Category Archives: news

Gerry Fink wins Gruber Genetics prize

Congrats are in order to Gerry Fink on winning the 2010 Gruber Foundation award for his work on the genetics of yeast and Arabidopsis. He has been a pioneer in the field developing molecular biology approaches and leading the field in study of genetics.  See the press release announcement for more details on the award – I got word of this thanks to the Genetics Society of America email.

Gerry’s had profound impact on the field of genetics and biology it is wonderful to see this awarded to him. Personally, he’s subtly influenced several things that have benefited my career : helping get the fungal genome initiative started, as the mentor of my grad advisor, serving on advisory boards like the one for my postdoc fellowship, and his leadership and ingenuity producing new tools and approaches to understanding genetics and fungal biology.  Well deserved award and it is great to see recognition of a stellar geneticist.

Busy, but here are some links

Dear Hyphal Tip reader-

I’m having a hard time making enough to blog about interesting papers at length, but to spell you I am putting up twitter msgs about papers that have interesting abstracts and are worth a followup look.  You’ll see these in the boringly titled “Weekly Twitter Updates” on Monday morning with a round up links from the week’s twitterings by @fungalgenomes.  If you are like me, sometimes just a survey of some interesting titles is enough to introduce a new paper that might be worth reading but you don’t have time to read a whole long post about a paper anyways.  Hopefully there will be some more time this summer to catch up on papers that could be blogged about.  I also plan on reorganizing some more of the links to accessible genome data and database resource to make it easier to mine and download this information.  With so many projects that are no longer specifically funded or directed by sequencing centers since every lab can pretty much do a fungal genome now, it is hard for the list to realistically expect to keep it  up to date without other contributors to it.

I’m also open and interested in other people with mycological interests providing short blogged reviews on papers or fungal genome database resources, but I understand the pull between spending time writing things that “count” (ie published, peer reviewed papers & reviews), getting work done, and blogging.

Other things here are afoot with work developing databases for fungal genome data, a bunch of new data loads for gbrowse tools that is competing with my time teaching and the work to get initial lab projects running that are takes up lots of time.  I co-submitted a couple of CSP proposals and tried to support other fungal groups’ proposals with some letters.  In the meantime I’ll keep blogging about what comes across my plate and hope to see you at a conference this summer or online.

CSP: Letter of support time!

Several groups working on Fungi are submitting proposals to the JGI Community Sequencing Program.  Several proposals relating to the JGI’s interest in an encyclopedia of fungal genomes sequencing genomes of ascomycete and basidiomycete yeasts, filamentous ascomycetes, basidiomycetes,  and early diverging fungi are being put forward.  If you haven’t been contacted by these community members but would like to write a letter of support in these areas, please get in touch as the deadline for the proposals in early next week. There are also other proposals going in for Neurospora mutant strain resequencing, more Fusarium species, transcriptomes of mycorrhizal fungi, and other topics.  If you are are a user of data from any of the previous fungal projects that you know how important these resources are in both comparative genomics and molecular biology work, so support to get additional sequences generated will benefit many in the community.

I don’t know if it is appropriate for me to post the text of the solicitation for letters here, differing to the privacy of the groups submitting proposals, but if you want to help out the community by writing a letter showing that you would benefit from these resources, I can try to put you in touch.

Tragic loss of Gopi Podila

I was so sad to learn of the death of Prof Gopi Podila at the shooting at University of Alabama in Huntsville.  I had only met him once at a MSA meeting but he was extremely respected scientist for his work on ectomycorrhizal fungi, plant-microbial interactions, and functional genomics to study plant stress.

My thoughts go out to the families of Dr Podila, Dr Maria Ragland Davis, and Adriel Johnson on this horrible and tragic loss.

Server moved

Migration

I’ve migrated some of the services from UCB to UCR so the blog and wiki server as well as Gbrowse V1 services have migrated to UCR machine.  The Gbrowse2 installation and migration of under-development services are still in progress but will hopefully be done in next two weeks.

This setup is more flexible and I’ll blog about geeky server details later, perhaps in a different forum. In the future we should be able to support additional project data in a simplified format.

I hope after this and a few more setup issues we can resume development of new tools and services for these data.

For your reading pleasure

Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news.  Here’s a short list of links and papers that are worth a look though.

  • “Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature)
  • NYT Science article sort of summarizing the good, bad, and ugly of fungi and human interactions
  • Attempts to save amphibians from chytridiomycosis “Riders of a Modern-Day Ark” (PLoS Biology)
  • Looks like Scott Baker with the JGI are in the process of resequencing several classical mutant strains of Phycomyces, Neurospora and Cochliobolus, Cryphonectria for sequence-based mapping of mutants (i.e. here and here and here).

Brown rotting fungal genome published

ResearchBlogging.orgPostia placenta genome is now published in early edition of PNAS.   Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters break down cellulose but cannot break down lignin or lignocellulose while white rotters (like the previously sequenced Phanerochaete chrysosporium) are able to break down the lignin.  This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author – go Diego!). It is also helpful to contrast the white and brown rotters to understand how their enzyme capabilities have changed and how these different lifestyles evolved.  There had been some issues with the initial assembly of this genome which is basically twice as big as one would expect because the dikaryon genome was sequenced – this is where two nuclei with different genomes are present as the result of fusion between two parents of opposite mating types.  When genome sequenced is performed it is hard to assemble these into a single assembly since there are really two haplotypes present.  So these haplotypes have to be sorted out to obtain the gene ‘count’ for the organism for those who like simple numbers. This is a similar situation to the Candida albicans genome, although those haplotypes are much more similar.  The main problem is that one has to generate twice as much sequence to get the same coverage of each haplotype without playing some tricks to collapse them into a consensus and them afterwards separate the haplotypes back out.  At any rate, this sequenced provided a good summary of the gene content and thus metabolic and enzymatic capabilities to match up functional data collected from LC/MS and transcriptional profiling. 

There are several other rotting fungi that are nearly done at JGI (but the task of writing and coordinating the analyses for the papers are ongoing!) include Schizophyllum commune and Pleurotus ostreatus. There are also several more mycorrhizal and plant pathogenic basidiomycete fungi as well as some classic model systems that have finished genomes and are in the process of finalizing papers.  It is an exciting time that is just beginning as these genome and transcriptional data are integrated and compared for their different ecological, morphological, and metabolic capabilities.

The article is unfortunately not Open Access so I haven’t even read it from home yet, but pass along this news to you, dear reader. Will get a chance to read through more than the abstract to see what glistening gems have been extracted from this genomic endeavor.
D. Martinez, J. Challacombe, I. Morgenstern, D. Hibbett, M. Schmoll, C. P. Kubicek, P. Ferreira, F. J. Ruiz-Duenas, A. T. Martinez, P. Kersten, K. E. Hammel, A. V. Wymelenberg, J. Gaskell, E. Lindquist, G. Sabat, S. S. BonDurant, L. F. Larrondo, P. Canessa, R. Vicuna, J. Yadav, H. Doddapaneni, V. Subramanian, A. G. Pisabarro, J. L. Lavin, J. A. Oguiza, E. Master, B. Henrissat, P. M. Coutinho, P. Harris, J. K. Magnuson, S. E. Baker, K. Bruno, W. Kenealy, P. J. Hoegger, U. Kues, P. Ramaiya, S. Lucas, A. Salamov, H. Shapiro, H. Tu, C. L. Chee, M. Misra, G. Xie, S. Teter, D. Yaver, T. James, M. Mokrejs, M. Pospisek, I. V. Grigoriev, T. Brettin, D. Rokhsar, R. Berka, D. Cullen (2009). Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0809575106

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.

Eigenfactors of mycology journals

Eigenfactor.org computes journal’s influence (akin to Impact Factor).  Here’s a plot of the influence and number of articles in journals classified as “Mycology”.  It shows bubbles representing eigenfactor and the lines are the representation of change over time – the animation is much more informative so click over to see it play out. Unfortunately a few mycology journals like Fungal Genetics and Biology/Experimental Mycology aren’t included.

Mycology Journals influence over time From http://eigenfactor.org
Mycology Journals influence over time. From http://eigenfactor.org