Program Book - 27th Fungal Genetics Conference

CONCURRENT SESSION ABSTRACTSFriday, March 15 3:00 PM–6:00 PMKilnPhylogenomicsCo-chairs: Jason Stajich and Joey SpataforaCharacterizing Gene Tree Incongruence on a Genome Scale. Dannie Durand. Biological Sciences, Carnegie Mellon University, Pittsburgh, PA.Gene families evolve through gene duplication and loss, and lateral gene transfer. Reconstructing these events is a powerful approach to understandingthe co-evolution of genes and species and the emergence of novel protein function. Gene duplication, loss, and transfer can all result in a gene tree thatdisagrees with the species tree. This incongruence can be exploited to infer the history of these events, as well as the ancestral lineage in which each eventtook place. This is achieved by fitting the gene family tree to the associated species tree, a process called reconciliation. I will discuss the benefits andchallenges of gene tree reconciliation, with special attention to genome scale analyses. The use of gene tree reconciliation will be compared with nonphylogeneticanalyses of gene family expansion and contraction. The problem of determining whether the observed incongruence is due to geneduplication, lateral transfer, or incomplete lineage sorting will also be discussed. I will present analyses of several large gene tree data sets from wellstudiedspecies lineages, as a practical demonstration of this approach. Our algorithms have been implemented in[http://www.cs.cmu.edu/~durand/Notung], a freely available software tool.Early fungi and their carbohydrate active enzymes. Mary L. Berbee 1* , Satoshi Sekimoto 2 , Joseph Spatafora 3 , Timothy James 4 , Teresita M. Porter 5 , RytasVilgalys 6 . 1) Dept Botany, Univ British Columbia, Vancouver, B.C., Canada; 2) Department Of Biological Sciences, The University Of Alabama, Tuscaloosa, AL;3) Oregon State University, Dept of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR; 4) University of Michigan, Dept of Ecology & Evol Biology,830 N University, Ann Arbor, MI; 5) 16 Yachters Lane, Etobicoke, ON, Canada; 6) Biology Department 130 Science Drive, Biological Sciences Rm 137, DukeUniversity Box 90338, Durham, NC.Early fungi are intermingled with some of the oldest fossils from vascular plants, dated at 400 Ma. However, what the fungi were doing for their nutritionbefore land plants were available has been difficult to reconstruct because in phylogenies of the earliest diverging fungal lineages, saprotrophs andparasites of plants as well as animals are intermingled, and which fungal life style came first is ambiguous. We are using phylogenetic analysis of enzymesinvolved in carbohydrate metabolism to reconstruct the enzymatic capabilities of some of the early terrestrial fungi. Our community sequencing proposalto the US Joint Genome Institute resulted in four new genome sequences for evolutionarily divergent lineages including aquatic fungi, the chytrids andBlastocladiomycota, and zygomycetes. Analysis of the genomes suggests that cellulases and pectinases to degrade plant wall carbohydrates were alreadypresent in the earliest fungal lineages but largely lost from the zygomycetes. This implies that fungi evolved in association with the green algal/green plantlineage. Even with complete genome sequences, the branching order among the aquatic fungi and zygomycetes remains problematical, and branchingorder conflicts from one analysis to another. The conflicts may reflect difficulties involved in modeling evolutionary processes across lineages.Alternatively, the conflicts may indicate that fungi, like animals, underwent a 'Cambrian Explosion' perhaps facilitated by rapid expansion of nutritionalresources offered by radiation of multicellular plants and animals.Better evolution through gene clustering. Jason Slot 1 , Matthew Campbell 2 , Han Zhang 1 , Martijn Staats 3 , Jan van Kan 4 , Antonis Rokas 1 . 1) BiologicalSciences, Vanderbilt University, Nashville, TN; 2) Botany, University of Hawai`i, Manoa, HI; 3) Biosystematics group, Wageningen University, Wageningen,The Netherlands; 4) Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.The recent availability of a large number of fungal genomes has facilitated systematic investigations of metabolic pathway evolution across the kingdom.Through combining phylogenetic and genomic techniques, we have recently examined the evolution of metabolic pathways across a well-sampled fungalphylogeny, and gained new insight into the role of metabolic gene clusters in fungal evolution. The occasional occurrence of horizontal gene transfer ofentire pathways between distantly related fungi via gene clusters suggests that fungal species have access to larger pan-genomes than previously thought.Furthermore, analysis of gene cluster decay suggests these transfers are underestimated by analyses of single strains, and that evolution within clusteredpathways is constrained by natural selection. Increased evolvability in fungi is also implied by the discovery of chromosomal loci that maintain largealternative secondary metabolite gene clusters within recombining lineages. Together, these phylogenomic analyses in fungi illustrate a multi-faceted roleof gene clustering in fungal evolution.Phylogenomics unveils secondary metabolites specific to mycoparasitic lineages in Hypocreales. C. Alisha Owensby, Kathryn E. Bushley, Joseph W.Spatafora. Botany & Plant Pathology, Oregon State University, Corvallis, OR.Hypocreales is an order characterized by a dynamic evolutionary history of interkingdom host jumping, with members that parasitize animals, plants, andother fungi. The monophyly of taxa attacking members of the same kingdom is not supported by molecular phylogenetics, however. For example,Trichoderma spp. and Elaphocordyceps spp. are both mycoparasitic, but are members of different families within Hypocreales, Hypocreaceae andOphiocordycipitaceae, respectively. In fact, both genera are more closely related to insect pathogens, than they are to each other. Multiple species ofTrichoderma have sequenced genomes, and recently genomes of several insect pathogens in Hypocreales have been completed (e.g. Metarhizium spp. andTolypocladium inflatum). The genus Elaphocordyceps represents a unique clade within Hypocreales, because whereas most species in the familyOphiocordycipitaceae are insect pathogens, most Elaphocordyceps parasitize truffles of the ectomycorrhizal genus Elaphomyces [Eurotiales, Ascomycota].To compare genes of a truffle pathogen with hypocrealean insect pathogens and mycoparasites, we sequenced the genome of Elaphocordycepsophioglossoides. Our draft assembly of the E. ophioglossoides genome is ~32 MB and has 10,779 gene models, 36 of which are predicted to producesecondary metabolites. We have identified three very large genes in E. ophioglossoides related to peptaibol producing nonribosomal peptide synthetase(NRPS) genes. Peptaibols, which disrupt osmoregulation by forming ion channels through lipid bilayers, have antibiotic and antifungal activity and are bestdescribed in Trichoderma spp. E. ophioglossoides and its beetle-pathogenic congener, T. inflatum, both possess three putative peptaibol synthetases whichwe identified through analysis of NRPS adenylation domains. Of the three peptaibol-specific domain clades, one is predicted to encode for thenonproteinogenic a-aminoisobutryic acid residues. We also show that, despite being very closely related, E. ophioglossoides and T. inflatum each possess27th Fungal Genetics Conference | 75