Tuesday March 30


Plenary Session I


Fungal Diversity and Evolution



Macroevolution as a unifying framework for integrative studies of fungal symbiotic systems

François Lutzoni

Duke University, Department of Biology, Durham, NC, USA 27708.



Major advancements in the study of symbiotic systems ranging from parasitism to mutualism are more likely to be attained through a coordinated multidisciplinary approach, involving the interplay of theoretical and empirical research including a reciprocal illumination process between cell and molecular biology and organismal biology. A synthesis of the results from evolutionary, genetic/genomic, and ecological studies centered on lichen symbiosis and endophytic systems will be presented as examples. Phylogenetics provides a logical and primary framework for this integrative research. A phylogenetically based reconstruction of the past sheds new light on our understanding of current biological trends. The testing of hypotheses derived from this more comprehensive knowledge has a greater potential to yield major discoveries in all fields of biology. Large-scale phylogenetic studies are essential to this endeavor and necessitate data management pipelines with adequate bioinformatic tools.




Genome insights into early fungal evolution and global population diversity of the amphibian pathogen Batrachochytrium dendroabatidis

Christina Cuomo1, Sharadha Sakthikumar1, Jason Stajich2, Nick Inglis3, Bernard Henrissat4, James Galagan1, Manfred Grabherr1, Robert Lintner1, Matthew Pearson1, Chinnappa Kodira1, Antonis Rokas5, Alan Kuo6, Jeremy Schmutz6,  Chad Nusbaum1, Michel Leroux3, Joyce Longcore7, Igor Grigoriev6, Timothy James8, and Bruce Birren1


1Broad Institute of MIT and Harvard, Cambridge, MA  2Univ. of California Riverside, Riverside, CA 3Simon Fraser University, Burnaby, BC, CANADA 4CNRS, Universités Aix-Marseille I & II, Marseille, FRANCE, 5Vanderbilt Univ., Nashville, TN 6Joint Genome Institute, Walnut Creek, CA   7University of Maine, Orono, ME 8University of Michigan, Ann Arbor, MI



Batrachochytrium dendrobatidis (Bd) is a fungal pathogen of amphibians implicated as a primary causative agent of amphibian declines.  The genome sequence of Bd was the first representative of the early diverging group of aquatic fungi known as chytrids. We have sequenced and assembled the genomes of two diploids strains: JEL423, isolated from a sick Phylomedusa lemur frog from Panama and JAM81, an isolate from Sierra Nevada, CA.  By identifying polymorphisms between these two assemblies with survey sequence from additional global isolates, we have characterized the genome-wide pattern of variation, and used conservation patterns to model the recent evolution of Bd strains.  By comparing the predicted proteins of Bd to that of other fungi and eukaryotes, we identified gene families expanded in Bd, some with potential roles in pathogenesis. The recent sequence of two additional chytrid genomes allows more specific characterization of such gene families within chytrids, and better delineation of expansions in the lineage leading to Bd. We have also characterized a set of genes conserved only with non-fungal eukaryotes, some of which play a role in flagella and centrosome structure in those species.  Comparative analysis with the additional chytrid genomes will strengthen this basal vantage point for genomic comparisons across the fungi as well as with the sister animal clade and other eukaryotes.


Effector diversity and gene innovations in Phytophthora

Francine Govers

Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands



Phytophthora literally means plant destroyer, a name coined by the founding father of mycology, Anton de Bary, when he proved that a microorganism was the causal agent of the devastating potato late blight disease. The genus Phytophthora belongs to the oomycetes, a distinct lineage of fungus-like eukaryotes within the supergroup Chromalveolates and related to brown algae and diatoms. The ~ 240 Mb genome of Phytophthora infestans is the largest and most complex in the chromealveolate lineage and its sequence reveals features that illuminate its success as a pathogen. Comparison to other Phytophthora genomes showed rapid turnover and massive expansion of specific families encoding effector proteins, including the host-translocated effectors sharing an RXLR motif. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome and may attribute to the rapid and successful adaptability of this pathogen to host plants. Other hallmarks reminiscent of a dynamic genome are copy number variations and gene innovations, the latter resulting in proteins with oomycete-specific domain combinations several of which probably have a function in signal transduction.





What have we learnt about pathogenicity from sequencing the Heterobasidion genome?

Jan Stenlid

Swedish University of Agricultural Sciences


Annosum root rot is one of the most devastating diseases in conifer forests. It is caused by the necrotrophic basidiomycete Heterobasidion annosum s.l. consisting of a species complex with partly overlapping geographic distributions and host ranges. Recently, the genome of H. annosum has been sequenced and annotated. We have found several key traits such as signaling pathways and transcription factors associated with pathogenicity in other pathogens also to be present in the H. annosum genome. The analysis of the gene content also showed presence of the basic gene sets necessary for wood decomposition. We have constructed a genetic linkage map, recently transferred to the physical gene map, and identified several QTLs that are associated with e.g. pathogenicity, wood decomposition, growth rate and fungal interactions, these also give candidate genes for host interactions. Interestingly, the density of evolutionary young transposable elements is high within the QTLs for pathogenicity. Transcriptome analysis resulted in gene sets that are significantly associated with growth as a pathogen, indicating that coping with oxidative stress, producing secondary metabolites, degrading wood components and detoxifying host defense reactions are part of the arsenal activated in contact with living host tissue. A subset of these genes is located within the QTLs for pathogenicity. Studies are on the way to silence or knock out candidate genes in the fungus to verify the importance of several of the indicated candidate genes.  We have also conducted a resequencing of a population of 24 isolates of H. annosum. This allows us to study population genomics in terms of size of linkage disequilibrium, signs of selection etc. and from there infer recent selective events. Gene models found in these genome areas are plausible target candidates for active selection.




Genomic encyclopedia of fungi: bioenergy prospective

Igor Grigoriev

DOE Joint Genome Institute


Already sequenced fungal genomes are biased towards organisms of medical importance and mostly represent a single phylum. At the same time, fungi are very important in many other areas of life including bienergy. Better understanding pathogens and symbionts is critical for a sustainable growth of feedstock plants. Fungi are most efficient organisms in degrading biopolimers such as lignocellulose. Since future biorefineries will rely on fungi that efficiently secrete cellulolitic enzymes and ferment sugars, discovery of new metabolic processes and enzymes is essential and depends on sequencing a broader spectrum of fungal genomes.

The Genomic Encyclopedia of Fungi project is aimed at sampling phylogenetic breadth and ecological diversity of fungi. Developing systematic approaches to sequencing and analysis of well designed groups of organisms rather than individual genomes should help to decode fungal inventions related to plant pathogenicity, symbiosis, cellulose degradation and fermentation as well as improve our understanding of fungal diversity and established industrial organisms.





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