Program Book - 27th Fungal Genetics Conference

FULL POSTER SESSION ABSTRACTS335. A draft genome of the ectomycorrhizal fungus Rhizopogon vesiculosus: Characterization of mating system and heterozygosity within the dikaryon.Alija Mujic, Joseph Spatafora. Botany and Plant Pathology, Oregon State University, Corvallis, OR.Species of Rhizopogon are EM symbionts of trees in family Pinaceae and produce basidiospores within hypogeous false truffles that are dispersed bymycophagous mammals. All known members of R. subgenus Villosuli form obligate EM relationships with Pseudotsuga spp. (Douglas Fir) and are the onlymembers of the genus known to possess this host association. R. vesiculosus, along with its cryptic sister species R. vinicolor, possess a sympatricdistribution where sampled within the range of their host tree, P. menziesii. While the sporocarp and EM morphology of these fungi may be highly similar;they possess striking life history differences with R. vesiculosus producing larger vegetative genets and displaying greater population structure at bothlocal and landscape scales. We have sequenced the genome of R. vesiculosus using dikaryotic tissue and a whole genome shotgun sequencing approach onthe Illumina HiSeq platform. De novo assembly of the genome was performed using VELVET 1.19 and gene predictions were made using AUGUSTUS withLaccaria bicolor as a training model. The draft genome assembled to a total length of 46 Mb in 6700 contigs with an N50 of 26,783, a maximum contig sizeof 446,818 bp, and 12,604 predicted genes. Here we characterize the mating system of R. vesiculosus, which possesses both an A-locus encoding aheterodimer transcription factor, as well a B-locus encoding transmembrane pheromone receptors and pheromone precursor genes. We presentcomparisons of the mating system of R. vinicolor and its similarities to other members of Boletales (e.g., Serpula) and differences with Agaricales (e.g.,Laccaria). Due to the dikaryotic nature of the genome sequence produced for R. vesiculosus, single nucleotide polymorphisms (SNPs) can be observed andused to characterize allelic variation. SNPs observed in protein coding regions of both MAT loci indicate that R. vesisculosus is likely heterothallic. We havealso characterized heterozygosity across the whole genome in order to identify hypervariable regions. This genome will allow for comparative analysis ofgene content, mating type system with other Basidiomycota and, ultimately, for population/species-level genomic studies within Rhizopogon.336. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi. Robin A Ohm 1 , Nicolas Feau 2 ,Bernard Henrissat 3 , Conrad L Schoch 4 , Benjamin A Horwitz 5 , Rosie E Bradshaw 6 , Lynda Ciuffetti 7 , Richard C Hamelin 2,8 , Gert HJ Kema 9 , ChristopherLawrence 10 , James A Scott 11 , Joseph W Spatafora 7 , B. Gillian Turgeon 12 , Pierre JGM de Wit 13 , Shaobin Zhong 14 , Stephen B Goodwin 15 , Igor V Grigoriev 1 ,Other members of the Dothideomycetes community. 1) United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, UnitedStates of America; 2) Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada; 3) Architecture et Fonction desMacromolécules Biologiques, Aix-Marseille Université, CNRS, Marseille, France; 4) NIH/NLM/NCBI, Bethesda, MD, United States of America; 5) Departmentof Biology, Technion - IIT, Haifa, Israel; 6) Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand; 7) Department of Botanyand Plant Pathology, Oregon State University, Corvallis, OR, United States of America; 8) Natural Resources Canada, Ste-Foy, QC, Canada; 9) Plant ResearchInternational, Wageningen, The Netherlands; 10) Virginia Bioinformatics Institute & Department of Biological Sciences, Blacksburg, VA, United States ofAmerica; 11) Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; 12) Departmentof Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, United States of America; 13) Laboratory of Phytopathology, WageningenUniversity, Wageningen, The Netherlands; 14) Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America; 15)United States Department of Agriculture, Agricultural Research Service, Purdue University, West Lafayette, Indiana, United States of America.The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broadrange of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyzegenome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in numberof (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequentlydemarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensablechromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis,secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, theCapnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of thesegenes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. Asyntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting apossible function in response to oxidative stress.337. Domains of meiotic DNA recombination and gene conversion in Coprinopsis cinerea (Coprinus cinereus). Patricia J. Pukkila 1 , Wendy Schackwitz 2 . 1)Dept Biol, Univ North Carolina, Chapel Hill, NC, USA; 2) US DOE Joint Genome Institute, Walnut Creek, CA, USA.We have shown previously that rates of meiotic recombination are highly non-uniform along the assembled chromosomes of C. cinerea (Stajich et al.PNAS 107: 11889-11894, 2010). That study revealed an over-representation of paralogous multicopy genes in regions with elevated levels of meioticexchange. In addition, retrotransposon-related sequences were not found in large segments of the genome with low levels of meiotic exchange. However,the study was limited by the available markers, and only 31 Mb of the 36 Mb genome could be mapped. More recently, we have resequenced 45 meioticsegregants and 4 complete tetrads. We developed a simple script to detect crossover and gene conversion events involving over 75,000 SNPs spanning 35Mb. The data were analyzed using MSTmap (Wu et al. PLoS Genetics 4: e1000212, 2008). The new dataset revealed sub-telomeric recombination hotspotsat every chromosome end, and 36% of the crossovers were associated with uninterrupted tracts of gene conversion. The conversion tracts (2-8 SNPs) werequite short (8-219 nt), and the median distance between the flanking SNP markers was also small (500 nt). Since these subtelomeric hotspots correspondto sites of synaptic initiation in C. cinerea (Holm et al. Carlberg Res. Commun. 46: 305-346, 1981), these data may contribute to our understanding of howhomologous chromosome pairing and synapsis are coordinated with meiotic recombination. Supported by the U.S. Department of Energy Joint GenomeInstitute Community Sequencing Program. The work conducted by the U.S. DOE JGI is supported by the Office of Science of the U.S. Department of Energyunder Contract No. DE-AC02-05CH11231.338. FungiDB: An integrated functional genomics database for fungi. Raghuraman Ramamurthy 1 , Edward Liaw 1 , Sucheta Tripathy 7 , John Brestelli 2,3 , SufenHu 3 , Wei Li 3 , Omar Harb 3,4 , Brian Brunk 3,4 , Steve Fischer 2,3 , Deborah Pinney 2,3 , Jessica Kissinger 5,6 , Brett Tyler 8 , David Roos 3,4 , Jason Stajich 1 . 1) Plantpathology and Microbiology, University of California, Riverside, Riverside, CA; 2) Department of Genetics, University of Pennsylvania School of Medicine,Philadelphia, PA; 3) Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA; 4) Department of Biology, University of Pennsylvania,Philadelphia, PA; 5) Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA; 6) Department of Genetics and Institute ofBioinformatics, University of Georgia, Athens, GA; 7) Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA; 8) Center for Genome27th Fungal Genetics Conference | 203