

Blogging about Peer-Reviewed ResearchFungi, like most organisms, take an active role in finding food for survival. When thinking about hostile takeovers by fungi, one probably thinks about mycelia growing towards nutrients, rotting plant matter, the ability to extract nutrients from a living host, or perhaps producing toxins or secondary metabolites that can affect the host. However, some fungi can take an even more active role and trap their animal hosts (when that animal isn’t much bigger than you). A paper from earlier this year on “Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences” describes the evolutionary history of a group of fungi able to trap and eat nematodes. Nematode trapping fungi have been investigated experimentally since at least the 30s (Drechsler, Mycologia. 1937, Drechsler, J Wash Acad Sci. 1933), and some more recent studies of the relationship of the groups (Rubner, Studies in Mycology. 1996).

In the recent PNAS paper, the authors used multi-locus sequencing to reconstruct a phylogeny and history of large group of carnivorous fungi and reconstruct the ancestral history the prey trapping mechanism of either through constricting rings or adhesive traps. They were able to reconstruct the likely order of the evolutionary steps needed to make the stalk and trapping cells. They found that the most common type of trap, an Adhesive Network, was the earliest evolved trap.

Some movies also demonstrate how these fungi make their living.