Program Book - 27th Fungal Genetics Conference

CONCURRENT SESSION ABSTRACTSpractical implications. While ecologists have long recognized the importance of scale on ecological processes, fungal communities have primarily beenstudied at small-scales, focusing on deterministic processes. To rectify this knowledge gap we are using next generation sequencing techniques to surveysoil fungi in North American pine forests with a sampling design that allows us to examine community structure from roots-to-biomes. Our results showthat soil fungal communities in these ecosystems are highly diverse and are structured primarily by large-scale, macroecological processes, rather thansmall-scale deterministic processes. Our results also show that there is high functional redundancy in soil fungal communities. This work demonstratesthat increasing the scale of observation is critical to a complete understanding of the ecological dynamics of soil fungi and the ecosystem processes theymediate.Genomic analysis of Mortierella elongata and its endosymbiotic bacterium. Gregory Bonito 1 , Andrii Gryganskyi 1 , Christopher Schadt 2 , Dale Pelletier 2 , AmySchaefer 3 , Gerald Tuskan 2 , Jessy Labbé 2 , Sofia Robb 4 , Rebecca Ortega 1 , Francis Martin 5 , Mitchel Doktycz 2 , Kurt LaButti 6 , Matt Nolan 6 , Robin Ohm 6 , IgorGrigoriev 6 , Rytas Vilgalys 1 . 1) Duke University, Durham NC; 2) Oak Ridge National Laboratory, Oak Ridge TN; 3) University of Washington, Seattle WA; 4)University of California, Riverside CA; 5) Institut National de la Recherche Agronomique, Nancy France; 6) Joint Genome Institute, Walnut Creek CA.Mortierella belong to a group of basal fungi (Mortierellomycotina) common to soils and the rhizosphere and endosphere of many plant species.Mortierella species are known for rapid growth and abundant lipid production. Mortierella elongata is one species commonly isolated from forest soils andhealthy plant roots where it grows asymptomatically as an endosymbiont. Mortierella elongata is a heterothallic species but can also reproduce asexuallythrough chlamydospores and sporangiospores. Recent reports indicate that some isolates of M. elongata host endosymbiotic bacteria, which may betransmitted vertically via spores. However, it is still unclear whether all Mortierella species host endosymbionts or whether these are lineage-specificassociations. Given the geographically widespread distribution of Mortierella elongata and its ubiquitous presence in forest soils and plants we chose tosequence its genome through the JGI Forest Metatranscriptome CSP. We also sought to assemble the genome of the bacterial endosymbiont to addresswhether there are genomic signatures of co-adaptation or co-evolution in the genomes of Mortierella and its endosymbiotic bacterium, which may impactthe function and growth of Mortierella elongata. The 50 Mb genome of M. elongata was sequenced to 112x coverage. Of the 220,113 putative proteinsidentified in M. elongata, 109,093 appear to be unique (e.g. only ~50% have orthologs in other fungal species having sequenced genomes). The M.elongata genome appears to be enriched in genes related to tryptophan metabolism, siderophore group nonribosomal peptides, glucan 1,4-alphaglucosidases, and in lipid metabolism (e.g. sphingolipids, etherlipids, and glycerophopholids) compared to genome sequences of other basal fungi. Theendosymbiotic bacterium sequenced along with the M. elongata isolate is related to Glomeribacter (endosymbiont of Gigospora, Scutellospora, and otherGlomeromycota) within the Burkholdariales. The ~2.6 MB endosymbiont genome is larger than that of Glomeribacter but quite reduced compared to freelivingisolates of Burkholdaria. The reduced genome size of this bacterium, and the fact that it has thus far evaded pure culture isolation, supports the viewthat this is an ancient and obligate symbiosis.Integrative genomics of poplar-fungal pathogen interactions. Richard C. Hamelin. Forest Sciences, University of British Columbia, Vancouver, BC, Canada.Poplar is an important tree, both from an ecosystemic point of view as riparian species, and as a commercial agro-forestry crop for the production ofwood and paper products and increasingly as a source of bioenergy. Fungi in the Urediniales and the Dothideomycetes are responsible for the mostimportant diseases of poplars. In most tree-fungal pathogen interactions, a few founder species are key determinants of the outcome. To betterunderstand these interactions at the landscape level and predict their outcome, we are using a variety of genome-based approaches. We have appliedDNA barcoding and multigene phylogeny to poplar pathogens to assess species diversity and host specificity both from environmental and herbariumderivedsamples. We have found a high level of fidelity in host tracking of pathogens vis-à-vis their host. However, this fidelity tends to break down whenpoplar is grown in intensive plantations or when interspecific hybrids are planted. To further investigate and understand this pattern, we sequenced thegenomes of 12 poplar pathogens with different host specificity. By comparing these genomes we identified core gene sets as well as genes that are uniqueto each species and are candidate determinants of the interaction outcomes. Annotation of these genome sequences with customized pipelines allowedus to assign putative functions to the candidate genes and detect effector-like sequence profiles. RNAseq profiling of the interaction of poplar rust ondifferent hosts and their hybrids confirms the uniqueness of expression patterns in host-specific infections. In addition, we are using population genomere-sequencing approaches to detect selection patterns at the genome level. Several of the candidate genes identified in the upstream analyses encodesecreted proteins and possess a signature of positive selection. Integration of this data can be used as predictive resources to determine the outcome ofpoplar-pathogen interactions in the environment.Fungal pathogen and endophyte genetics within the context of forest community dynamics. M.-S. Benitez 1 , M. H. Hersh 2 , L. Becker 1 , R. Vilgalys 3 , J. S.Clark 1,3 . 1) Nicholas School of the Environment, Duke University, Durham, NC; 2) Department of Biology, Eastern Michigan University, Ypsilanti, MI; 3)Department of Biology, Duke University, Durham, NC.Fungal pathogens play important roles in forest community dynamics, particularly through negative-density dependent regulation. Negative-densitydependence regulation is hypothesized to be regulated by the presence of host-specific pathogens. Studies on forest pathogens, however, indicate thepredominance of generalist seedling pathogens, capable of infecting more than one host species. To understand the mechanisms through which“generalist” pathogens contribute to forest-community dynamics we conducted extensive surveys of seedling pathogens in temperate hardwood forestsof the eastern U.S.A. Species in the genera Colletotrichum and Ilyonectria were among the most commonly isolated and recovered amplicon sequencefrom seedlings of multiple host species showing disease symptoms. Further, co-infection by both Colletotrichum and Ilyonectria species decreases hostsurvival, as quantified by posterior model probabilities. To investigate molecular mechanisms associated with multi-host generalism and co-infection, andto determine whether these “generalist” pathogens are distinct species or species-complexes, the genomes of three common species in our dataset (e.g.C. fioriniae, C. gloesporoides and Ilyonectria europea) were sequenced. The largest genome of the three belonged to Ilyonectria at 63.66 Mb, which alsocontained the highest number (22,250) of genes. The smallest genome belonged to C. fioriniae with 50.04 Mb and 15,777 genes. Genome size and numberof predicted genes appears expanded, confirming their role as seedling pathogens. For instance, three out of four polysaccharide lyase (PL) enzymedomains found in fungal genomes, are enriched in these three species. PL enzymes are relevant in plant pathogenicity since they may contribute to initialstages of host penetration. The genome sequence of these fungal groups will serve as a reference set for population level studies to address hostspecificityand local adaptation within our isolate database.96