Tag Archives: mushroom

Postdoc: Agaricus bisporus genomics and transcriptomics

Applications are invited for a bioinformatics postdoctoral position in
the research group of David Fitzpatrick (Department of Biology, Maynooth University, Ireland). My group is interested in genomics,
transcripomics, proteomics and molecular evolution of fungal species.
The project start date is the 1st of February 2015 and sets out to
investigate the genome of Agaricus bisporus.

Agaricus bisporus strain A15 is the most widely cultivated white
mushroom strain in Europe. Currently there are significant financial and time costs associated with ensuring A15 inoculum is genetically
identical to parent culture. This project sets out to undertake an
extensive genetic analysis of A. bisporus A15, via genomic and
transcriptomic sequence analysis. Ideally this genetic characterisation will act as the starting point for development of a molecular diagnostic test to determine if new inoculum is genetically identically to parent culture. We also aim to produce a high quality map for the genome of A. bisporus A15. This will be invaluable for future breeding of new A. bisporus strains.

The position will last for 18 months, with the possibility of extension.
I am looking for somebody who has experience in genome/transcriptomic assembly and experience in handling large datasets. The successful candidate will have published in peer reviewed literature and have their PhD awarded by the start of the project.

Send a CV and covering letter to david.fitzpatrick@nuim.ie with the
subject line “post-doc position on Agaricus bisporus ”


Dr. David Fitzpatrick
Genome Evolution Laboratory
Department of Biology
Maynooth University
Maynooth
Co. Kildare
Ireland.

E: david.fitzpatrick@nuim.ie
T: +353-1-7086844
F: +353-1-7083845
M: +353-860681715
W: https://www.maynoothuniversity.ie/people/david-fitzpatrick
W: http://bioinf.nuim.ie/

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

 

Love, Sex and Mushrooms: Adventures of a Woman in Science

[Reposted from FGSC news]

Cardy Raper, University of Vermont Professor Emerita, Microbiology and Molecular Genetics, has just published a memoir titled “Love, Sex and Mushrooms: Adventures of a Woman in Science” (ISBN 978-0-615-43440-7). As Peter R. Day, coauthor of “Plant-Fungal Pathogen Interaction” remarked: “Books about sex in fungi rarely reward the casual interest of the general reader generated by ‘sex’ in their titles….Cardy Raper’s autobiography is a refreshing exception….What makes it so readable and engrossing is her frank account of her circumstances both in and out of the laboratory. This book will encourage aspiring students, men as well as women, in how to overcome difficulties.” And Lorna Casselton, FRS, commented: “Cardy Raper succeeded in being what she dreamed of as a young girl, a successful scientist with her own laboratory. But it was not a conventional path to success….This is the personal story of an exceptional woman scientist.”

Copies of the book will be available at this year’s Fungal Genetics Conference at Asilomar, in March. 

 

Genome sequence of mushroom Schizophyllum commune

Schizophyllum CommuneI 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

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)

Underwater mushrooms?

ResearchBlogging.org 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

a mushroom and a microsporidia walk into a bar

These papers got lost in my drafts of things to write about.  Grants and overdue manuscripts are keeping me away from the blog.

  • Published work from Gary Foster’s lab in Applied Env Micro show progress on genetic engineering tools to express introduced genes in the basidiomycete mushroom system Clitopilus passeckerianus. C. passeckarianus produces an antibiotic, pleuromutilin, an important antibiotic. Cover photo [Press] They also showed the  5′ intron is important for efficient expression, something that has been shown several times in fungi and provides more evidence for the role of introns in promoting or regulating an aspect of gene expression or translation. Perhaps by splicing-dependent export.
  • Corradi et al – the genome of the microsporidia parasite of Daphnia (water flea). It’s as big as a fungal genome at 24Mb (S.cerevisiae is about 12Mb, Neurospora crassa about 40Mb) but only has about 2,100 genes (S.cerevisiae has ~6,000, N.crassa ~ 10,000). DOI: 10.1186/gb-2009-10-10-r106

Please be sure of your mushroom’s identity before eating

Amanita PhalloidesSFChronicle has an article on musroom poisining from Amanita phalloides over this holiday season. They come in a variety of colors during their development depending on moisture and their surroundings. These are definitely beautiful and attractive mushrooms, but they are not to be eaten! Please be sure of what you are have found before eating. Waiting for that spore print is worth it when in doubt (at all!).  Get a copy of a good book especially if you are collecting in a new environment.

Also see Richard Eshelman’s survial from a mushroom poisoning experience.