Tag Archives: coprinus

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.

Coprinopsis cover

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.

Mature Coprinus cinereus (Coprinopsis cinerea)

Coprinopsis cinereus genome annotation updated

Coprinus cinereus genome projectThe Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across the globe including a BAC map from H. Muraguchi.  Thanks to Jonathan Goldberg and colleagues at the Broad Institute for getting this updated annotation out the door.

 

This updated annotation is able to join and split several sets of genes and the gene count sits at just under 14k genes in this 36Mb genome. There are a couple of hiccups in the GTF and Genome contig/supercontig file naming that I am told will be fixed by early next week.  Additional work to annotate the “Kinome” by the Broad team provides some promising new insight to this genome annotation as well.

We’re using this updated genome assembly address questions about evolution of genome structure by studying syntenic conservation and aspects of crossing over points during meiosis.  The C. cinereus system has long been used as model for fungal development and morphogensis of mushrooms as it is straightforward to induce mushroom fruiting in the laboratory.  It also a model for studying meiosis due to the synchronized meiosis occurring in the cells in the cap of the mushroom.

Happy genome shrooming.

Coprinus on the heart?

Here’s a fungal infection you don’t hear much about. One of the fungi we work on, a model for mushroom development as it can be fruited in the lab is Coprinopsis cinerea (previously named Coprinus cinereus). C. cinerea is a saprobric coprophillic fungus so it is usually found on dung.  Although rare in human infections there are a few reports in immunocopromised patients.  Below is an abstract describing isolation of C. cinerea from an implanted heart valve from a pig. This definitely not its typical habitat and Coprinus growing in yeast form I’m sure I’ve really heard of either.  Would be great to see if the clinical strains are still sexually competent and/or are significantly different in other ways (growth rate, resistance to drugs and oxidative stress) from the wild or laboratory strains.

A 77-year-old female initially presented with symptomatic mitral valve stenosis involving a bioprosthesis that had been implanted 8 months earlier for myxomatous mitral valve disease and severe valvular regurgitation. The patient was taken for a second mitral valve replacement due to stenosis. Intraoperatively, the bioprosthetic mitral valve was noted to have an unusual clot-like mass on the atrial side. Initial fungal smears were positive for yeast stains, and pathology revealed extensive colonization by thick filamentous fungus with apparent true hyphae, pseudohyphae, and yeast forms. The fungus was identified as Hormographiella aspergillata, the asexual form of Coprinus cinereus, a common inky cap mushroom that grows in the lawn.

Continue reading Coprinus on the heart?

Linkathon

Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I’ve been remiss in reviewing the paper myself, but they’ve created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. corn smut

The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut.

Chris and Tom took some more Coprinus pictures while I was away from the lab.

Little Coprinus mushroom pictures

Coprinus cinereus (renamed Coprinopsis cinerea) growing in the lab. The genome was sequenced, assembled into chromosomes, and annotated and we are working on the final analysis of it to describe some of the interesting biology about this little Coprophilic fungus. I’m excited to put up a few of my pictures of the tiny mushrooms growing in the lab (although others have better ones). A few more days and I might have better shots.

Coprinus cinereus Coprinus

Coprinus

Update: Chris Ellison in the Taylor Lab sent this post from Cornell Mushroom Blog which has a video of Coprinus comatus (shaggy mane) fungi deliquescing.

Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

Continue reading Fungal Genetics 2007 details