I’m at the JGI user meeting, which is starting with a Basidiomycete genomics workshop/jamboree, later a meeting of JGI fungal genome advisory board, and the main show: the User Meeting. Looking forward to catching up with scientists from a wide variety of projects and some twitter/blogger types and twittering about it @#JGIUM.
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!
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.
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
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
Announced today at the 10th Frontiers in Fungal Biology meeting in Ensenada, Baja California: In honor of his contributions to research in cell biology fungi, in particular the growth of hyphae in fungi, critical work supporting the characterization of the Spitzenkörper, development numerous approaches for microscopic and biochemical characterization of fungal cell walls, and uncovering molecular mechanisms for growth and morphogenesis in filamentous fungi, a named award will be established for Salomón Bartnicki-García, Director in the Department of Microbiology at CICESE and Professor Emertius at UC Riverside. He has been honored in the past upon his retirement from UCR in a special issue in Fungal Genetics and Biology and by the Mycological Society of America as a Distinguished Mycologist. He truly defined a field in fungal biology and is well deserving of a named award at MSA. It is fitting that the announcement was made during a meeting he co-organized in Ensenada and also on the 50th anniversary of his 1st publication (BARTNICKI-GARCIA S AND W. J. NICKERSON. The yeast-like form of Mucor rouxii. 1959; Abst. IX Intern. Botan. Congr. (Montreal), v. 2, p. 22.).
There is an ongoing collection for donations to found this award both in direct monetary gifts and through the sale of some fantastic calendars designs and T-shirts. I am not sure if the T-shirts and calendars will be available online at all, but I expect additional fund raising through MSA auction and other events will work to raise the necessary capital to endow this award. Contact Terry Hill and Meritxell Riquelme for more information or to make a contribution.
[This was postponed due to Eyjafjallajökull – see a recent post about the 2011 conference]
New and Emerging Fungal Diseases of Animals and Plants : evolutionary aspects in the context of global changes
April 17, 2010
The CNRS and Conferences Jaques Monod are hosting a 4-day meeting at the French Marine Biology research station in Roscoff, Brittany on the evolution and dynamics of emerging fungal pathogens. This meeting will focus on the widening impacts that fungi are having on human, plant and animal health by considering the factors that drive their emergence within an evolutionary context. Specifically, the meeting will consider whether environmental change is facilitating fungal range expansions and genotypes, and to what extent this is predictable. The meeting will bring together leading evolutionary biologists, theoreticians and fungal biologists/ecologists in a beautiful setting to consider these questions and to formulate new research strategies.
For those of you with cameras at Fungal Genetics this year, I’ve started a Flickr pool to archive and shared pictures. Feel free to join in and post pictures you’d like to share from the current or past Asilomar or European Fungal Genetics meetings.
The abstract book is posted for Fungal Genetics 2009 with a whopping 319 pages to read on your flight/drive/bike ride to the Asilomar conference center in Pacific Grove, CA this week.
See you there!
The scientific program is up on the FGSC website. Plan out your dash between sessions, or where you will get that coffee break meeting. This will be the largest attended fungal genetics meeting yet so will be fun to see so many people enthusiastic about the field. Look forward to seeing some of the blog readers and encouraging some guest post contributions in the future as well.