title: The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics.
abstract: BACKGROUND
  Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described from Trichoderma species of Hypocreaceae. Peptaibiotics are produced by nonribosomal peptide synthetases (NRPSs) and have antibiotic and antifungal activities. Tolypocladium species are mainly truffle parasites, but a few species are insect pathogens.
  
  
  RESULTS
  The draft genome sequence of the truffle parasite Tolypocladium ophioglossoides was generated and numerous secondary metabolite clusters were discovered, many of which have no known putative product. However, three large peptaibiotic gene clusters were identified using phylogenetic analyses. Peptaibiotic genes are absent from the predominantly plant and insect pathogenic lineages of Hypocreales, and are therefore exclusive to the largely mycoparasitic lineages. Using NRPS adenylation domain phylogenies and reconciliation of the domain tree with the organismal phylogeny, it is demonstrated that the distribution of these domains is likely not the product of horizontal gene transfer between mycoparasitic lineages, but represents independent losses in insect pathogenic lineages. Peptaibiotic genes are less conserved between species of Tolypocladium and are the product of complex patterns of lineage sorting and module duplication. In contrast, these genes are more conserved within the genus Trichoderma and consistent with diversification through speciation.
  
  
  CONCLUSIONS
  Peptaibiotic NRPS genes are restricted to mycoparasitic lineages of Hypocreales, based on current sampling. Phylogenomics and comparative genomics can provide insights into the evolution of secondary metabolite genes, their distribution across a broader range of taxa, and their possible function related to host specificity.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. alishaq@umich.edu.|Present address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA. alishaq@umich.edu.
authors.forename: C Alisha
authors.initials: CA
authors.lastname: Quandt
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, MN, USA. kbushley@umn.edu.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Bushley
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. joseph.spatafora@oregonstate.edu.
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Spatafora
mesh_terms: D000818:Animals; D000935:Antifungal Agents / Q000378:metabolism*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D016681:Genome, Fungal; D006999:Hypocreales / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D007313:Insecta / Q000382:microbiology; D005810:Multigene Family; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D064210:Secondary Metabolism
chemical_list: D000935:Antifungal Agents; D005656:Fungal Proteins