Program Book - 27th Fungal Genetics Conference

FULL POSTER SESSION ABSTRACTSfound that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins from various spiecies, expansions leading intoseveral paralogs in vertebrates and plants were identified. We illustrate insertion/deletions (indels) in the conserved domain of BEM46 protein, whichallow differentiating fungal classes such as ascomycetes from basidiomycetes. Furthermore, we analyze several duplicates of this gene in different animaland plant genomes to understand possible mechanisms of evolution after separation from the fungal lineage. In addition, we unravel that BEM46 proteinfrom N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments, hinting there is need to re-define the motifs inconserved in various protein sequences as over a million of genome sequences will be available in next decade.303. Sugar ‘cubed’ - A Comparative Systems Analysis of Plant Cell Wall Polysaccharide Recognition and Degradation Using the Model FilamentousFungus Neurospora crassa. J.P. Benz, S. Bauer, N.L. Glass, C.R. Somerville. Energy Biosciences Institute, UC Berkeley, Berkeley, CA.Filamentous fungi are currently the primary source of plant cell wall degrading enzymes for the production of biofuels from lignocellulosic feedstocks.However, despite tremendous improvements of these enzyme cocktails over the last years, they are still rather inflexible and will not work optimally insituations such as complicated with a changing variety of feedstocks. Fungi have evolved with their host plants in a long and intricate relationship, and adetailed understanding of their responses to the various building blocks present in the plant cell wall material will also help to improve the industrialapplicability and versatility of these enzyme cocktails. In recent years, the ascomycete Neurospora crassa has been developed as a model system to studycellulose and xylan degradation by filamentous fungi. As a complement to these studies, here we performed a systems analysis of pectin degradation, thethird major plant cell wall polysaccharide. A combination of proteomics and transcriptomics was used to define the “toolbox” N.crassa uses to degrade thishighly complex heteropolysaccharide, and to identify new components that seem to work both synergistically and antagonistically in this process.Moreover, in combination with the data from two earlier studies, describing the responses to cellulose and xylan, the acquired knowledge allowed for thefirst time to put the individual responses to each of these three main plant cell wall polysaccharides into perspective. Central to this analysis was theconstruction of a co-expression matrix covering the most relevant carbon source-related inducing conditions. The applicability of this matrix could bedemonstrated by successfully guiding in the functional characterization of an unknown sugar transporter, which was identified to mediate L-arabinoseuptake. Only if we understand the building blocks of the carbon-related response pathways we can attempt to put them together into the “bigger picture”.The comparative approach presented here therefore is an important step towards a more profound understanding of the fungal degradation process ofcomplex biomass.304. Building upon whole genome resequencing in Neurospora. Kevin McCluskey, Aric Wiest, Robert Schnittker. Sch Biological Sci, Univ Missouri, KansasCity, Kansas City, MO.The availability of whole genome sequence allows immediate comparison between polymorphisms that have physiological impact and those that areneutral. We are exploiting this as we characterize genes responsible for Acriflavine resistance. Preliminary analysis showed that despite a wealth ofpolymorphisms among whole genome sequenced strains, the ORF NCU09975 encoding an abc3 transporter is not altered in the acriflavine resistant strainFGSC 1215. Additional analyses have pointed to the transcription factor gene NCU09974 and the polymorphism in this gene in the acriflavine resistantstrain is unique both in comparison to the reference genome strain and among the growing number of strains subject to whole sequencing. Continuingwork aims to test whether transfer of the NCU09974 allele from the acriflavine resistant strain to an otherwise sensitive strain will confer resistance.Additional studies will investigate whether the broad resistance seen in classical acriflavine resistant mutants can allow identification of a compound thatcan be used as a selectable agent in combination with the newly identified allele.305. Genome based phylogeny of early diverging fungal lineages. A. P. Gryganskyi 1 , G. Bonito 1 , M. Rodriguez-Carres 1 , T. M. Porter 2 , Y. Chen 3 , S. Robb 4 , H.-L. Liao 1 , I. M. Anishchenko 5 , O. V. Savytskyi 6 , R. Ortega 1 , J. E. Stajich 4 , J. Heitman 3 , A. P. Litvintseva 7 , T. Y. James 8 , S. Sekimoto 9 , J. Spatafora 10 , R. Vilgalys 1 . 1)Biology, Duke University, Durham, NC; 2) Ecology and Evolutionary Biology, McMaster University, Hamilton, ON, Canada; 3) Duke University MedicalSchool, Durham, NC; 4) Plant Pathology and Microbiology, University of California, Riverside, CA; 5) Institute of Botany, NASU, Kyiv, Ukraine; 6) Institute ofMolecular Biology and Genetics, NASU, Kyiv, Ukraine; 7) Centers for Disease Control and Prevention, Atlanta, GA; 8) Ecology and Evolutionary Biology,University of Michigan, Ann Arbor, MI; 9) Biological Sciences, The University of Alabama, Tuscaloosa, AL; 10) Botany and Plant Pathology, Oregon StateUniversity, Corvallis, OR.The phylogeny of the early diverging fungal lineages remains controversial in spite of a growing database of morphological, ultrastructural, biochemicaland molecular evidence. Here we present a comprehensive molecular phylogeny for the basal fungi using metagenomic data from 30 fungal taxa for whichwhole genomes or ESTs are available. Taxa include a dozen flagellated lineages, ten zygomycetous taxa, and key representatives of the Glomeromycota,Ascomycota, and Basidiomycota. Phylogenetic trees built from 434 orthologs (some missing data) and 29 orthologs (no missing data) are congruent andstatistically well supported. Our results show a clear separation of most flagellated fungi from terrestrial taxa. An analysis of the presence of the genesassociated with the flagellar apparatus supports the hypothesis that the flagellum was lost once concomitant with fungi transitioned to terrestrial habitats.Zygomycetous lineages occupy an intermediate position between flagellated fungi and the Dikarya with Entomophthoromycotina and Kickxellomycotinarepresentatives as a basal clade.306. Comparative analysis of 35 basidiomycete genomes reveals diversity and uniqueness of the phylum. Robert Riley 1 , Asaf Salamov 1 , Robert Otillar 1 ,Kirsten Fagnan 1 , Bastien Boussau 3 , Daren Brown 4 , Bernard Henrissat 5 , Anthony Levasseur 5 , Benjamin Held 6 , Laszlo Nagy 2 , Dimitris Floudas 2 , EmmanuelleMorin 7 , Gerard Manning 8 , Scott Baker 9 , Robert Blanchette 6 , Francis Martin 7 , David Hibbett 2 , Igor Grigoriev 1 . 1) Joint Genome Istitute, Lawrence BerkeleyNational Lab, Walnut Creek, CA; 2) Clark University, Worcester, MA; 3) UC Berkeley, Berkeley, CA; 4) USDA, Peoria, IL; 5) AFMB, Marseille, France; 6) UMN,St. Paul, MN; 7) INRA, France; 8) Salk Institute, La Jolla, CA; 9) Pacific Northwest National Lab, Richland, WA.Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37% of the described fungi, and are important in forestry, agriculture, medicine,and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of thisphylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes ofgenome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all availableprotein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48% of basidiomycete proteins are uniqueto the phylum with nearly half of those (22%) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genessuggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotinasubphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCAanalysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, althoughneither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth27th Fungal Genetics Conference | 195