Program Book - 27th Fungal Genetics Conference

FULL POSTER SESSION ABSTRACTSinner membrane complexes I, III, IV and V are identified. Additional protein-coding ORFs (sum 39) are predicted including a gene for ribosomal protein(rps3), a viral RNA-directed DNA polymerase (reverse transcriptase), and a gene for bacterial-originated DNA-directed DNA polymerase II of family B(dpoB). Total of 57 intron-homing endonucleases with core LAGLIDADGD and GYI-YIG domains were recognized in over 30 group I and II type introns, up to3.4 kb in length, in ten of the fifteen conserved genes (cox1,2,3; cob; nad1,2,4,4L,5; rnl). Multigene phylogeny of the conserved proteins confirms currentfungal taxonomy and a common, single origin of the mtDNA within Basidiomycota. Conclusions. The exceptionally large mt genome is explained by longintergenic stretches of DNA carrying repetitive and partially overlapping sequence elements, presence of additional open reading frames with unknownfunction, existence of the 6.1 kb duplication-inversion, and due to frequent intron splicing of the coding sequences. A few of the qualities indicate plasmidor viral origin, such as the dpoB, and the cob gene-interrupting long group II intron with reverse-transcriptase ORF. These features together with theduplicated inversion and dense repeat stretches, and the long introns with intron-associated homing endonucleases are indications of genetic flexibility,not previously recognized to such extent in fungal mitochondrial genomes. Thus, it may be concluded that DNA recombination as well as regulation ofgene transcription are allowed and on-going events in the P. radiata mt genome.290. De Novo Assembly of Fungal Genomes and Detection of Structural Variation using Extremely Long Single-Molecule Imaging. Nicholas R. Rhind 1 ,Alex Hastie 2 , Ernest Lam 2 , Andy Nguyen 2 , Han Cao 2 . 1) Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, WorcesterMA; 2) BioNano Genomics, San Diego CA.De novo genome assemblies using only short read data are generally incomplete and highly fragmented due to the intractable complexity found in mostgenomes. This complexity, consisting mainly of large duplications and repetitive regions, hinders sequence assembly and subsequent comparativeanalyses. We have overcome these problems in four fungal genomes by assembling whole genome shotgun (WGS) contigs with a high resolution longrange physical-mapping strategy. We used a single molecule genome analysis system (Irys) based on NanoChannel Array technology that linearizesextremely long DNA molecules for observation. This high-throughput platform automates the imaging of single molecules of genomic DNA hundreds ofkilobases in size to measure sufficient sequence uniqueness for unambiguous assembly of complex genomes. High-resolution genome maps assembled denovo from the extremely long single molecules retain the original context and architecture of the genome, making them extremely useful for structuralvariation and assembly applications.We have built full genome assemblies of the four fission yeast genomes: Schizosaccharomyces pombe, S. japonicus, S. octosporus and S. cryophilus. The S.pombe assembly is similar to the published finished S. pombe genome, but reveals several complicated genomic features that were mis-assembled by aclone-based approached. In addition, we have resolved centromeric and telomeric repeats that had not been assembled by traditional approaches. The S.japonicus and S. octosporus assemblies identify a number of mis-assemblies in the published WGS genomes. The S. cryophilus genome is the first genomescaleassembly of what was a draft assembly of WGS contigs.Our strategy combining genome map-based scaffolding with deep sequencing offers an integrated pipeline for whole genome de novo assembly solvingmany of the ambiguities inherent when using sequencing alone. Additionally, genome maps serve as a much-needed orthogonal validation method toWGS assemblies. As a result, genome maps improve contiguity and accuracy of whole genome assemblies, permitting a more comprehensive analysis offunctional genome biology and structural variation.291. Discovering host specificity candidate genes of Sporisorium reilianum by genotyping mixed-variety offspring. T. Wollenberg 1,2 , J. Donner 2 , J.Schirawski 1,2 . 1) Microbial Genetics, RWTH Aachen University, Aachen, Germany; 2) Molecular Biology of Plant-Microbe Interaction, Georg-August-University Göttingen, Göttingen, Germany.The biotrophic plant pathogenic basidiomycete Sporisorium reilianum exists in two host-specific varieties, S. reilianum f. sp. zeae (SRZ) and S. reilianum f.sp. reilianum (SRS). SRS causes head smut of sorghum and leads to weak symptoms on maize, such as phyllody in the inflorescences. SRZ causes head smutof maize and leads to the formation of red phytoalexin-containing spots on inoculated sorghum leaves. Plant infection results after pairwise mating ofcompatible haploid cells that fuse to form an infective dikaryotic filament. The fungus persists in the host plant until flowering time, and in theinflorescences develops into diploid spores that germinate by meiotic division to haploid cells. Haploid cells of the two varieties are mating competent andare able to infect both maize and sorghum with a very low infection rate. To identify the genetic basis for the difference in host specificity, we analyzedvirulent and non-virulent segregants of a mixed-variety (SRZ x SRS) infection both phenotypically and genotypically by a PCR-based approach. Weidentified twelve chromosomal regions that were associated to the phenotypic behavior of the strains. This shows that host adaptation is a multi-genictrait. To identify associated genes we genotypically analyze a larger set of strains by genome-wide SNP comparison after Illumina re-sequencing. Genomecomparison of mixed-variety offspring is a powerful tool to discover candidate genes involved in host specificity.292. Comparing comparative “omics” in Coccidioides spp. Emily A. Whiston, John W. Taylor. Plant & Microbial Biology, U.C. Berkeley, Berkeley, CA.The mammalian pathogens Coccidioides immitis and C. posadasii are the only dimorphic fungal pathogens that form spherules in the host. Furthermore,all of Coccidioides’ closest known relatives are non-pathogenic. In this project, we are interested in genome changes between the Coccidioides lineage andits relatives, and how these changes compare to recently published comparative and population genomics, and transcriptomics studies in Coccidioides.Coccidioides and its closest sequenced relative, Uncinocarpus reesii, are estimated to have diverged 75-80 million years ago. Here, we have sequenced thegenomes of four species more closely related to Coccidioides than U. reesii: Byssoonygena ceratinophila, Chrysosporium queenslandicum, Amauroascusniger and A. mutatus. For each of these four species, we prepared genomic DNA Illumina sequencing libraries; the resulting genome assemblies rangedfrom 23-34Mb, with N50 of 90kb-205kb. Predicted genes were confirmed by RNAseq; the total number of genes ranged from 8,179-9,184. We assessedindividual gene gain/loss, and gene family expansion/contraction in Coccioides using these new genomes and other recently published genomes from theOnygenales order, including the yeast-forming dimorphic pathogens Histoplasma and Paracoccidioides, and the dermatophytes Microsporum andTrichopyton. We have compared these results to genes identified in recently published Coccidioides “omics” studies that show evidence of positiveselection, introgression and/or differential expression.293. The transcriptional response during cell-fusion incompatibility in Podospora anserina. Frédérique Bidart, Sven J. Saupe, Corinne Clavé. IBGC, CNRS,Bordeaux, France.Heterokaryon incompatibility is a form of non-self recognition common in filamentous fungi that occurs when filaments of different isolates of the samespecies fuse. Compatibility is controlled by so-called het loci and fusion of strains of unlike het genotype triggers a complex incompatibility reaction thatleads to the death of the fusion cell. Herein, we analyze the transcriptional changes during the incompatibility reaction in Podospora anserina. Theincompatibility response was found to be associated with a massive transcriptional re-programming: 2248 genes were up-regulated by a factor 2 of moreduring incompatibility. In turn, 2463 genes were down-regulated. HET and NACHT domains previously found to be involved in the control of heterokaryon192