After the BWF Fungal DB meeting

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!

Preparing for meeting on Fungal Genome databases

Washington monument at nightNext 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.

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.

Origins and evolution of pathogens 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

In bookstores now

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.