Program Book - 27th Fungal Genetics Conference

CONCURRENT SESSION ABSTRACTSthree different peptaibol-like genes, only two of which appear to be located in syntenic regions. The current distribution of fungi possessing peptaibolgenes is restricted to mycoparasitic lineages of Hypocreales and is generating hypotheses about the role of secondary metabolites in mycoparasitism.Comparative analysis of 35 basidiomycete genomes reveals diversity and uniqueness of the phylum. Robert Riley 1 , Asaf Salamov 1 , Robert Otillar 1 , KirstenFagnan 1 , Bastien Boussau 3 , Daren Brown 4 , Bernard Henrissat 5 , Anthony Levasseur 5 , Benjamin Held 6 , Laszlo Nagy 2 , Dimitris Floudas 2 , Emmanuelle Morin 7 ,Gerard Manning 8 , Scott Baker 9 , Robert Blanchette 6 , Francis Martin 7 , David Hibbett 2 , Igor Grigoriev 1 . 1) Joint Genome Istitute, Lawrence Berkeley NationalLab, 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 growthassays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.Genome evolution of fungal pathogens from the Magnaporthe oryzae/grisea clade. Helene Chiapello 1,2 , Ludovic Mallet 1,3 , Cyprien Guérin 1 , GabrielaAguileta 4 , François Rodolphe 1 , Annie Gendrault 1 , Jonathan Kreplak 3 , Joelle Amselem 3 , Enrique Ortega-Abboud 5 , Marc-Henri Lebrun 6 , Didier Tharreau 5 ,Elisabeth Fournier 7 . 1) INRA, UR MIG, 78352 Jouy-en-Josas, France; 2) INRA, UR BIA, 31326 Castanet-Tolosan, France; 3) INRA, URGI, 78026 Versailles,France; 4) CRG, Barcelone, Spain; 5) CIRAD, UMR BGPI, TA 54K, 34398 Montpellier, France; 6) INRA, UMR BIOGER, 78850 Thiverval-Grignon, France; 7)INRA, UMR BGPI, TA 54K, 34398 Montpellier, France.The GEMO project aims at characterizing genomic determinants of pathogenicity and evolutionary events involved in adaptation of 9 isolates from theM. oryzae/grisea clade differing in their host specificity. Eight strains from M. oryzae species complex and one of the related species M. grisea have beensequenced and assembled. De novo structural gene annotation was carried out using Eugene (Schiex, 2001) to predict genes and REPET (Flutre, 2011) toannotate Transposable Elements (TEs) in these 9 genomes. Four of them exhibited large supplementary genomic regions potentially issued from anunknown bacterial strain of the Burkholderia genus. An original strategy based on Gotham software (Ménigaud, 2012) was used to accurately quantifythese regions in all the affected genome scaffolds. Functional gene annotations were performed using InterProScan. Databases and interfaces relying onthe GMOD tools (gmod.org) were set up to browse annotations and facilitate further evolutionary analyses. In order to identify gene families, the entireset of the predicted and known proteins of the M. oryzae/grisea genomes were clustered using OrthoMCL (Li, 2003). A total of 20443 clusters (15326assigned to M.oryzae/grisea and 5117 to Burkholderia) were obtained, including 8154 clusters comprising single copy genes shared by all genomes (coregenome) and variable number of genome specific gene families (305-1550). Genes encoding putative Secreted Proteins (SPs) were identified in 2522OrthoMCL clusters (2271 of M. oryzae/grisea and 251 of Burkholderia). Further analyses regarding genome-specific and rice-infecting specific genes andSPs will be presented. OrthoMCL families were processed to infer the phylogenetic reference genealogy of the M. oryzae/grisae complex. We alsoevaluated the ability of individual genes to recover the same topology as that supported by most of the genes by using a recent method based on multipleco-inertia analysis (de Vienne, 2012). Most of the genes exhibit a concordant topology with the reference tree except a small set of ‘outliers’. Furtherinvestigations are currently being performed to determine possible causes for incongruities. Finally, we present preliminary results regarding thecomparison of TE distribution in M. oryzae/grisea species taking into account the reference genealogy of the strains.Leptosphaeria maculans 'brassicae': "Transposable Elements changed my life, I feel different now". Jonathan Grandaubert 1 , Conrad Schoch 2 , HosseinBorhan 3 , Barbara Howlett 4 , Thierry Rouxel 1 . 1) INRA-BIOGER, Thiverval-Grignon, France; 2) NCBI, National Institutes of Health, Bethesda, MD, USA; 3) AAFSaskatoon, Canada; 4) School of Botany, University of Melbourne, Australia.The Dothideomycetes phytopathogens Leptosphaeria maculans and Leptosphaeria biglobosa form a complex of 8 species and putative subspeciessuggested to have diverged “recently”. In 2007, the sequencing of an isolate of Leptosphaeria maculans 'brassicae' (Lmb) provided the first referencegenome for this fungus. The 45-Mb genome has an unusual bipartite structure, alternating large GC-equilibrated and AT-rich regions. These AT-rich regionscomprise one third of the genome and are mainly composed of mosaics of truncated Transposable Elements (TEs) postulated to have “invaded” thegenome 5-10 MYA; they also comprise 5% of the predicted genes of which 20% encode putative effectors. In these regions, both genes and TEs areaffected by Repeat Induced Point mutation (RIP). To investigate when and how genome expansion took place in the evolutionary series, and theconsequences it had on fungal adaptability and pathogenicity, the genomes of five members of the species complex showing contrasted host range andinfection abilities were sequenced. In silico comparison of the reference genome with that of 30-32-Mb genome of L. maculans 'lepidii' (Lml), L. biglobosa'brassicae', L. biglobosa 'thlaspii' and L. biglobosa 'canadensis', showed these species have a much more compact genome with a very low amount of TEs(