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By Jason Stajich, on March 17th, 2010
By Jason Stajich, on February 25th, 2010
We had an impressive marshaling of fungal biologists, database builders, and sequencing centers to discuss what would be important for researchers, developing use cases to demonstrate what is needed by the community, and plotting some courses on how to get there. A more formal meeting report is being prepared, but I can summarize that everyone wants improvements with access, standardization, and web & data interface to interact with not only the 200 genomes we current have for Fungi & Oomycetes. but the expected 1000s in the next few years and certainly 10,000 in less than 10 years.
There will be more updates and possibility of input from the community in the form of descriptive “Use cases” to describe the types of research questions that use tools to integrate genomic data.
In summary a great meeting!
By Jason Stajich, on February 20th, 2010
 Next week a collection of international scientists with stakes in seeing fungal genome databases evolve and rise to meet the tide of genome data being produced and analyzed from fungi will be meeting in DC. I am hopeful we’ll come up with some strategies and principles that can guide how this data can be more effectively managed and provided to researchers. This includes web-based resources, tools, and simply adhering to a standardized formats for genome annotations (like GFF3), automated methods for gene ontology associations on newly annotated genomes, and integration of what I expect to be the major amount of data in the years to come: individual lab produced genomic, ChIP, resequencing, and RNA-sequencing results. This means the integration (and sharing) of individual labs produced genomic data with the public data will be key along with cross-species comparisons of this information. Tools like Ensembl and UCSC-browser provide great portals for animal data and some plant data with a few fungi sprinkled in as outgroups. (Okay UCSC does have some data for close relatives to Saccharomyces data in their “other clade” that provides data from the Phastcons paper and Ensembl is now serving up a few Fungi). Tools like Phytozome are attempting to integrate some of the plant genomic data in one place as well. However the resources for fungal researchers with a wide collection of highly detailed manually curated genomes to shotgun sequenced and automated annotation are available and the tools to search, compare, and integrate are still insufficient for what is needed by the community.
I expect will also be discussing how databases that incorporate the data from all the genomes can have some centralized aspects so comparative analyses are possible, and importantly, how can these types of resources be sustainably funded by public and private money.
Fungi are important in a wide variety of human and ecosystem processes, from pathogens of agriculture crops to human disease causing to symbiotic relationships with plants to industrial agents in food, chemical, and biofuel production. The study of them needs modern tools including genomic resources for molecular studies of these species. The current tools and data are quite useful and important in our current research but with the increasing amount of new sequence and phenotype data, and a need to effectively connect data from different experimental, model, and pathogen study systems needs to be much improved.
I hope to provide some updates on what are some of the ideas of what we discuss about “Pan-fungal” genome resources and will be interested in helping engage a wider audience on how tools and resources should be built to meet our needs as researchers.
By Jason Stajich, on February 13th, 2010
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.
By Jason Stajich, on February 8th, 2010
 An article in PLoS Pathogens by Morris et al describe a hypothesis about the evolution and origins of plant pathogens applying the parallel theories to the emergence of medically relevant pathogens. The authors highlight the importance of understanding the evolution of organisms in the context of emerging pathogens like Puccinia Ug99 for our ability to design strategies to protect human health and food supplies. Both bacterial and fungal pathogens of plants are discussed but I (perhaps unsurprisingly) focus on the fungi here. Continue reading Origins and evolution of pathogens
By Jason Stajich, on February 4th, 2010
 I am excited to dig into the newly published Cellular and Molecular Biology of Filamentous Fungi edited by my next door neighbor Katherine Borkovich and Daniel Ebbole from Texas A&M which was recently published by ASM Press. The book is a comprehensive look at biology of filamentous fungi including ascomycetes and basidiomycetes and covers cellular biology and structure, metabolism, growth, organelles, photobiology, sexual and asexual development, and mutualistic and pathogenic interactions with plants & animals. I’ve yet to get my own yet but I’ve leafed through a copy and this looks to be an excellent reference for those wanting a review of current knowledge on many aspects of fungal biology and I anticipate important reading for new students and postdocs in the field.
By Jason Stajich, on January 28th, 2010
Registration for the 9th International Mycological Congress, held 1-6 of August, is now open. This looks to be an exciting, dynamic, and broad conference on fungal biology covering a great breadth of topics. These include: intricate look at fungal cell biology using microscopy, genetic and molecular biology tools; Evolution of fungi through systematics and comparative biology and new aspects of taxonomy; genetics and genomics of fungi; Studies of plant and animal pathogens. The meeting is only held every 5 years so I hope you can advantage of it! This year it will be held in Edinburgh, Scotland, UK. The early registration is 5 February and you have until 9 April to submit abstracts.
Hope to see you there
By Jason Stajich, on January 25th, 2010
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
By Jason Stajich, on January 22nd, 2010
Don’t forget to register for Neurospora 2010 held at the beautiful Asilomar Conference center in Pacific Grove, CA held April 8-11, 2010. Get your filamentous fungi fix here!
Also save the date for some other important upcoming conferences you may consider attending
- American Society of Microbiology, Candida and Dimorphic Fungi Meeting, March 22-26, Miami, FL, USA
- Joint Genome Institute, 2010 User Meeting, March 24-26, Walnut Creek, CA, USA
- New and emerging fungal diseases of animals and plants, April 17-21, Roscoff Biological Station (near Brest), Brittany, FRANCE
- American Society of Microbiology, 110th Annual Meeting, May 23-27, San Diego, CA, USA
- Cellular and Molecular Fungal Biology Gordon Conference, June 13-18, Holderness, NH, USA
- Mycological Society of America meeting, June 28-July 1, Lexington, KY, USA
- 9th International Mycological Congress, August 1-6, Edinburgh, Scotland, UK
Other evolutionary and genomics meetings
- Biology of Genomes, May 11-15, Cold Spring Harbor, NY, USA
- Evolution Meetings, June 25-29, Portland, OR, USA
- Society of Molecular Biology and Evolution, July 4-8, Lyon, FRANCE
- International Society of Computational Biology, ISMB2010, July (9-10) 11-13, Boston, MA, USA
By Jason Stajich, on January 12th, 2010
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
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