If you are interested in Polypores check out the NSF funded PEET site for the Taxonomy of the Polyporales from David Hibbett and colleagues.
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Category Archives: basidiomycota
The Alaskan Goo demystified
Another delightful well written piece by Jennifer Frazer in her SciAm blog. She presents a solution to a unknown fungus that showed up as a blanket of orange spores in the water near the town of Kivalina, Alaska. “Mystery of Alaskan “Goo” Rust Solved at Last”. Jennifer writes that the rust spores are from:
Spruce-Labrador Tea Needle Rust, Chrysomyxa ledicola, a parasite of both spruce trees and arhododendron — a flowering woody shrub common to conifer understories the world over — called Labrador Tea.
Schizophyllum genome update
Robin Ohm at the JGI has announced the release of version 2 of the Schizophyllum commune genome. This is great news on the heels of the announcement that one of the funded 2012 CSPs will include detailed functional genomics experiments in this mushroom.
I am pleased to announce the public release of the JGI annotation and portal for the improved assembly of Schizophyllum commune. Annotations of the assembly are now publicly visible at http://jgi.doe.gov/Scommune2 . Annotation and editing privileges remain password-protected but all other tools are now available to the general public.
A detailed set of statistics on the assembly and annotation can be found on the Info page of that portal: http://genome.jgi-psf.org/Schco2/Schco2.info.html
Myco-bio-diesel
Previously I posted on an article on making biodiesel using the fungus Gliocladium roseum. Here is a new study reporting conversion of lipids to biodiesel using the basidiomycete Cryptococcus curvatus. There has been also other progress in this area where Mucor circinelloides can also be used to produce oils suitable for biodiesel production as reported in the paper and the press release - though it is a pathogenic fungus with interesting spore size dimorphism.
Thiru M, Sankh S, & Rangaswamy V (2011). Process for biodiesel production from Cryptococcus curvatus. Bioresource technology PMID: 21930373
Orange goo is in fact rust spores in Alaska waters
Previously incorrectly identified as eggs, the ‘orange goo’ floating off the shore of a small Alaskan village has now been identified as a rust fungus.
If they had known that a hoard of Mycologists were descending on Alaska for our annual meeting! I guess the exact identification is still being determined by NOAA labs – hope they can PCR ITS up and figure it out (and maybe save a culture for deposition somewhere).
(Thanks to Blake Billmyre for passing along the story)
Genome sequence of mushroom Schizophyllum commune
I am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers. The data and analyses from these efforts are presented in a publication appearing in Nature Biotechnology today.
Studies in mushrooms can have important impact on other research areas. They can be useful in biotechnology as protein biosynthesis factories for producing compounds or even as an edible delivery mechanism for new drugs. What we found in the analysis of this genome include clues to mechanisms of how white rotting fungi degrade lignin through analysis of enzyme families. We also saw evidence for extensive antisense transcription during different developmental stages suggesting some important clues as to how some gene regulation could impact or control developmental progression. Through gene expression comparison (by MPSS) a large number of transcription factors were shown to be differentially regulated during sexual development. A knockout out two of these (fst3 and fst4) resulting in changes in ability to form mushrooms (fst4) or smaller mushrooms (fst3).
Several more interesting findings in this work that I hope to add back to this post when there is a little more time -
Ohm, R., de Jong, J., Lugones, L., Aerts, A., Kothe, E., Stajich, J., de Vries, R., Record, E., Levasseur, A., Baker, S., Bartholomew, K., Coutinho, P., Erdmann, S., Fowler, T., Gathman, A., Lombard, V., Henrissat, B., Knabe, N., Kües, U., Lilly, W., Lindquist, E., Lucas, S., Magnuson, J., Piumi, F., Raudaskoski, M., Salamov, A., Schmutz, J., Schwarze, F., vanKuyk, P., Horton, J., Grigoriev, I., & Wösten, H. (2010). Genome sequence of the model mushroom Schizophyllum commune Nature Biotechnology DOI: 10.1038/nbt.1643
A mushroom on the cover
I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus. You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper.
Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D., Palmerini, H., Ramesh, M., Rehmeyer, C., Roe, B., Shenoy, N., Stanke, M., Ter-Hovhannisyan, V., Tunlid, A., Velagapudi, R., Vision, T., Zeng, Q., Zolan, M., & Pukkila, P. (2010). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Proceedings of the National Academy of Sciences, 107 (26), 11889-11894 DOI: 10.1073/pnas.1003391107
An Inky-cap mushroom genome
Francis Martin has written up a delightful summary pointing to our publication of the genome of Coprinopsis cinereus which appears in the early edition of PNAS and will grace the cover at the end of the month. I encourage you to take a look at Francis’s post and the paper, available as Open Access from PNAS. I’ll do my best to post a summary of the paper when I get a free moment.
For now I’ll leave you with a picture of this cute little mushroom fruting in the lab and a link to many more at Flickr.
I’ll have the truffles and huitlacoche
A couple of papers should have captured your attention lately in the realm of fungal genomics.
One is the publication of the genome of the black truffle Tuber melanosporum. This appears as an advanced publication at Nature (OA by virtue of Nature’s agreement on genome papers) along with a NYT writeup and is a tasty exploration of the genome of an ascomycete ectomycorrhizal (ECM) fungus. There are several gems in there including the differences in transposable element content, content of gene families related to carbohydrate metabolism. This genome helps open the doorway for exploring the several independent origins of ECM in both ascomycete and basidiomycete fungi.
I’ll also point out there is some work on the analysis of mating type locus found in this genome has applied aspects suggesting that inoculation of roots with both mating types may increase truffle yields in truffle farms. Evidence for sexual reproduction is also discovered from this genome analysis based on the sexual cycle genes present and the structure of the MAT locus. Much like what was revealed in the genome analysis of the previously ‘asexual’ species Aspergillus fumigatus (and later reconstitution of a sexual cycle), the Tuber genome has the potential for mating and is a heterothallic (outcrossing) fungus based on its mating type locus -just like many other filamentous Ascomycete species.
A second paper I encourage you take a look at (those with a Science subscription) is from Virginia Walbot’s lab on the formation of tumors by U. maydis in Maize. These tumors end up destroying the corn but can produce a delicious (to some) dish that is huitlacooche. The idea that the fungus is co-opting the host system by secreting proteins that acted in the same way as native proteins and that it has a tissue or organ specific repertoire was one that her lab has been pursuing. U. maydis can grow inside corn without detection and the formation of tumors seems to be a manipulation of the plant as much as it is the pathogen directly taking resources from the plant. It reminds me a bit of the production of secondary metabolites that can control plant growth like gibberellins produced by fungi. This kind of manipulation and also ability to evade detection suggests a pretty specific set of controls that prevent the fungus from doing the wrong thing at the wrong time (to avoid detection). So they set out to see if there are a set of organ specific genes that the fungus uses during infection that would suggest a very host-specific strategy by this corn smut.
In this paper the authors evaluate the role of fungal genes specifically expressed in infection of different organs and also the role of secreted proteins in colonization of the organs. In what is impressive and elegant work, the authors show through the use of microarrays and genetics that there is plant tissue specific gene expression of U. maydis – so infections in leaves express a different set of genes than those in seedlings. Genetic and phenotypic evaluation of fungal strains with knockouts of sets of the predicted secreted proteins was able to confirm a role for specific secreted proteins that previously may have not had any discernible phenotype. They infect strains with knockouts of sets of genes that encode secreted proteins and compare the virulence when these strains infect individual organs of the maize host. They showed there is significantly different virulence in the various tissues for a some of the mutants suggesting an organ-specific role for virulence of secreted proteins. They also go on to show that some of this organ specific infection requires organ-specific gene expression by evaluating maize mutants and the ability of the fungus to infect different organs.
Future work will hopefully followup to see what these secreted proteins are manipulating in the host and how they either enable virulence by protecting the pathogen, avoiding detection by turning of host responses, or co-opting host gene networks in some other way.
Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buée M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marçais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, & Wincker P (2010). Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature PMID: 20348908
Skibbe DS, Doehlemann G, Fernandes J, & Walbot V (2010). Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen. Science (New York, N.Y.), 328 (5974), 89-92 PMID: 20360107
Underwater mushrooms?
The cover of the Jan/Feb Mycologia has a picture of a pretty weird place to find a mushroom growing – a new species of mushroom that was found fruiting underwater in the Rogue river in Oregon. This was reported about two years ago for a discovery that was made in 2005, but this is a formal publication on the finding and species description of Psathyrella aquatica. It is quite cool to see discovery of a new habitat for mushrooms, but I expect some more work will be required to fully understand the mechanics and development dealing with the challenges of underwater growth. I think it would be interesting to see what kind of dispersal mechanisms there are since the spores are probably forced to float downstream, if there is an animal or wind dispersal mechanism at some later stage too or whether one finds mycelium growing in the soil near and around the rivers.
The important part of identifying the species and sequencing identifying molecular marker like ITS is that when later metagenomics studies of soil are performed, the anonymous sequenced clones can be matched up to know species, and we can identify where else this fungus is found.
Frank, J., Coffan, R., & Southworth, D. (2009). Aquatic gilled mushrooms: Psathyrella fruiting in the Rogue River in southern Oregon Mycologia, 102 (1), 93-107 DOI: 10.3852/07-190